key: cord-011558-ls6cdive authors: zhang, jingping; du, yonghao; bai, lu; pu, jiantao; jin, chenwang; yang, jian; guo, youmin title: an asymptomatic patient with covid-19 date: 2020-06-01 journal: am j respir crit care med doi: 10.1164/rccm.202002-0241im sha: doc_id: 11558 cord_uid: ls6cdive nan our case verified the asymptomatic infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) as previously reported (3, 4) and suggested that 1) the transmission of covid-19 seemingly could occur during the incubation period and may cause a potential threat to public health, and 2) the ct examination is very helpful for the early diagnosis of covid-19 because the abnormalities (e.g., unilateral or bilateral subpleural multifocal ground-glass opacities of the lungs) associated with covid-19 could be visualized on ct while subjects remain asymptomatic (5) . n author disclosures are available with the text of this article at www.atsjournals.org. detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr novel wuhan (2019-ncov) coronavirus evidence of sars-cov-2 infection in returning travelers from wuhan, china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-toperson transmission: a study of a family cluster radiological findings from 81 patients with covid-19 pneumonia in wuhan, china: a descriptive study key: cord-352797-xuaqump9 authors: bian, xiaoen; fan, xiaoli; wang, yanfeng title: influence of asymptomatic carriers with covid-19 on transplantation resumption in wuhan date: 2020-06-22 journal: transplantation doi: 10.1097/tp.0000000000003356 sha: doc_id: 352797 cord_uid: xuaqump9 nan xiaoen bian, md, xiaoli fan, md, and yanfeng wang, md w uhan is not only the first city to experience covid-19 but is also among the first to emerge from the pandemic and currently has only 5 confirmed cases. the existence of asymptomatic carriers poses a threat for disease resurgence and also for virus transmission through transplantation. there are 2 types of asymptomatic carrier: the first is a recessive infection, with persistent but asymptomatic viral detection over 14 days or more, but with a relatively low-infectivity risk in the general community and unknown infection transmission risk from organ donation. the second group of asymptomatic cases are in the early stages of the incubation of the disease and become symptomatic over time but are contagious in the asymptomatic phase. to identify all asymptomatic carriers, wuhan has carried out sars-cov-2 nucleic acid tests (nat) for all city dwellers since may 14. as of may 24, 6 574 093 nat tests have been completed, with a total of 227 new asymptomatic carriers and 1 new confirmed case 1 . the asymptomatic infection rate in wuhan has dropped from 0.5 per 1000 people 2 to 0.03 per 1000 people. the outbreak of covid-19 greatly slowed and then stopped organ donation and transplantation in wuhan, but the decrease in the number of infections has allowed hospitals in wuhan to carefully resume deceased donor organ donation and transplantation. hyo-lim hong et al 3 and stephen lagana et al 4 have reported 2 cases of donor-derived transmission of covid-19, therefore a strategy is needed to prevent donor-derived transmission from all potential asymptomatic carriers. due to the superficial understanding of covid-19 and presence of asymptomatic infection in wuhan, we instituted a protocol to prevent organ donor transmission of covid-19. before transplantation both deceased donors and potential recipients undergo sars-cov-2 nat and antibody tests as well as ct scans, which are repeated twice, to avoid the known false negative rates of single tests in covid-19 patients and detect patients in the early stages of developing symptomatic disease. donors and recipients must test negative twice to be eligible for transplant. to minimize transmission caused by asymptomatic carriers, potential deceased donors are quarantined in intensive care for >7 days while being tested. suspected or confirmed covid-19 patients would be eliminated from the donation process. from april 8, when wuhan was reopened, to may 25, 43 cases of organ donation after brain death and 125 cases of organ transplant have been completed in wuhan hospitals. there have been no cases of covid-19 detected among organ transplant donors and recipients. this protocol may serve as a complex but necessary learning model for others. epidemic situation of covid-19 in wuhan wuhan reopened for a week, and no case of asymptomatic infection was confirmed a case of coronavirus disease 2019-infected liver transplant donor covid-19 associated hepatitis complicating recent living donor liver transplantation key: cord-275765-58iul47s authors: yao, wenlong; wang, xueren; liu, tianzhu title: critical role of wuhan cabin hospitals in controlling the local covid-19 pandemic date: 2020-04-22 journal: infection control and hospital epidemiology doi: 10.1017/ice.2020.167 sha: doc_id: 275765 cord_uid: 58iul47s nan to the editor-covid-19 is quickly spreading all over the world. the total number of confirmed cases has exceeded 1.6 million in just 2 months. 1 patients with a variety of respiratory symptoms have flooded into hospitals in a relative short time, posing an enormous challenge to every healthcare system. wuhan was the first center of the pandemic, and it had the highest number of cases in china. but the pandemic in wuhan was controlled by 2 months of lockdown beginning january 23, 2020, and newly detected cases of covid-19 have now decreased to zero. among a series of preventive approaches, 2 cabin hospitals played a critical role in isolating mild and asymptomatic cases. here, we evaluate the role of cabin hospitals in controlling the covid-19 pandemic by retrospectively analyzing the correlation between available beds in cabin hospitals and epidemic data. we obtained the data regarding total daily beds available in cabin hospitals from the official website of the wuhan municipal government, and we extracted daily numbers of newly diagnosed cases, newly cured cases, and new deaths, and we calculated the overall recovery rate and mortality from covid-19 in wuhan from the official website of the national health commission of the people's republic of china. covid-19 cases were diagnosed according to history, symptoms, chest ct, and nucleic acid test. 3 from february 12 to february 14, a clinical diagnosis of covid-19 was applied to make sure that every patient received immediate treatment in wuhan. therefore, the number of cases diagnosed in these 3 days dramatically increased, and we was excluded these data from our analysis. we used spss version 19.0 software (ibm, armonk, ny) for the statistical analysis. a pearson correlation analysis was performed by correlating cabin beds with all epidemic data. p < .05 was considered a significant difference. the official government website reported a total of 28 designated hospitals with 8,254 beds for covid-19 patients in wuhan before february 4, 2020. the utilization ratio of beds was as high as 99.1%. on february 4, 2020, the first cabin hospital in hongshan stadium opened with 1,000 beds. by february 26, 2020, a total of 17 cabin hospitals with 35,499 beds had been set up in wuhan; overall these cabin hospitals received~12,000 mild cases of covid-19. the final utilization ratio of cabin beds was 33.8%. all epidemiological data and their fluctuating trends with the increase in cabin beds are shown in figure 1 . by statistical analysis, the number of newly diagnosed cases showed a highly negative correlation with the availability of cabin beds (r = −0.833; p < .0001). we detected a highly negative correlation between the number of new death cases and the number of cabin beds (r = −0.859; p < .0001). the overall recovery rate was positive correlated with cabin beds (r = 0.961; p < .0001). in addition, we detected a significantly decrease of severe cases in the hospital with the increase of cabin beds (r = −0.977; p < .0001). the approaches for prevention and control of covid-19 can vary from city to city. however, the principle of controlling contagious diseases is to isolate the source of infection, to cut off transmission, and to protect vulnerable populations. 4 although both covid-19 and sars are respiratory diseases caused by coronavirus, covid-19 differs from sars 5 in that many mild and asymptomatic cases of covid-19 also have transmissibility, and these cases are often missed and not isolated. therefore, the management of mild or asymptomatic covid-19 cases is equally important as the treatment of severe cases. our analysis showed that, with the increase of available beds by cabin hospitals, the newly diagnosed cases and severe cases decreased. thus, the cabin hospitals played an important role in controlling the covid-19 pandemic. they effectively prevented family infection or community spread. early treatment of mild cases can prevent covid-19 cases from deteriorating. cabin hospitals were mainly responsible for the treatment of mildly ill patients. all admitted patients were diagnosed by a positive nucleic acid test, concern regarding cross infection was alleviated. in these temporary hospitals, patients were also cared for by professional medical staff. when a case became severe, the patient was transferred to a designated infectious hospital immediately. food, accommodation, medication, and examination were paid by the government. these incentives greatly increased the motivation of mildly ill patients to be admitted to cabin hospitals, which reduced social mobility and the risk of community infection. at the same time, timely medical treatment also improved prognoses, avoiding exacerbation of the disease. 6 in addition, initiation of cabin hospitals reduced the workload of designated infectious hospitals, so the limited public medical resources could be used to treat severe patients and thus reduce the death rate. according to xu et al, 7 the cost of cabin hospitals was low enough that the government could support the roll out on a large enough scale to ensure rapid sequester of cases. short-term training should be employed to equip cabin hospital staff with self-protection and medical care. psychological counseling for patients and medical staff should be provided to alleviate anxiety and panic. we also advocate communication and entertainment activity between patients. online visits for comprehensive mental consultation were also available. a cabin hospital is like a large community clinic. home quarantine and community isolation play an important role in the treatment of mild cases, but there is a risk of neglecting some cases, which could lead to community transmission, and a percentage of patients become severely ill. in wuhan, cabin hospitals connected traditional community clinics and hospitals to achieve early diagnosis, timely treatment, and effective isolation of covid-19 patients. in conclusion, these cabin hospitals were an important part of effectively controlling the covid-19 pandemic in wuhan. supplementary material. to view supplementary material for this article, please visit https://doi.org/10.1017/ice.2020.167 covid-2019) situation reports. world health organization website association of public health interventions with the epidemiology of the covid-19 outbreak in wuhan clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study viral shedding patterns of coronavirus in patients with probable severe acute respiratory syndrome can we contain the covid-19 outbreak with the same measures as for sars? viral dynamics in mild and severe cases of covid-19. the lancet infectious diseases establishing and managing a temporary coronavirus disease 2019 specialty hospital in wuhan, china the relationships between total beds of cabin hospitals and epidemic data of covid-19 in wuhan. data were obtained from national health commission of china and people's government of wuhan to acknowledgments. none.financial support. no financial support was provided relevant to this article.conflicts of interest. all authors report no conflicts of interest relevant to this article. key: cord-265206-ddg87zxv authors: kanny, g. title: maladies respiratoires, allergies et infections à covid-19. premières nouvelles de wuhan date: 2020-04-01 journal: rev fr allergol (2009) doi: 10.1016/j.reval.2020.03.003 sha: doc_id: 265206 cord_uid: ddg87zxv nan sciencedirect www.sciencedirect.com plusieurs études ont attiré l'attention sur l'association entre infections virales et asthme [1] . toutefois, il apparaît que les infections à coronavirus jouent un rôle mineur dans les exacerbations d'asthme. nos confrères de wuhan [2] nous informent sur l'impact de l'infection à ce nouveau virus, covid-19 chez les personnes asthmatiques, allergiques ou porteuses de bronchopneumopathie obstructive chronique. zhang et al. ont étudié les caractéristiques cliniques et le statut allergique de 140 patients infectés par covid-19 hospitalisés du 16 janvier au 3 février 2020 dans un hôpital de wuhan [2] . l'infection a été confirmée pour chacun par rt-pcr. le diagnostic d'infection sévère se base sur la présence d'un des critères suivants: • détresse respiratoire avec une fréquence ≥ 30/mn; • saturation pulsée en oxygène ≤ 93 % au repos; • indice d'oxygénation (pao 2 /fio 2 ) ≤ 300 mm hg. la guérison est définie par le jour de la disparition de tous les symptômes. parmi les 140 patients, 58 ont été classés comme sévères. le ratio homme/femme est de 1/1. l'âge moyen des patients est de 57 ans avec des extrêmes allant de 25 à 87 ans. la majorité (70 %) avaient plus de 50 ans. l'âge moyen des patients identifiés comme sévères était de 64 ans et pour les cas non-sévères de 51,4 ans. aucun patient ne rapportait une exposition directe avec le marché de huanan ou des animaux sauvages. ils s'agissaient d'infections communautaires. trois professionnels hospitaliers étaient infectés. parmi eux, 90 (64,3 %) avaient au moins une comorbidité : 79,3 % dans les formes sévères et 53,7 % dans celles non-sévères. les plus fréquentes étaient l'hypertension (30 %) et le diabète (12,1 %). une hypersensibilité médicamenteuse était rapportée par 11,4 % des patients et une urticaire par 2 patients. l'asthme ou une autre maladie allergique (rhinite, allergie alimentaire, dermatite atopique) ne sont pas rapportés par ces patients alors que la prévalence de l'asthme est estimée à 4,3 % en chine [3] et la rhinite allergique à 17,2 % à wuhan en 2011 [4] . la bronchopneumopathie chronique obstructive (bpco) qui a une prévalence de 13,7 % en chine concerne seulement 2 patients (1,4 %), ce qui est proche de la prévalence de 1,1 % rapporté par guan et coll. [5] et celle de 3 % rapportée par zhou et coll. [6] . le tabagisme est actif pour 2 sujets, arrêté pour 7 autres. ces taux sont faibles eu égard à la prévalence de la bpco chez les sujets de plus de 40 ans en chine qui est de 13,7 % la majorité (99,3 %) présentait des images caractéristiques au scanner. la lymphopénie est présente chez 75,4 % des patients, l'éosinopénie dans 52,9 % des cas. le taux de pcr était augmenté chez 91,9 % des patients. la faible prévalence des patients porteurs de bpco ou fumeurs est surprenante. cette population avait été identifiée à risque pour le middle east respiratory syndrome coronavirus (mers-cov) : la cible de ce coronavirus est la dipeptidyl peptidase iv (ddp4) qui est plus exprimée dans cette population [8] . l'enzyme de conversion de l'angiotensine 2 (eca2), très exprimée dans les cellules épithéliales des voies aériennes est identifiée comme étant le récepteur de sars-cov et joue un rôle crucial dans les lésions pulmonaires [9] . elle vient également d'être identifiée comme le récepteur du covid-19 [10] . d'autres études sont nécessaires pour étudier le rôle d'eca2 dans la pathogénie des lésions pulmonaires induites par ce nouveau coronavirus et étudier l'expression d'eca2 dans les cellules épithéliales des patients porteurs de bpco et des fumeurs. ces données préliminaires sont rassurantes. l'asthme, les maladies allergiques et la bpco n'apparaissent pas comme étant des facteurs de risque dans cette population de patients hospitalisés. il conviendra de confirmer ces données en population générale et en europe. la période de confinement que nous traversons aura des effets bénéfiques pour les personnes présentant une pollinose en les exposant moins à l'air extérieur riche en pollens en cette période de l'année et à la pollution automobile qui diminue. il conviendra cependant de veiller à la qualité de l'air intérieur de nos domiciles en évitant l'utilisation de substances volatiles irritantes ou allergisantes: fumée de tabac, produits d'entretien, parfums d'intérieur, combustions (bougies, encens avec émission de benzène. . .), etc. il est conseillé d'aérer son domicile tôt le matin et à la tombée de la nuit. la fédération franç aise d'allergologie rappelle que les personnes allergiques doivent poursuivre la prise du traitement prescrit par leur médecin et en particulier les corticoïdes inhalés pour les asthmatiques afin que leur maladie soit bien contrôlée. au-delà des symptômes respiratoires, il conviendra d'être particulièrement attentif à l'apparition de symptômes inhabituels tels que la fièvre, la fatigue, des céphalées, des courbatures, des troubles gastro-intestinaux, une perte de l'odorat (anosmie) et du goût (agueusie). l'auteur déclare ne pas avoir de liens d'intérêts. https://doi.org/10.1016/j.reval.2020.03.003 1877-0320/© 2020 elsevier masson sas. tous droits réservés. viruses and bacteria in acute asthma exacerbations-a ga2len-dare* systematic review clinical characteristics of 140 patients infected with sars-cov-2 in wuhan, china prevalence, risk factors, and management of asthma in china: a national cross-sectional study an increased prevalence of self-reported allergic rhinitis in major chinese cities from clinical characteristics of coronavirus disease 2019 in china clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study prevalence and risk factors of chronic obstructive pulmonary disease in china (the china pulmonary health [cph] study): a national cross-sectional study dpp4, the middle east respiratory syndrome coronavirus receptor, is upregulated in lungs of smokers and chronic obstructive pulmonary disease patients a crucial role of angiotensin converting enzyme 2 (ace2) in sars coronavirus-induced lung injury evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission france adresse e-mail : gisele.kanny@univ-lorraine disponible sur internet le xxx key: cord-262693-z9dolxky authors: nishiura, hiroshi; linton, natalie m.; akhmetzhanov, andrei r. title: initial cluster of novel coronavirus (2019-ncov) infections in wuhan, china is consistent with substantial human-to-human transmission date: 2020-02-11 journal: j clin med doi: 10.3390/jcm9020488 sha: doc_id: 262693 cord_uid: z9dolxky reanalysis of the epidemic curve from the initial cluster of cases with novel coronavirus (2019-ncov) in december 2019 indicates substantial human-to-human transmission. it is possible that the common exposure history at a seafood market in wuhan originated from the human-to-human transmission events within the market, and the early, strong emphasis that market exposure indicated animal-to-human transmission was potentially the result of observer bias. to support the hypothesis of zoonotic origin of 2019-ncov stemming from the huanan seafood market, the index case should have had exposure history related to the market and the virus should have been identified from animals sold at the market. as these requirements remain unmet, zoonotic spillover at the market must not be overemphasized. the clinical summary of the earliest cases of 2019 novel coronavirus (2019-ncov) infections in wuhan, china was recently published [1] , showing the majority of cases were exposed to the huanan seafood market, which also had wild animals, suggesting the possibility of zoonotic transmission in the market. this suggestion of zoonotic spillover was quoted by international organizations, including the world health organization (who), and as a result early research focused on zoonotic rather than direct human-to-human transmission of 2019-ncov. however, the index case had no exposure history related to the seafood market, indicating that huanan seafood market-related zoonotic spillover may have been an overblown hypothesis. here, we reanalyze the epidemic data of the initial cluster of cases with 2019-ncov infections to demonstrate that the epidemic curve is consistent with substantial human-to-human transmission in december 2019. three important arguments are made here with respect to epidemiological interpretation of the epidemic dataset. first, figure 1a shows the epidemic curve of cases in wuhan, distinguishing case generations by color. the index case developed symptoms on 1 december 2019, with cases 2-4 having onset nine days later, and cases 5-6 five days after that. together, these intervals indicate a possible serial interval (si)-the time between illness onset in an earlier case to that in a secondary case-with a mean of 7.4 days, consistent with the mean si of severe acute respiratory syndrome [2] . the latter is also consistent with the mean si estimate of 7.5 days presented in the preliminary epidemiological study [3] . although it is possible that the sis are shorter than quoted here [4] , the epidemic curve is still in agreement with the existence of asymptomatic and unascertained mild cases between diagnosed cases. epidemic curve is still in agreement with the existence of asymptomatic and unascertained mild cases between diagnosed cases. the expected number of cases in each subsequent generation was assumed to follow a poisson distribution, and the 95% confidence intervals of the reproduction number (whiskers) were derived from the profile likelihood. second, assuming a constant si of 8 days, the epidemic curve of cases by the date of illness onset can be transformed to that by generation of cases. the number of cases in each generation is therefore 1, 3, 4, 27, and 6 cases, respectively. these numbers allow for the estimation of generation-dependent reproduction numbers-the average number of secondary cases per primary case for each generation [5] ( figure 1b ). assuming that the offspring distribution is poisson distributed, the reproduction numbers can be estimated at 3.0 (95% confidence interval (ci): 0.75, 7.8), 1.3 (95% ci: 0.4, 3.1), 6.7 (95% ci: 4.5, 9.6), and 0.2 (95% ci: 0.1, 0.5)-broadly in line with preliminary basic reproduction number estimates of 1.5-3.5 quoted by the who and presented elsewhere [6, 7] . third, the common exposure supports secondary transmission events taking place in the market. although the virus has been identified in market environmental samples [8] , this does not exclude the likelihood of secondary transmission. that is, it is possible that the common exposure history at the huanan seafood market in wuhan originated from the human-to-human transmission events within the market. unfortunately, early emphasis that market exposure implied animal-to-human transmission considerably delayed global recognition of exportation of the virus from wuhan, especially during the first half of january [9, 10] . the emphasis on market-based zoonotic transmission may have been the result of observer bias-i.e., the bias that originates from having preconceptions or subjective feelings about what is being studied that could influence epidemiological observation and even recording information. for example, the zoonotic origin of another relatively recently emerged coronavirus with predominantly zoonotic transmission-the virus causing middle east respiratory syndrome (mers)-may have served as a strong reference for reducing concern about epidemic levels of sustained human-to-human transmission. in conclusion, we believe that zoonotic spillover at the market should not be overemphasized, because the epidemic curve is consistent with substantial human-to-human transmission in december 2019. there are two important take homes for any future investigations that begin with a similar scenario: first, to verify that zoonotic spillover is related to the exposure in question, the index case must be verified to have that exposure history. second, without identifying the virus in second, assuming a constant si of 8 days, the epidemic curve of cases by the date of illness onset can be transformed to that by generation of cases. the number of cases in each generation is therefore 1, 3, 4, 27, and 6 cases, respectively. these numbers allow for the estimation of generation-dependent reproduction numbers-the average number of secondary cases per primary case for each generation [5] ( figure 1b) . assuming that the offspring distribution is poisson distributed, the reproduction numbers can be estimated at 3.0 (95% confidence interval (ci): 0.75, 7.8), 1.3 (95% ci: 0.4, 3.1), 6.7 (95% ci: 4.5, 9.6), and 0.2 (95% ci: 0.1, 0.5)-broadly in line with preliminary basic reproduction number estimates of 1.5-3.5 quoted by the who and presented elsewhere [6, 7] . third, the common exposure supports secondary transmission events taking place in the market. although the virus has been identified in market environmental samples [8] , this does not exclude the likelihood of secondary transmission. that is, it is possible that the common exposure history at the huanan seafood market in wuhan originated from the human-to-human transmission events within the market. unfortunately, early emphasis that market exposure implied animal-to-human transmission considerably delayed global recognition of exportation of the virus from wuhan, especially during the first half of january [9, 10] . the emphasis on market-based zoonotic transmission may have been the result of observer bias-i.e., the bias that originates from having preconceptions or subjective feelings about what is being studied that could influence epidemiological observation and even recording information. for example, the zoonotic origin of another relatively recently emerged coronavirus with predominantly zoonotic transmission-the virus causing middle east respiratory syndrome (mers)-may have served as a strong reference for reducing concern about epidemic levels of sustained human-to-human transmission. in conclusion, we believe that zoonotic spillover at the market should not be overemphasized, because the epidemic curve is consistent with substantial human-to-human transmission in december 2019. there are two important take homes for any future investigations that begin with a similar scenario: first, to verify that zoonotic spillover is related to the exposure in question, the index case must be verified to have that exposure history. second, without identifying the virus in animals sold at the market, it is difficult to conclude with certainty that any zoonotic transmission occurred at the market. author contributions: h.n. conceived the study, and all authors participated in the study design. h.n. collected the data and a.r.a. and h.n. analyzed the data. all authors jointly drafted the manuscript. all authors gave comments on the earlier versions of the manuscript. all authors have read and agreed to the published version of the manuscript. the authors declare no conflicts of interest. clinical features of patients infected with 2019 novel coronavirus in wuhan, china. lancet transmission dynamics and control of severe acute respiratory syndrome early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia serial interval of novel coronavirus (2019-ncov) infections assessing dengue control in tokyo transmissibility of 2019-ncov real time estimation of the risk of death from novel coronavirus (2019-ncov) infection: inference using exported cases china detects large quantity of novel coronavirus at wuhan seafood market the extent of transmission of novel coronavirus in wuhan, china, 2020 the rate of underascertainment of novel coronavirus (2019-ncov) infection: estimation using japanese passengers data on evacuation flights key: cord-342268-azi9i2a8 authors: zhao, shi; zhuang, zian; cao, peihua; ran, jinjun; gao, daozhou; lou, yijun; yang, lin; cai, yongli; wang, weiming; he, daihai; wang, maggie h title: quantifying the association between domestic travel and the exportation of novel coronavirus (2019-ncov) cases from wuhan, china in 2020: a correlational analysis date: 2020-02-20 journal: j travel med doi: 10.1093/jtm/taaa022 sha: doc_id: 342268 cord_uid: azi9i2a8 nan in the end of 2019, a novel coronavirus (2019-ncov) emerged in wuhan, china and was causing a serious outbreak of acute respiratory illness. 1 wuhan locates in the centre of mainland china with a population of 14 million and is very conveniently connected to other parts of china through airlines and highspeed rails. 2 as of 31 january 2020 (5:00 p.m., gmt + 8), there were 9809 confirmed 2019-ncov cases in mainland china, including 213 deaths and 180 discharges. 3, 4 cases infected in wuhan were also detected in many foreign countries or regions including thailand, japan, republic of korea, the united states, canada and some european countries. 4 the world health organization (who) has declared that the novel coronavirus outbreak is a public health emergency of international concern. official reports on the newly confirmed cases are released very rapidly (several times a day) after january 16, 3-5 as the official diagnosis protocol was released by the who on january 17. 6 recent studies indicated the likelihood of travel-related risks of 2019-ncov spreading both domestically and internationally. 7 , 8 many major cities in mainland china reported the finding of imported cases, including beijing, shanghai, guangzhou and shenzhen. the outbreak is still on-going with an increasing trend in daily new cases. 3, 4 before the wuhan lockdown (official travel restriction) on january 23, virtually all cases found in other major cities were exported cases from wuhan. population flow data between major cities in mainland china are available online due to the rapid development of internet in recent decades, see https://qianxi.baidu.com/ (in chinese). in this work, we quantified the association between the domestic travel load and the number of cases exported from wuhan to other cityclusters in mainland china. our city-clusters are the pool of top five cities in the top 10 provinces (in number of cumulative cases). thus, we included 10 city-clusters in the analysis, and the details of the selected city-clusters can be found in supplementary data s1. we examined the association between the load of domestic passengers departed from wuhan and the number of confirmed cases to the 10 city-clusters (including the three municipalities, beijing, shanghai and chongqing). data sets of the daily numbers of domestic passengers were obtained from the location-based services database of baidu company from january 1 to 20. we selected the top 10 provincial regions (except hubei) with the largest cumulative number of cases, which accounts for 68% of all cases reported outside hubei, before the implementation of the city lockdown, on 23 january 2020. cases from other provinces are scattered and showed no clear pattern. the daily numbers of passengers from wuhan to the city-clusters of each province were adopted to measure the load of domestic passengers departed from wuhan to that cluster. from now on, province means the city-clusters in that province. the daily number of cases time series are obtained via the online outbreak situation reports. 3 , 4 daily cases for each cluster are scaled from daily province total. the detail is given in supplementary data. the association was formulated as follows: here, c i,t represents the daily number of new cases in the ith provincial region on day t. the function e(·) is the expectation; the 'province i ' denotes the dummy variable for the ith provincial region in accounting for the heterogenicity among different provinces, and thus, α i is a locality-varying interception term. term ξ i is the daily number of passengers from wuhan to the ith province. the time index was denoted by t, and the term τ modelled the delay from exposure to being detected. the ε represented the daily number of new cases in wuhan. hence, the product term (ξ ·ε) was proportional to the rate of cases exported from wuhan to other places, and this setting was consistent with the framework in imai et al., 9 which estimated the outbreak size through exported 2019-ncov cases overseas, as well as in more complex frameworks. 10 the β is the regression coefficient to quantify the association between the load of passengers multiplied by the local infectivity in wuhan and the number of cases reported outside wuhan. hence, the change rate, denoted by ∆ = [exp(β × 100) − 1] × 100%, may be interpreted as the expected percentage change in the daily number of cases offsite found associated with per 100 increase in the daily number of passengers departed from wuhan where there was one new case daily. we estimated β for three means of transportation, and the p-value less than 0.05 was considered as statistical significance. we also considered a baseline version of the model by replacing term 'β·ξ i,t−τ ·ε t−τ ' in equation (1) with 'β 0 ·ξ i,t−τ ', which ignored the variation in the force of infection in wuhan, thus a constant, as in equation (2) log the likelihood ratio (lr) test was adopted to justify the model structure in equation (1) against the baseline form in equation (2) . for the delay term (τ ), it was expected to be equivalent to the incubation period, which was reported to be 5.2 days (95% ci: 4.1-7.0) in. 1 finally, we examined the association with τ varying at 3, 4, 5, 6 and 7 days in sensitivity analysis. the lr test yielded statistically significant outcomes, which suggests that the model in equation (1) is more reasonable than the baseline form in equation (2) . through the goodness-of-fit in terms of the mcfadden's pseudo-r-squared, we found that τ = 5 days attains the best fitting performance to explain the patterns of the cases offsite detected. this well matched the estimate of the mean incubation period of the infection at 5.2 in. 1 we found a statistically significant positive association between the load of passengers multiplied by the local infectivity in wuhan and the number of cases reported outside wuhan, see table 1 . we estimated that per 100 cases increase in the daily number of newly reported cases in wuhan together with per 100 persons increase in the daily number of passengers departed wuhan were likely to cause a 16.25% (95% ci: 14.86-17.66%) increase in the daily number of cases offsite detected on average. the sensitivity analysis by varying τ suggested this fundamental relationship holds, and the details can be found in table 1 and the supplementary data s2. this analysis has limitations. the data used in this study are in the early phase of the outbreak and may not represent subsequent waves. we aim at quantifying the association between domestic travel and 2019-ncov exportation in china. although the differences in case ascertainment in different cities clusters are considered in the model by the dummy term 'province i ', the association could also bear heterogeneity. temporal and spatial correlations were not addressed in this simple modelling analysis due to lack of data. the 2019-ncov surveillance data were too scattered and short at this early stage to consider temporal and spatial correlation. the correlation between population flow, number of cases offsite detected, and source infection prevalence was addressed in this work. our modelling framework would be extended to a more complex and realistic form for exploring the potential spatial correlations, and benefit from more detailed disease surveillance and travel population flow data. supplementary data are available at jtm online. early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the association between domestic train transportation and novel coronavirus outbreak in china, from 2019 to 2020: a data-driven correlational report situation report of the pneumonia cases caused by the novel coronavirus', released by the national health commission of the people's republic of china novel coronavirus (2019-ncov) situation reports, released by the world health organization (who) news press and situation reports of the pneumonia caused by novel coronavirus laboratory testing for 2019 novel coronavirus (2019-ncov) in suspected human cases: interim guidance, released on january 17, 2020 by the world health organization (who) pneumonia of unknown etiology in wuhan, china: potential for international spread via commercial air travel nowcasting and forecasting the wuhan 2019-ncov outbreak preprint published by the school of public health of the university of hong kong estimating the potential total number of novel coronavirus (2019-ncov) cases in wuhan city, china preprint published by the nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study the authors would like to acknowledge colleagues for helpful comments. the authors declared no competing interests. all authors conceived the study, carried out the analysis, discussed the results, drafted the first manuscript, critically read and revised the manuscript and gave final approval for publication. the funding agencies had no role in the design and conduct of the study; collection, management, analysis and interpretation of the data; preparation, review or approval of the manuscript; or decision to submit the manuscript for publication. the ethical approval or individual consent was not applicable. all data and materials used in this work were publicly available and also available based on request. not applicable. key: cord-347257-s0w95qdn authors: kraemer, moritz u. g.; yang, chia-hung; gutierrez, bernardo; wu, chieh-hsi; klein, brennan; pigott, david m.; du plessis, louis; faria, nuno r.; li, ruoran; hanage, william p.; brownstein, john s.; layan, maylis; vespignani, alessandro; tian, huaiyu; dye, christopher; pybus, oliver g.; scarpino, samuel v. title: the effect of human mobility and control measures on the covid-19 epidemic in china date: 2020-03-25 journal: science doi: 10.1126/science.abb4218 sha: doc_id: 347257 cord_uid: s0w95qdn the ongoing covid-19 outbreak expanded rapidly throughout china. major behavioral, clinical, and state interventions have been undertaken to mitigate the epidemic and prevent the persistence of the virus in human populations in china and worldwide. it remains unclear how these unprecedented interventions, including travel restrictions, affected covid-19 spread in china. we use real-time mobility data from wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across china and ascertain the impact of control measures. early on, the spatial distribution of covid-19 cases in china was explained well by human mobility data. following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases were still indicative of local chains of transmission outside wuhan. this study shows that the drastic control measures implemented in china substantially mitigated the spread of covid-19. the incubation period is the time interval between infection and symptom onset. we assumed that cases travelling from wuhan were exposed during their stay in wuhan. we estimated the incubation period from 38 travelling cases returning from wuhan with known dates of symptom onset, entry and exit. the end of the exposure period was assumed to be the exit travel date except if symptom onset occurred prior to the exit date (in which case exposure was assumed to have occurred prior to symptom onset). the start of the exposure period corresponded to the entry date. we assumed that the incubation period could not exceed 30 days. for each case, the minimum and maximum incubation period was derived from the dates of entry, exit and symptom onset we fitted a truncated gamma distribution (0 to 30 days) and estimated the mean and variance of the incubation period using markov chain monte carlo (mcmc) in a bayesian framework using an uninformative prior distribution. we derived the likelihood as follows: = 5 ( ≤ #$% + 1) − 5 ( ≤ #/0 ) 5 a metropolis-hastings algorithm was implemented in r. marginal posteriors were sampled from a chain of 5,000 steps after discarding a burn-in of 50 steps. convergence was inspected visually. age and sex distributions are important in understanding risk of infection across populations. assuming risk to be distributed relatively equally across a population, as an outbreak evolves age and sex distributions should follow the underlying population structure. varying degrees of immunity and exposure may shift these distributions (30) . to examine whether the ongoing outbreak shifted from an epidemic concentrated in wuhan and among travelers from wuhan to an epidemic that was self-sustained in provinces across china we use age and sex data from different periods of the outbreak for individuals with reported travel history and no known travel history. we define two periods of the outbreak, an "early" phase, starting with the first reports in early december and ending a set number of days after the wuhan shutdown. this was selected to be 8 days after the wuhan shutdown, which conservatively corresponds to one incubation period + 1sd (see above) after the shutdown. after that date (i.e. 1 st feb 2020; the "later" phase) we assume that most reported transmissions in provinces outside of wuhan are the result of local transmission. we further divided our data in those that had cases with known travel history to wuhan and those who did not. then we produce the following summary statistics: we cannot exclude the possibility that shifts in distributions may be due to heightened awareness among the general population which may have increased reporting in female cases later in the epidemic. further, more work will be necessary to understand the differential risk of severe or symptomatic disease to fully understand the age and sex distributions in this outbreak. for example, why there are relatively few reports of cases <18y old. however, as for other respiratory pathogens symptomatic and severe infection were more concentrated in older populations. we do not intend to make any general statements about differential risk but were more interested in shifts in reported cases across multiple geographies in china. we extract human mobility data from the baidu qianxi web platform, which presents daily population travels between cities or provinces tracked through the baidu huiyan system. the data do not represent numbers of individual travelers but rather an index of relative movements constructed by baidu's proprietary methods which are correlated with human mobility (31) (http://qianxi.baidu.com/). in particular, two pieces of information are collected. first, we extract a series of migration scale indices for traveling out of wuhan, from january 1st to february 10, both in 2019 and 2020. second, we obtain the proportion of human movement from wuhan were bound for each of 31 provinces in china. these proportions are available for january 1st -february 10, 2020. based on this data we had access to both changes in mobility volume and changes in mobility direction. see more detailed descriptions of the human movement data here: (32, 33) . as of 2017, baidu inc's. mapping service had a 30% market share in china (34) . we reviewed the literature and online social media to understand the key timings of interventions and announcements that are relevant for disease transmission across china. we collated information about the type (e.g., announcement of outbreak, travel restrictions, isolation of patients, etc.), geographic location (e.g., city where available, province), and timing (specific date or date range). definitions of probable and confirmed covid-19 cases have changed throughout the epidemic. we collected data from official sources describing the timing and specifics of the case definitions. probable: need to satisfy (i) and (ii): i. clinical symptoms: (1) fever; (2) imaging showing pneumonia typical of the disease; (3) during early disease, total white cells normal or reduced, or lymph cell count reduced. ii. epidemiologic history: (1) within 2 weeks of symptom onset, wuhan travel or resident history; or within 2 weeks of symptom onset, contact with persons from wuhan who had fever with respiratory symptoms; or belong to a cluster. confirmed: need to satisfy criteria for probable case and have a real-time quantitative polymerase chain reaction (rt-qpcr) positive result from sputum, nasopharyngeal swabs, lower respiratory tract secretions or other sample tissue, or genome sequencing highly similar with known sars-cov-2. available strains. probable: need to satisfy (i) and any one epidemiologic history described in (ii): i. clinical symptoms: (1) fever; (2) from january 27-february 5: probable: need to satisfy any two of the symptoms described in (i) and any of the january 2020 and 0 before (which represents one median incubation period from 22nd january 2020). models were fit to province-level data. the three models were compared using differences in bayesian information criteria (bic), where larger values indicate models with lower relative support, and bic>4 considered the cutoff for substantial model improvement. we performed a detailed sensitivity analysis on the availability of rt-qpcr tests, doubling time, and incubation periods. we obtained qualitatively similar results for model 1 (poisson glm fit to daily case counts), model 2 (negative binomial glm fit to daily case counts), and model 3 (loglinear regressions fit to cumulative cases), see table s2 . in addition, we provide a full time series analysis of the optimal lag structure for cases and mobility for each province. additionally, although bic is considered more conservative, model selection results were confirmed using aic for model selection (see fig. 4 and table s2 ). lastly, we validated our model selection results using elastic-net regression and n-fold cross validation as implemented in the r package glmnet v. 2.0-18 (35, 36) . to estimate the epidemic doubling time across each province, we fit a mixed effects poisson glm of daily case counts to days since the first case report in each province (fixed effect) and a random effect for each province on the slope and intercept, using the r package lme4 v. (37) . all code and data are available here (38) . to ascertain whether earlier travel restrictions could have prevented the wide-spread increase in cases witnessed in late-january we constructed a simple forecasting model for covid-19. briefly, we forecast the cumulative number of cases in each chinese province by simply doubling the number of cumulative cases reported six days prior. for dates prior to jan. 28th and after feb 3rd, this naive forecast produces an accurate estimate of the cumulative number of cases in each province (fig. s4) . however, the cumulative number of cases reported on jan 28th is poorly estimated using this model (fig. s4) . in order to accurately forecast the number of cases on jan 28th, we must also include the relative amount of mobility out of wuhan into various provinces in the regression model. in fig. s4 , we show how a model including only movement from wuhan on january 22nd fit to the residuals from fig. s4 is once again able to accurately forecast cumulative cases. this indicates that for any hope of success of controlling the spread of an epidemic, movement restrictions must be prompt. table s1 . covid-19 control in china during mass population movements at new year china novel coronavirus investigating and research team, a novel coronavirus from patients with pneumonia in china the impact of transmission control measures during the first 50 days of the covid-19 epidemic in china risk for transportation of 2019 novel coronavirus disease from wuhan to other cities in china nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study quantifying the association between domestic travel and the exportation of novel coronavirus (2019-ncov) cases from wuhan, china in 2020: a correlational analysis coronavirus disease 2019 (covid-19) situation report epidemiological data from the covid-19 outbreak, real-time case information middle east respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility incubation periods of acute respiratory viral infections: a systematic review incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china generalized linear models" in statistical models in pattern of early human-to-human transmission of wuhan reporting, epidemic growth, and reproduction numbers for the 2019 novel coronavirus (2019-ncov) epidemic metapopulation dynamics of infectious diseases" in ecology, genetics and evolution of metapopulations multiscale, resurgent epidemics in a hierarchical metapopulation model characteristics of and important lessons from the coronavirus disease, 2019 (covid-19) outbreak in china: summary of a report of 72,314 cases from the chinese center for disease control and prevention novel coronavirus pneumonia emergency response epidemiology team, the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in china temporally varying relative risks for infectious diseases: implications for infectious disease control factors that make an infectious disease outbreak controllable substantial undocumented infection facilitates the rapid dissemination of novel coronavirus code for: the effect of human mobility and control measures on the covid-19 epidemic in china kraemer; open covid-19 data curation group, open access epidemiological data from the covid-19 outbreak a database of geopositioned middle east respiratory syndrome coronavirus occurrences the chi-square test of independence handbook of biological statistics (sparky house genomic and epidemiological monitoring of yellow fever virus transmission potential past and future spread of the arbovirus vectors aedes aegypti and aedes albopictus the impact of traffic isolation in wuhan on the spread of population movement, city closure and spatial transmission of the 2019-ncov infection in china mobile map app research report: which of the highest, the baidu, and tencent is strong? fitting linear mixed-effects models using lme4 regularization paths for generalized linear models via coordinate descent open covid-19 data working group pseudo r-squared measures for poisson regression models with over-or underdispersion regression models for count data in r key: cord-348327-rgikd4g8 authors: ueyama, hiroki; kuno, toshiki; takagi, hisato; krishnamoorthy, parasuram; vengrenyuk, yuliya; sharma, samin k.; kini, annapoorna s.; lerakis, stamatios title: gender difference is associated with severity of coronavirus disease 2019 infection: an insight from a meta-analysis date: 2020-06-19 journal: crit care explor doi: 10.1097/cce.0000000000000148 sha: doc_id: 348327 cord_uid: rgikd4g8 objectives: coronavirus disease 2019 is a novel infection now causing pandemic around the world. the gender difference in regards to the severity of coronavirus disease 2019 infection has not been well described thus far. our aim was to investigate how gender difference can affect the disease severity of coronavirus disease 2019 infection. data sources: a comprehensive literature search of pubmed and embase databases was conducted from december 1, 2019, to march 26, 2020. an additional manual search of secondary sources was conducted to minimize missing relevant studies. there were no language restrictions. study selection: studies were included in our meta-analysis if it was published in peer-reviewed journals and recorded patient characteristics of severe versus nonsevere or survivor versus nonsurvivor in coronavirus disease 2019 infection. data extraction: two investigators independently screened the search, extracted the data, and assessed the quality of the study. data synthesis: our search identified 15 observational studies with a total of 3,494 patients (1,935 males and 1,559 females) to be included in our meta-analysis. males were more likely to develop severe coronavirus disease 2019 infection compared with females (odds ratio, 1.31; 95% ci, 1.07–1.60). there was no significant heterogeneity (i(2) = 12%) among the studies. conclusions: this meta-analysis suggests that the male gender may be a predictor of more severe coronavirus disease 2019 infection. further accumulation of evidence from around the world is warranted to confirm our findings. c oronavirus disease 2019 (covid-19) is a novel infection caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) (1). since the first cluster of its disease in wuhan, china, was reported in december 2019, the infection has rapidly expanded worldwide, making world health organization (who) to declare this as a pandemic on march 11, 2020 (2) . the clinical manifestation of the disease varies from fever, myalgia, nonproductive cough to acute respiratory distress syndrome, fulminant myocarditis, and death (3, 4) . recognition of the clinical risk factors of severe covid-19 infection is a high priority to effectively manage this emerging threat of the new virus. reports have consistently shown that the older age and comorbidities such as hypertension, respiratory system disease and, cardiovascular disease are associated with worse outcomes of covid-19 (5, 6) . gender difference in its association with susceptibility and severity of infectious disease is reported in the past for several other infectious organisms (7) . however, the gender difference in regards to the severity of covid-19 infection has not well been delineated thus far. therefore, the aim of this study was to investigate how gender difference can affect the disease severity of covid-19 infection. this meta-analysis was performed in accordance with the preferred reporting items for systematic reviews and meta-analyses guidelines (8) . we performed a comprehensive literature search of pubmed and embase databases from december 1, 2019, to march 26, 2020. the following search terms were applied to include all relevant studies documenting gender information on covid-19 infection and its association with outcomes: "coronavirus 2019 or 2019-ncov or sars cov 2 or covid-19 or covid; sex or gender or male or female or clinical characteristic or clinical features of clinical course or risk factor. " we conducted an additional manual search of secondary sources, including commentaries and citations of initially identified articles to minimize the risk of missing relevant studies. studies were included in our meta-analysis when it was: 1) published in peer-reviewed journals and 2) study that recorded patient characteristics of severe versus nonsevere or survivor versus nonsurvivor in covid-19 infection. there was no restriction on publication language. duplicate reports from the same study population were excluded. no contact was made to the authors since there were no missing outcomes for the analysis. the search was screened by two investigators (h.u., t.k.) independently to assess the eligibility of each study. after the initial screen through titles and abstracts, the full-texts of articles were retrieved and assessed if there were any potential correlations. any disagreement in the process of study selection and data extraction were resolved by input from the third author (h.t.) (9) . for each eligible study, we extracted the study characteristics (author name, study design, location of the study), patient characteristics (number of patients, age, gender, and comorbidities), and outcome measures. the newcastle-ottawa assessment scale was used for each study to assess the quality of the studies (10). the endpoints were the rate of severe covid-19 infection and death. severe covid-19 infection was defined by each study. for each included study, the total number and event number for each gender were extracted in regard to each outcome. the pooled results were presented as odds ratios (ors) and 95% ci. review manager version 5.3 (the cochrane collaboration, copenhagen, denmark) was used to conduct statistical analysis. a randomeffect model was used for the analysis. mantel-haenszel effect model was used to calculate the pooled or and 95% ci of categorical variables. a total of 403 articles were identified after initial database searching and additional records review. after title and abstract screening, 39 articles were extracted for full-text article assessment. two studies were excluded due to reporting duplicate of the same population (1, 11) , two were excluded due to the meta-analysis nature of the original article, four were excluded due to lack of information on gender, and 16 were excluded due to the lack of comparison between severity of the infection. finally, our search identified 15 observational studies (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) to be included in our meta-analysis (fig. 1) . eleven studies compared characteristics of severe versus nonsevere and four compared survivors versus nonsurvivors of covid-19 infection. the analysis included a total of 3,494 patients with 1,935 (55.4%) males and 1,559 (44.6%) females. the details of the study and patient characteristics are summarized in table 1 . all except one report were from china. the median age ranged from 42.0 to 60.0. the definition of severe covid-19 infection for each included study is summarized in table s1 (supplemental digital content 1, http://links.lww.com/ccx/a208). the result of quality assessment by the newcastle-ottawa assessment scale is summarized in table s2 (supplemental digital content 1, http:// links.lww.com/ccx/a208). males were more likely to develop severe covid-19 infection compared with females (or, 1.31; 95% ci, 1.07-1.60). there was no significant heterogeneity (i 2 = 12%) among the studies (fig. 2) . there was no significant difference in mortality between males and females (or, 1.53; 95% ci, 0.87-2.69) without significant heterogeneity (i 2 = 17%) among studies (fig. 3) . the salient findings of this meta-analysis are that males were more likely to develop severe covid-19 infections compared with females, while there was no significant difference in mortality between gender. studies have reported significant differences between men and women in regards to prevalence, severity, and even response to vaccination to several other viral illnesses, partially explained by the biological difference in antiviral, inflammatory, and cellular immune response to viruses (27, 28) . these differences are not only limited to virus but also seen in certain bacteria and parasites (29) . understanding the epidemiology of gender difference in susceptibility and vulnerability to a certain outbreak of infection may be important to effectively respond to or prepare for the public health crisis by minimizing the health, economic and social impact of the emerging outbreak (7, 30) . reports from who europe and chinese centers for disease control and prevention widely agree that the covid-19 infections are seen more frequently in males compared with females (53.6% (15) have found males to be associated with refractoriness of covid-19 infection. by performing a meta-analysis of studies comparing severe versus nonsevere covid-19 infection, we were able to provide the largest scale of evidence on gender disparity of severity of covid-19 infection, concluding that males were more likely to develop severe covid-19 infection compared with females. in our analysis, mortality was not significantly different between the gender; however, it is likely that the study population was small to exhibit significant differences. interestingly, similar findings of males being more susceptible and mounting more severe reaction to virus have been reported in severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers), an infection caused by a similar yet different stream of coronavirus. a report from hong kong investigating characteristic of sars have documented males to have significantly higher case fatality rate compared with females (33) . furthermore, mers has been reported to have a significantly higher incidence in males compared with females (7, 34) . the observed findings of gender difference in susceptibility and vulnerability to covid-19 infection may be multifactorial. gender differences in behavior may contribute to our findings of males being more susceptible to severe covid-19 infection. for instance, in the chinese population, men are reported to have a higher prevalence of smoking compared with women (35) . since all except one of the studies included in the present analysis are reported from china, this could have affected our result. however, to date, there is no firm evidence that smoking is the risk factor of severe covid-19 infection. furthermore, underlying differences in gene expression may be associated with different rates of severe covid-19 infection between gender. for instance, an expression of angiotensin-converting enzyme 2 (ace2) may also have a significant role in the observed gender difference in covid-19 infection outcomes. emerging evidence has suggested that ace2 is a co-receptor for sars-cov-2 viral entry into the human cell that plays a significant role of the pathogenesis of this virus (36) . the recent study has suggested that ace2 expression was higher in asian males (37) , which may have potentially contributed to the findings of this analysis. other explanations to why men were associated with severe outcomes compared with women in response to covid-19 infection may involve differences in immunologic reaction and the lack of protective effect of estrogen signaling seen in females; an insight derived from a study of mers and sars (38) . the present analysis has several limitations. first, the included studies were retrospective observational studies, and the pooled or are unadjusted. furthermore, the lack of individual patientlevel data limits our ability to adjust for potential confounders. however, our meta-analysis is valuable since previous studies have shown conflicting results of gender difference in the severity of covid-19. second, the definition of severe illness was variable among the studies. therefore, the results must be cautiously interpreted in regard to potential heterogeneity. finally, all but one of the included studies were reported from china, potentially limiting its applicability to other countries and races. nonetheless, this report is thus far the largest study comparing gender difference of vulnerability to this emerging covid-19 infection. this meta-analysis suggests that the male gender may be a predictor of more severe covid-19 infection but does not predict mortality. further accumulation of evidence from around the world is warranted to confirm our findings. supplemental digital content is available for this article. direct url citations appear in the html and pdf versions of this article on the journal's website (http://journals.lww.com/ccejournal). the authors have disclosed that they do not have any potential conflicts of interest. for information regarding this article, e-mail: hiroki.ueyama@mountsinai.org clinical features of patients infected with 2019 novel coronavirus in wuhan, china world health organization: rolling 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transcatheter aortic valve implantation critical evaluation of the newcastle-ottawa scale for the assessment of the quality of nonrandomized studies in meta-analyses clinical characteristics of refractory covid-19 pneumonia in wuhan, china diagnostic utility of clinical laboratory data determinations for patients with the severe covid-19 clinical characteristics of coronavirus disease 2019 in china dysregulation of immune response in patients with covid-19 in wuhan, china host susceptibility to severe covid-19 and establishment of a host risk score: findings of 487 cases outside wuhan characteristics of covid-19 infection in beijing clinical features and treatment of covid-19 patients in northeast chongqing clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical features of 69 cases with coronavirus disease risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease epidemiologic features and clinical course of patients infected with sars-cov-2 in singapore clinical characteristics of 140 patients infected with sars-cov-2 in wuhan, china abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study association of radiologic findings with mortality of patients infected with 2019 novel coronavirus in wuhan, china clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study the xs and y of immune responses to viral vaccines emerging and zoonotic infections in women sex differences in infectious diseases-common but neglected overcoming the 'tyranny of the urgent': integrating gender into disease outbreak preparedness and response the novel coronavirus pneumonia emergency response epidemiology team: the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) world health organization: covid-19 situation update for the who european region: data for the week of 16-22 do men have a higher case fatality rate of severe acute respiratory syndrome than women do? mers-cov outbreak in jeddah-a link to health care facilities prevalence and patterns of tobacco smoking among chinese adult men and women: findings of the 2010 national smoking survey a pneumonia outbreak associated with a new coronavirus of probable bat origin single-cell rna expression profiling of ace2, the putative receptor of wuhan sex-based differences in susceptibility to severe acute respiratory syndrome coronavirus infection key: cord-350338-lcsa06gm authors: wang, kun; zuo, peiyuan; liu, yuwei; zhang, meng; zhao, xiaofang; xie, songpu; zhang, hao; chen, xinglin; liu, chengyun title: clinical and laboratory predictors of in-hospital mortality in patients with covid-19: a cohort study in wuhan, china date: 2020-05-03 journal: clin infect dis doi: 10.1093/cid/ciaa538 sha: doc_id: 350338 cord_uid: lcsa06gm background: this study aimed to develop mortality-prediction models for patients with coronavirus disease 2019 (covid-19). methods: the training cohort were consecutive patients with covid-19 in the first people’s hospital of jiangxia district in wuhan from january 7, 2020 to february 11, 2020. we selected baseline clinical and laboratory data through the stepwise akaike information criterion and ensemble xgboost model to build mortality-prediction models. we then validated these models by randomly collecting covid-19 patients in the infection department of union hospital in wuhan from january 1, 2020, to february 20, 2020. results: 296 patients with covid-19 were enrolled in the training cohort, 19 of whom died during hospitalization and 277 were discharged from the hospital. the clinical model developed with age, history of hypertension and coronary heart disease showed auc of 0.88 (95% ci, 0.80-0.95); threshold, -2.6551; sensitivity, 92.31%; specificity, 77.44% and negative predictive value (npv), 99.34%. the laboratory model developed with age, high-sensitivity c-reactive protein (hscrp), peripheral capillary oxygen saturation (spo2), neutrophil and lymphocyte count, d-dimer, aspartate aminotransferase (ast) and glomerular filtration rate (gfr) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with auc of 0.98 (95% ci, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and npv, 100.00%. in the subsequent validation cohort (n=44), the aucs (95% ci) were 0.83 (0.68, 0.93) and 0.88 (0.75, 0.96) for clinical model and laboratory model, respectively. conclusions: we developed two predictive models for the in-hospital mortality of patients with covid-19 in wuhan and validated in patients from another center. we developed a clinical model and laboratory model for predicting the in-hospital mortality of covid-19 patients, the aucs (95% ci) were 0.88 (0.80, 0.95) and 0.98 (0.92, 0.99) in training cohort, and 0.83 (0.68, 0.93) and 0.88 (0.77, 0.95) in validation cohort, respectively. several cases of "unknown viral pneumonia" have been reported in wuhan, hubei 2 province, china since december 2019. the causative agent was revealed as a novel 3 coronavirus named as severe acute respiratory syndrome coronavirus 2 (sars-cov-2) by the 4 international committee on taxonomy of viruses. the disease caused by sars-cov-2 was 5 named coronavirus disease 2019 (covid-19) by the world health organization (who). 1 6 this infectious disease has rapidly spread from wuhan to other chinese regions 2 . since mid-7 march 2020, cases have been detected in most countries worldwide and community spread is mild acute respiratory infection symptoms, such as fever, dry cough, and fatigue, 13 commonly occur in the early stages of covid-19, but some patients might rapidly develop 14 acute respiratory distress syndrome, acute respiratory failure, multiple organ failure, and other 15 fatal complications. 3, 4 no specific treatment has been fully developed for covid-19; thus, 16 early identification of patients with poor prognosis may facilitate the provision of proper 17 supportive treatment in advance and reduce mortality. the participants in the training cohort were all the consecutive patients diagnosed with 28 covid-19 in the first people's hospital of jiangxia district in wuhan, a major hospital in 29 the jiangxia district. we collected data on patients hospitalized from january 7, 2020, 17:58 30 to february 11, 2020, 22:01. a total of 296 patients with final outcome (i.e. discharged or 31 dead) were enrolled in this study before february 12, 2020, 14:00. we then randomly 32 collected patients with covid-19 who had been hospitalized in the infection department of 33 union hospital in wuhan from january 1, 2020, to february 20, 2020 to form our validation 34 cohort. a flow diagram is showed in figure 1 . 35 the data of these participants were used to construct two predictive models for in-36 hospital mortality. the study protocol was approved by the medical ethics committee of the 37 first people's hospital of jiangxia district and union hospital, and was complied with the 38 declaration of helsinki. we verbally informed the patients that their data would be used 39 anonymously for medical studies and obtained their permission. written informed consent 40 was not gathered, because the data were anonymous and the study was observational. 41 previous medical history, age, cough and fever (the oral temperature>37.5 ℃, the 43 axillary temperature>37℃, or the body temperature fluctuates more than 1℃ in a day) for 44 every subject were obtained by trained nurses. the laboratory data of the first examination 45 after admission of every subject were also collected. 46 all blood and urinary samples were processed within two hours of collection. routine 47 106 range (iqr), 8.6-15.5] days, respectively. the mean and median hospital stay of the 107 survivors were 6.2 ± 5.0 and 4.9 (iqr, 2.6-10.5) days, respectively. the mean and median 108 time interval between symptom onset and admission of the non-survivors were 5.2 ± 3.7 and 109 5.0 (iqr, 3.0-7.0) days, respectively. and for the survivors were 6.8 ± 4.0 and 5.5 (iqr, 3.0-110 9.2) days, respectively. 111 baseline clinical and laboratory characteristics of study population by training and 112 validation cohort are shown in table 1 . we observed significant differences between the two 113 cohorts in age, outcome, symptoms, and clinical indicators. the patients in validation cohort 114 were remarkably older, with higher rates of diabetes and hypertension, lower spo2, and 115 worse markers of inflammation, clotting status, and liver and kidney function. 116 the comparison between the survivors and the non-survivors were shown in table 2 . the 117 mean age of the non-survivor group was remarkably higher than that of the survivor group in 118 both cohorts. medical history showed that the non-survivor group had a higher proportion of 119 basic disease. no substantial difference was observed in the sex composition and habits of 120 smoking and drinking between survivors and non-survivors. in the training cohort, non-121 survivors had remarkably lower spo2 than survivors. inflammatory cells, namely, wbc and 122 neutrophil, were considerably higher whereas lymphocyte was remarkably lower in the non-123 survivor group than in the survivor group. meanwhile, hscrp, a marker of inflammation, was 124 also substantially elevated in the non-survivor group. in terms of blood coagulation indexes, 125 the non-survivor group had higher d-dimer and thrombin time and lower activated partial 126 thromboplastin time than the survivor group. cr, bun, alt, ast, ldh, and blood ammonia 127 were remarkably higher whereas gfr and serum alb were significantly lower in the non-128 survivor group. 129 in the model-development phase, the clinical model developed according to age, history 130 of hypertension and coronary heart disease showed good discriminatory power with auc of table 4 ) 142 the roc of the two models in training and validation cohort were plotted in figure 2 . exhibited relatively good discriminatory power the and the external verification was also 151 satisfactory. we believe that this is the first study to establish models for predicting the 152 mortality of patients with covid19 . 153 the clinical model based on age, history of hypertension, and coronary heart disease had 154 achieved good predictive power. elderly people are at higher risks for chronic diseases and 155 more susceptible to infection. age might be the risk factor for worse outcomes in patients 156 with covid-19 partially because age-related immune dysfunctions result from low-grade 157 chronic inflammation according to our speculation. 5, 11 in addition, elderly patients may 158 possess other risk factors, such as comorbidities and sarcopenia. hypertension is one of the 159 most common diseases in the elderly. history of hypertension is an important risk indicator in 160 the mulbsta score, which is a viral pneumonia death warning model developed by chinese 161 scholars. 12 our results are consistent with the above research. in addition, angiotensinwith chd history and infected with sars-cov-2 has to work harder to ensure that sufficient 168 blood oxygen is provided throughout the body. the problem of increased heart burden will 169 become more prominent. reasonable precautions must be taken to prevent these patients from 170 the viral infection. 171 xgboost showed that hscrp was the most important predictor for the mortality of patients 172 with covid-19, followed by age, spo2, ast, neutrophil count, d-dimer, gfr and 173 lymphocyte count. this finding is consistent with our clinical observation. 174 a low spo2 level suggests that the patients might have a serious illness at the time of 175 admission. we found that most of the patients with covid-19 had mild acute respiratory 176 infection symptoms initially; however, the conditions of some patients would rapidly 177 exacerbate and result in multiple organ failure or even death. we suspected this exacerbation 178 was primarily due to the "cytokine storm" and consequent immunologic abnormality. 179 cytokine storm is an important cause of death in severe acute respiratory syndrome (sars), 180 middle east respiratory syndrome coronavirus, and influenza a virus subtype h1n1 181 infection. [15] [16] [17] cytokine storm also seems to be a remarkable mechanism in the present 182 outbreak of covid-19 and contributed to the death of several patients, especially young 183 patients. a recent study showed that patients requiring icu admission had higher 184 concentrations of granulocyte colony-stimulating factor, interferon-induced protein 10, 185 monocyte chemoattractant protein 1, macrophage inflammatory protein 1 alpha, and tumor 186 necrosis factor alpha than those who did not require icu admission, suggesting that cytokine 187 storm is associated with disease severity. 4 a remarkable finding of our study was that the 188 increasing level of hscrp and neutrophil counts had prominent power in predicting fatal 189 outcomes in patients with covid-19. neutrophil chemotaxis and transmigration are essential 190 components for host defense during infections, but excessive neutrophil infiltration 191 contributes to deleterious inflammatory processes, 18 which might deeply interact with 192 cytokine storm during virus invasion. 193 the substantially depressed total lymphocytes in the non-survivor group indicated that 194 sars-cov-2 might act on t lymphocytes, and high replication of the virus leads to the 195 depletion of t lymphocytes, which suppresses the body's immunity. 19 in addition, patients 196 with severe illness are more likely to be co-infected with bacteria because of depressed 197 immune function, which is another possible reason for the increased level of neutrophils and 198 hscrp. further studies are necessary to elucidate the cytokine storm and immunologic 199 abnormality in sars-cov-2 infection. 200 we found that coagulation indicators might play a role in identifying severe cases as 201 well. we observed that d-dimer was negatively associated with in-hospital mortality. high specificity and ppv were demonstrated in clinical models in the validation cohort, as 244 opposed to the training cohort. we hypothesized that the probable reason was that there were 245 more deaths in patients with a history of hypertensive or coronary artery disease in the 246 validation cohort. more external validation is needed to demonstrate the robustness of the 247 model, and we currently recommend that clinical models with limited information only be 248 used for preliminary screening of high-risk populations. 249 by comparing the training and validation populations in table 1 , we had observed 250 significant differences between the two groups in age, symptoms, and examination index 251 wk and lc conceived and designed the study. wk, zp, cx analyzed the data, and wrote the first draft of the manuscript. wk, ly, zm, zx, xs and zh recruited patients, gathered data and participated in manuscript revision. lc provided study oversight and participated in manuscript revision. all authors had access to study data and approved the decision to submit the manuscript. we thank the patients and families who agreed to participate in this important study. we there was no funding directly relevant to this work. chengyun liu received a grant from the national natural science foundation of china (81974222) within the last 36 months, which was not directly related to this study. and all of the authors declare that they have no conflict of interest. roc curves of in-hospital mortality from logistic regression models of patients with clinical data (red ) and laboratory data (black) using bootstrap resampling (times = 500). roc = receiver operator characteristic. auc = area under the curve. spo2=peripheral capillary oxygen saturation. ast=aspartate aminotransferase. gfr= glomerular filtration rate. alb=albumin. glo=globulin. ck=creatine kinase. -data not collected in the validation cohort. auc=area under the curve. aic= akaike information criterion. *bootstrap resampling (times = 500). outbreak of covid-19-an urgent need for good science to silence our fears? nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with 2019 novel coronavirus in wuhan clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster machine learning for the prediction of volume responsiveness in patients with oliguric acute kidney injury in critical care boosted tree model reforms multimodal magnetic resonance imaging infarct prediction in acute stroke transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (tripod) comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach innate immune responses in the ageing lung clinical features predicting mortality risk in patients with viral pneumonia: the mulbsta score genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding from gene to proteinexperimental and clinical studies of ace2 in blood pressure control and arterial hypertension preparing for the next influenza pandemic an interferon-γ-related cytokine storm in sars patients corticosteroid treatment ameliorates acute lung injury induced by 2009 swine origin influenza a (h1n1) virus in mice the trafficking protein jfc1 regulates rac1-gtp localization at the uropod controlling neutrophil chemotaxis and in vivo migration understanding the t cell immune response in sars coronavirus infection biochemical aspects of coronavirus replication and virus-host interaction abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia specific ace2 expression in cholangiocytes may cause liver damage after 2019-ncov infection clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province 25 national health commission. treatment scheme of covid-19 key: cord-029550-qodmamov authors: jandrić, petar title: review of fang fang (2020). wuhan diary: dispatches from a quarantined city. trans. m. berry: new york: harpercollins. 377 pp. isbn 9780063052659 (e-book) date: 2020-07-23 journal: postdigit sci educ doi: 10.1007/s42438-020-00173-w sha: doc_id: 29550 cord_uid: qodmamov nan on 25 january 2020, day one of the lunar new year and two days after the city of wuhan entered lockdown, the famous chinese writer fang fang started writing her online diary in her flat not far from the local huanan seafood wholesale market identified as a possible source of covid-19 (maron 2020) . this powerful spatio-temporal symbolic, combined with fang's poignant writing and her 3.8 million strong social media following at the time of publishing her first entry, has soon launched her online wuhan diary towards huge popularity. in early april, the '"fang fang diary" has had 380m views, 94,000 discussions, and 8,210 original posts' on chinese social network weibo (davidson 2020) and was also mirrored on numerous other places throughout the web. on 24 march, after 60 consecutive days of writing, fang published her last entry. on 15 may, english translation of fang's online diary was compiled into a book and published as wuhan diary: dispatches from a quarantined city (fang 2020) . following fang's huge online success, the book has become a best seller in less than a month after its publication, and translations to several other languages are on their way (siqi 2020) . when she started writing the diary, fang did not plan to compile her online entries into a book. this lack of planning clearly shows in text's less-than-perfect transition from short online vignettes to a 377-page volume. furthermore, the diary has been translated in real time, and such urgency left no time for deep editing. in translator's afterword, michael berry describes huge efforts needed to publish the book in english mere 3 weeks after fang wrote her last entry in chinese. 'so for 46 days, from february 25 through april 10, 2020, i translated roughly 5,000 words a day (minus a week's break to recover from illness), living amid an unfolding pandemic' (berry in fang 2020: 356) . urgent publication of translation of wuhan diary (fang 2020) to english and other languages is fully justified by book's relevance for the world locked down in anti-pandemic measures. translating the book from his home in los angeles, berry writes that 'translating a diary written one month in the past, which somehow, simultaneously, offered glimpses into our future' (berry in fang 2020: 356). as the pandemic slowly spread around the globe, this insight into wuhan's reality has become a window into the future for the whole world (see jandrić 2020). it also opens up a myriad of questions for western governments and individuals. why did we not listen to these early warnings? why did we not care? the western world has largely ignored what happened in china in early days of the covid-19 pandemic, and only few months later, it has paid a dire price for its arrogance (jackson 2020) . as it becomes clear that covid-19 is here to stay (sharping 2020) , wuhan diary gives a powerful lesson in humility to everyone who thinks that suffering in china, or anywhere else in the world, is not their business. the world has become one, both metaphorically and literally, and covid-19 teaches citizens of the whole world what it means to live in the anthropocene. the world may have become one, but that does not mean we are all the same. fang's words build a unique rhythm, slow yet powerful, which (for a western reader) requires some getting used to. most entries start with innocent weather reports and chatter about fang's extended family and neighbours. within these trivial details, fang masterfully interweaves diverse topics including courage and resilience of everyday people, reports from hospitals and morgues, troubles with obtaining face masks, government's responsibility, censorship, and many others. this slow build-up occasionally culminates in a very open critique of various responses to the covid-19 pandemic by doctors, government officials, and the communist party. on 6 february, fang reported about the death of dr. li wenliang. 'he was one of the eight doctors who were penalized for speaking out about the virus early on, and later he himself was infected with the novel coronavirus. right now everyone in this city is crying for him. and i am heartbroken' (fang 2020: 61) . until the end of the book, fang occasionally returns to dr. li wenliang; with each subsequent mention, her grief turns into a deeper and deeper social critique and a call to responsibility: i realized that this was precisely why we were all so angry about the death of li wenliang. after all, he was the first to speak out, even if all he did was warn his own friends, but by doing that he revealed the truth. but after he spoke out, dr. li wenliang was punished, forced to sign a confession, and later he sacrificed his life-no one ever apologized to him before his death. when that is the result of speaking out, moving forward, how can we expect anyone else to speak the truth? (fang 2020: 64) in places, her critique almost sounds like a call for action. 'dr. ai fen already sounded the alarm; dr. li wenliang also made some noise; but who is there to carry on their mission? the sound of the whistleblowers has disappeared under the triumphant songs and laughter blaring from those two big media companies.' (fang 2020: 275-276) fang's critique of dr. li wenliang's death is one of many gateways into her deep and poignant critique of the chinese society. yet many would say that her critique is not strong enough (e.g. diterbitkan 2020). fang is a well-known chinese writer and a former president of the hubei writers' association, who has lived in the literary and arts federation compound for 30 years, surrounded by other writers and artists recognized and approved by the chinese government. at the time of writing the diary, fang was not a superstar, but she was definitely a well-respected member of the chinese society, and she never tried to hide that. in a moment of self-reflection, fang writes: my lifestyle is indeed a bit different from your average person's because i'm a professional writer who has published nearly 100 books. there are a lot of people out there who have read my work and they seem to respect me, especially people here in wuhan. the fact that i have won a small amount of notoriety for my writings certainly has led some people to go out of their way to help me out; i have to admit that. sometimes when i go out to eat, the restaurant owner will bring out a special dish, and i even once had a cab driver who refused to accept the cab fare after he recognized me. i am very thankful and moved by all these people's generosity. (fang 2020: 262) it is safe to assume that fang would not be able to maintain such lifestyle, had she been significantly out of the party line. and yet, fang is far from a typical regime writer, and wuhan dairy is not her first clash with the chinese establishment. in 2017, her awardwinning novel soft burial situated in the age of mao zedong's land reform campaign was banned for being too radical (lam 2017) . this places fang's critique somewhere in the middle: strong enough to stir a lot of water, yet mild enough to keep fang in good terms with the establishment. as soon as her diary appeared online, it was strongly censored. in china, fang's diary has triggered polarized views, 'where some call her a truth-teller but others view her as a liar and traitor' (siqi 2020) . some examples of this critique include following excerpts from the media. 1 'bravo fang fang. you're giving western countries ammunition to target china,' said one post about her on the country's twitter-like weibo platform. 'you've shown your treacherous nature', it said. another accused fang of making money off wuhan's nearly 4000 virus victims, writing: 'how much did you sell the diary for?' (agence france presse 2020). 'wuhan diary is a knife handed over to foreigners and a bullet shooting at chinese', said one poster on weibo. another wrote: 'the woman only writes articles in her own small blog, and does not know the overall situation of our country at all. maybe she does not admit that she is unpatriotic, she thought we were extreme, in fact she was just a stupid old lady' (davidson 2020) . yue zhongyi, a 63-year-old resident of wuhan, said a lot of the criticism represented nationalist sentiment rather than the views of the city's people. 'i asked all of my neighbours and friends and all of them said they support fang fang', he said. 'her diaries represent our experiences and our feelings'. the writer's critics misunderstood the notion of patriotism, he said (lau and xie 2020). fang has received death threats, and her home address has been posted online (agence france-presse 2020). michael berry, translator of wuhan diary, has also 'received thousands of angry emails and death threats for simply translating her writing' (feng 2020) . in the west, fang's work has attracted almost unanimously positive reactions. fang's publishing house, harpercollins, claims that '[t] he stark reality of this devastating situation drives fang fang to courageously speak out against social injustice, corruption, abuse, and the systemic political problems which impeded the response to the epidemic' (in siqi 2020). the diplomat claims that 'the daily account of the locked down city's millions of inhabitants' untold sufferings during the ongoing health crisis has recast fang fang from a well-known literary figure into china's most revered living literary voice of dissent. 'her fans in china are already proclaiming her to be the conscience of wuhan' (adlakha 2020) . alice su of la times writes: hers is a voice of rare authenticity, an antidote to the flood of chinese propaganda celebrating the country's victory over the coronavirus. she weeps, she shouts, she describes corpses in bags, dragged away and burnt while their loved ones mourn alone. she curses those who concealed the truth and will not apologize even as thousands die. while state media trumpets hero stories and upbeat slogans, fang fang speaks plainly of her people's suffering. (su 2020) in wuhan diary (2020), and also elsewhere, fang repeatedly insists that her diary is not in any way aimed against the establishment. in an interview for caixin (2020), she makes a point that 'there's no tension between me and the country, and my book will only help the country' and that her 'diary is by no means about the so-called negative things in china or deliberately peddling misery as misinterpreted by extremists. they take it out of context.' so how do we make sense of all this? has freedom of speech in china achieved such progress that the chinese government and communist party decided not to censor fang? or has fang's online diary taken them by surprise, so after the diary has become viral, they had no other choice but to play neutral while orchestrating attacks from below? or should we perhaps believe the independent analyst wu qiang's hypothesis about the chinese art of censorship? also, despite the backlash she had faced, fang-who is a former president of the officially affiliated hubei writers' association-was still considered a 'politically trustworthy figure', wu said, and her work was still available on china's internet. 'many voices from wuhan have been silenced. the fact that her work was allowed to survive is the art of censorship: to let out a relatively moderate voice to avoid the embarrassment of a completely blank canvass', he said (diterbitkan 2020) for a western person lacking in deep understanding of chinese culture and society, many domestic implications of wuhan diary (fang 2020) will forever remain a mystery. many answers may be left to mystery, yet there is no doubt that that the historical significance of fang's work reaches well beyond her original thoughts and ideas. the assemblage of wuhan diary: dispatches from a quarantined city (fang 2020 ) and its responses is an almost perfect example of a postdigital dialogue (jandrić 2017; jandrić et al. 2019) and an exercise in we-think, we-learn, and we-act (jandrić 2019; jandrić and hayes 2020). as i wrote in my last year's editorial for postdigital science and education, '[a] ny thinking, individual or collective, is derived from and produces learning. any thinking and learning might have been derived from the actions of someone or something else or might provoke new thinking, learning, or action, by someone or something else' (jandrić 2019: 278) . furthermore, the trialectic of we-think, we-learn, and we-act is meaningless without our personal feelings (jandrić and hayes 2020) and also myth, custom, and religion (mclaren and jandrić 2020: 256) . sitting at the edge between the online and the offline world, and at the intersections of all these forces, wuhan diary: dispatches from a quarantined city (fang 2020) is a truly postdigital book written in a and for our postdigital times. many commentators argue that fang's critique is too strong, and just as many commentators argue that her critique is too weak. to each their own, depending on perspective, both conclusions can be supported by solid arguments. however, there is no doubt that fang's style of critique is strong enough to attract massive global attention and weak enough to make it into the mainstream. in result, fang's work has ignited in a hugely important global postdigital dialogue about individual and social responses to the covid-19 pandemic. whether we agree with fang or not, wuhan diary: dispatches from a quarantined city (fang 2020) is a true exercise in postdigital critical pedagogy. fang fang: the 'conscience of wuhan' amid coronavirus quarantine. the diplomat chinese writer faces backlash for 'wuhan diary wuhan diary author -there is no tension between me and the country chinese writer faces online backlash over wuhan lockdown diary. the guardian coronavirus: chinese writer hit by nationalist backlash over diary about wuhan lockdown wuhan diary: dispatches from a quarantined city wuhan diary' brings account of china's coronavirus outbreak to english speakers weary from the future, hong kong learning in the age of digital reason we-think, we-learn, we-act: the trialectic of postdigital collective intelligence postdigital research in the time of covid-19 postdigital we-learn china bans 'soft burial', an award-winning novel about the deadly consequences of land reform coronavirus: chinese writer hit by nationalist backlash over diary about wuhan lockdown. south china morning post wet markets' likely launched the coronavirus. here's what you need to know postdigital dialogues on critical pedagogy, liberation theology and information technology could we be living with covid-19 forever? discover magazine chinese vigilant on deifying writer fang fang amid publication of wuhan diary in english. global times two months into coronavirus lockdown, her online diary is a window into life and death in wuhan key: cord-267548-7mcfehzc authors: mizumoto, kenji; chowell, gerardo title: estimating risk for death from coronavirus disease, china, january–february 2020 date: 2020-06-17 journal: emerg infect dis doi: 10.3201/eid2606.200233 sha: doc_id: 267548 cord_uid: 7mcfehzc since december 2019, when the first case of coronavirus disease (covid-19) was identified in the city of wuhan in the hubei province of china, the epidemic has generated tens of thousands of cases throughout china. as of february 28, 2020, the cumulative number of reported deaths in china was 2,858. we estimated the time-delay adjusted risk for death from covid-19 in wuhan, as well as for china excluding wuhan, to assess the severity of the epidemic in the country. our estimates of the risk for death in wuhan reached values as high as 12% in the epicenter of the epidemic and ≈1% in other, more mildly affected areas. the elevated death risk estimates are probably associated with a breakdown of the healthcare system, indicating that enhanced public health interventions, including social distancing and movement restrictions, should be implemented to bring the covid-19 epidemic under control. s ince the first case of coronavirus disease (covwas identified in december 2019 in the city of wuhan in the hubei province of china, the novel virus (severe acute respiratory syndrome coronavirus 2 [sars-cov-2]) has continued to spread around the world, resulting in several thousand reported cases in multiple countries. in china, the cumulative number of reported deaths was 2,858 as of february 28, 2020, a figure that already dwarfed the number of persons that succumbed to severe acute respiratory syndrome during 2002-2003 (1) . in the context of an emerging infectious disease with pandemic potential, assessing its efficiency at spreading between humans is critical, as is determining the associated risk for death from the disease. in particular, the type and intensity of public health interventions are often set as a function of these epidemiologic metrics. in the absence of vaccines against sars-cov-2 or antiviral drugs for the treatment of covid-19, the implementation of handwashing and other hygiene-related interventions, as well as nonpharmaceutical interventions such as social distancing and movement restrictions (all of which are the basic strategies available to mitigate disease spread in the population), also generate considerable pressure on the global economy (2) . as interventions are gradually implemented and calibrated during the course of an outbreak, early estimates of the case-fatality ratio (cfr) provide crucial information for policymakers to decide the intensity, timing, and duration of interventions. however, the assessment of epidemiologic characteristics, including the cfr, during the course of an outbreak tends to be affected by right censoring and ascertainment bias (3) (4) (5) . the phenomenon of right censoring is caused by the gap in illness onset to death between the vulnerable population and the healthy population, resulting in underestimation, whereas ascertainment bias is attributable to the unreported bulk of infected persons who have mild symptoms or asymptomatic infections, potentially leading to overestimation. assuming that ascertainment bias is consistent, we can adjust for right censoring by using established methods and available data (6, 7) . to assess the current severity of the epidemic in china, we derived estimates (and quantified uncertainty) of the time-delay adjusted cfr for covid-19 for the city of wuhan and for china excluding wuhan, with quantified uncertainty. we used 2 different types of epidemiologic data in our analysis. first, we extracted the daily series of confirmed cases and deaths in china from daily reports published by the respective governments of china, hubei province, and the city of wuhan (8) (9) (10) (11) (12) . we then obtained from several sources a total of 50 epidemiologic descriptions of patients who died from covid-19 (9) (10) (11) . after we checked for duplication and missing data, the sample size with data available was 39 patients for observed delays from illness onset to death and 33 for observed delays from hospitalization to death. we fitted a gamma distribution, an exponential distribution, and a lognormal distribution to these distributions and selected the best model based on the akaike information criterion (aic) (appendix 1, https://wwwnc.cdc.gov/ eid/article/26/6/20-0233-app1.pdf). the gamma distribution yielded the best fit for the distribution of delays from hospitalization to death (aic 202.0), whereas the log-normal distribution gave the best fit for the distribution of delays from illness onset to death (aic 263.3). on the basis of these 2 delay distributions, we incorporated the distribution of delays from hospitalization to death into the model. we defined crude cfr as the number of cumulative deaths divided by the number of cumulative cases at a specific point in time. to estimate cfr in real time, we used the delay from hospitalization to death, h s , which is assumed to be given by h s = h(s) -h(s-1) for s>0 where h(s) is a cumulative density function of the delay from hospitalization to death and follows a gamma distribution with mean 10.1 days and sd 5.4 days, obtained from the available observed data. if π a,ti os the time-delay adjusted cfr on reported day ti in area a, the likelihood function of the estimate π a,ti is where c a,t represents the number of new cases with reported day t in area a, and d a,ti is the cumulative number of deaths until reported day t i in area a (6,7). among the cumulative cases with reported day t in area a, d a,ti have died, and the remainder have survived the infection. the contribution of those who have died with biased death risk is shown in the middle parenthetical term, and the contribution of survivors is shown in the right parenthetical term. we assume that d a,ti is the result of the binomial sampling process with probability π a,ti . we estimated model parameters by using a markov chain monte carlo method in a bayesian framework. we estimated posterior distributions of the model parameters by sampling from the 3 markov chains. for each chain, we drew 100,000 samples from the posterior distribution after a burn-in of 20,000 iterations. we evaluated convergence of markov chain monte carlo chains by using the potential scale reduction statistic (13, 14) . estimates and 95% credibility intervals (cris) for these estimates are based on the posterior probability distribution of each parameter and based on the samples drawn from the posterior distributions. all statistical analyses were conducted in r version 3.6.1 (r foundation for statistical computing, https://www.r-project.org) using the rstan package. as of february 11, 2020, a total of 44,795 cases of co-vid-19 had been reported in china, 1,117 of which had resulted in death (9we charted the cumulative cases and deaths in wuhan, hubei province excluding wuhan, and china excluding hubei province (figure 1 ). the curve of the cumulative number of deaths grows after that of the cumulative number of cases. moreover, the increase in the number of deaths in wuhan occurred more rapidly and the associated mortality rate was much higher than for the rest of china, whereas the cumulative case counts for the 3 areas in china are relatively similar. we also charted the observed and model-based posterior estimates of crude cfr and the model-based posterior estimates of the time-delay adjusted cfr for wuhan, hubei province excluding wuhan, and china excluding hubei province (figure 2 ). our model-based crude cfr fitted the observed data well throughout the course of the epidemic except for the very early stage. during the course of the outbreak, our model-based posterior estimates of time-delay adjusted cfr have much higher values than the observed crude cfr, except for the early stage in wuhan and the later stage in china excluding hubei province. our estimates of the time-delay adjusted cfr appear to be decreasing almost consistently in hubei province excluding wuhan and in china excluding hubei province, whereas in wuhan, estimates were low at the early stage and then increased and peaked in the middle of the study period; the wuhan estimates then followed a decreasing trend similar to the other 2 areas, reaching ≈12%. as of february 11, estimates of the time-delay adjusted cfr were 12.2% (95% cri 11.3%-13.1%) in wuhan, 4.2% (95% cri 3.7%-4.7%) in hubei province excluding wuhan, and 0.9% (95% cri 0.7%-1.1%) in china excluding hubei province. the observed crude cfr was 4.2% (95% ci 3.9%-4.5%) in wuhan, 1.8% (95% ci 1.6%-2.0%) in hubei province excluding wuhan, and 0.43% (95% ci 0.32%-0.57%) in china excluding hubei province (table; figure 3 ). we have derived estimates of the cfr for the ongoing covid-19 epidemic in china. we have estimated time-delay adjusted cfr in 3 different geographic areas in china and found that the most severely affected areas were wuhan as well as hubei province excluding wuhan, whereas the rest of china (china excluding hubei province) experienced a less severe impact. our latest estimates (as of february 11, 2020) of the delay-adjusted cfr in wuhan reach values as high as 12.2% (95% cri 11.3%-13.1%), an estimate that is 3-fold higher than our estimate for hubei province excluding wuhan and ≈14-fold higher than our estimate for china excluding hubei province. these findings suggest that the situation in wuhan has been particularly dire compared with the other affected areas in china. we note that the upward trend of cfr during the early phase generally indicates increasing ascertainment bias. an upward trend in the cfr should be interpreted with caution. diagnosing cases of covid-19 is difficult because the associated symptoms are not specific. further, the fraction of asymptomatic patients with sar-cov-2 infection and covid-19 patients who have mild symptoms is not minor; this fact complicates detection and diagnosis early after illness onset, leading to ascertainment bias (15, 16) . indeed, out of a total of 566 residents of japan who evacuated wuhan by government-chartered plane during january 29-31, a total of 5 asymptomatic and 4 symptomatic covid-19 patients were detected after undergoing detailed medical examinations (17). however, considering that this underestimation occurred during the course of outbreak and the number of deaths is reported fairly accurately, the upward trend indicates that the temporal disease burden exceeded the capacity of healthcare facilities and the surveillance system probably missed many cases during the early phase. in addition, hospital-based transmission has occurred, potentially affecting healthcare workers, inpatients, and visitors at healthcare facilities, which might explain an increasing trend and the elevated cfr estimates. indeed, thousands of healthcare workers have succumbed to the disease in china (18), a pattern that resembles past nosocomial outbreaks of middle east respiratory syndrome (mers) and severe acute respiratory syndrome (19, 20) . during past mers outbreaks, inpatients with underlying disease or elderly persons infected in the hospital setting have raised the cfr to values as high as 20% (21, 22) . a growing body of evidence indicates that covid-19 transmission is facilitated in confined settings; for example, a large cluster (634 confirmed cases) of covid-19 secondary infections occurred aboard a cruise ship in japan, representing about one fifth of the persons aboard who were tested for the virus. this finding indicates the high transmissibility of covid-19 in enclosed spaces (23, 24) . a downward trend in cfr is suggestive of the extent of improvements in epidemiologic surveillance. in addition, this pattern indirectly indicates a substantial number of mild or asymptomatic cases in wuhan and that the underlying transmission might prolong the end of the outbreak or further transmission to other areas unless effective social distancing measures are implemented until a vaccine becomes available. furthermore, given that the delay-adjusted cfr and crude cfr estimates in wuhan are ≈14fold higher than our estimates for china excluding hubei province, a breakdown in healthcare delivery probably occurred, underscoring the critical need for urgent medical support in the epicenter of the epidemic. we also found that the estimates of the delayadjusted cfr for hubei province excluding wuhan and for china excluding hubei province showed a declining trend as the epidemic progressed. a similar trend was previously reported for the 2015 mers outbreak in south korea, where a substantial fraction of the case-patients were elderly or had underlying conditions (19, 20) . the high proportion (27) . our study has limitations. first, our cfr estimate is influenced by ascertainment bias, which might influence estimates upward. for those infectious diseases characterized by a large fraction of patients with mild illness or asymptomatic infections, the infection-fatality risk (e.g., the number of deaths divided by the total number of persons infected) is a more appropriate index of disease burden (28, 29) . therefore, mass serologic surveillance and surveys to assess the presence or absence of symptoms is strongly recommended to disentangle the threat of emerging infectious diseases, including covid-19. in addition, because our estimates of cfr are based on the number of confirmed cases reported before the february 12 change in the case definition, caution will be needed when comparing our estimates with other cfr estimates that include epidemiologic data from on or after february 12, which would be lower. second, in our estimation we employed a distribution of delays from illness onset to death (n = 39 patients), which was obtained from secondary sources, but the available epidemiologic data does not include either the date of illness onset or the date of confirmation. for this reason, we used the time delay from hospitalization to death (n = 33 patients). in conclusion, our estimates of the risk for death from covid-19 in china as of february 11, 2020, were as high as 12% in the epicenter of the epidemic and as low as ≈1% in the less severely affected areas in china. because the risk for death from covid-19 is probably associated with a breakdown of the healthcare system in the absence of pharmaceutical interventions (i.e., vaccination and antiviral drugs), enhanced public health interventions (including social distancing measures, quarantine, enhanced infection control in healthcare settings, and movement restrictions), as well as enhanced hygienic measures in the general population and an increase in healthcare system capacity, should be implemented to rapidly contain the epidemic. world health organization. summary of probable sars cases with onset of illness from 1 sars outbreaks in ontario, hong kong and singapore: the role of diagnosis and isolation as a control mechanism methods for estimating the case fatality ratio for a novel, emerging infectious disease case fatality rate for ebola virus disease in west africa non-parametric estimation of the case fatality ratio with competing risks data: an application to severe acute respiratory syndrome (sars) early epidemiological assessment of the virulence of emerging infectious diseases: a case study of an influenza pandemic dynamics of the pneumonic plague epidemic in madagascar assessing the severity of the novel influenza a/h1n1 pandemic the state council of the people's republic of china. update on new coronavirus pneumonia health commission of hubei province. china. pneumonia epidemic prevention and control of new coronavirus infection wuhan municipal commission of health and health on pneumonia of new coronavirus infection the state council of the people's republic of china. clinical guideline for covid-19, version 5 markov chain monte carlo: stochastic simulation for bayesian inference inference from iterative simulation using multiple sequences transmission of 2019-ncov infection from an asymptomatic contact in germany ministory of health, labour and welfare over 1,700 frontline medics infected with coronavirus in china, presenting new crisis for the government transmission characteristics of mers and sars in the healthcare setting: a comparative study evaluating the potential impact of targeted vaccination strategies against severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) outbreaks in the healthcare setting real-time characterization of risks of death associated with the middle east respiratory syndrome (mers) in the republic of korea estimating the risk of middle east respiratory syndrome (mers) death during the course of the outbreak in the republic of korea estimating the asymptomatic proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess cruise ship transmission potential of the novel coronavirus (covid-19) onboard the diamond princess cruises ship characteristics of covid-19 infection in beijing china medical treatment expert group for covid-19. clinical characteristics of coronavirus disease 2019 in china clinical characteristics of 50466 hospitalized patients with 2019-ncov infection infection fatality risk of the pandemic a(h1n1)2009 virus in hong kong new york city swine flu investigation team. the severity of pandemic h1n1 influenza in the united states key: cord-339044-qy4jab37 authors: li, man; cheng, biao; zeng, wen; chen, sichao; tu, mengqi; wu, meng; tong, wei; wang, shipei; huang, yihui; long, wei; zhou, wei; chen, danyang; zhou, lin; wang, min; xu, haibo; deng, aiping; liu, zeming; guo, liang title: analysis of the risk factors for mortality in adult covid-19 patients in wuhan: a multicenter study date: 2020-08-25 journal: front med (lausanne) doi: 10.3389/fmed.2020.00545 sha: doc_id: 339044 cord_uid: qy4jab37 objectives: an outbreak of coronavirus disease (covid-19) in 2019 in wuhan, china, has spread quickly worldwide. however, the risk factors associated with covid-19-related mortality remain controversial. methods: a total of 245 adult patients with laboratory-confirmed covid-19 from two centers were analyzed. chi-square, fisher's exact, and the mann-whitney u-tests were used to compare the clinical characteristics between the survivors and non-survivors. to explore the risk factors associated with in-hospital death, univariable and multivariable cox regression analyses were used. results: of the 245 patients included in this study, 23 (9.4%) died in the hospital. the multivariate regression analysis showed increased odds of in-hospital deaths associated with age, d-dimer levels >1,000 ng/l, platelet count <125, and higher serum creatinine levels. conclusions: we identified risk factors that show significant association with mortality in adult covid-19 patients, and our findings provide valuable references for clinicians to identify high-risk patients with covid-19 at an early stage. in december 2019, infectious pneumonia broke out in wuhan, hubei province. it was caused by a new coronavirus, which was named "sars-cov-2" by the world health organization (who) on february 13, 2020 (1) . meanwhile, the infectious disease caused by sars-cov-2 was named "covid-19." in china, according to the national health commission (2), a total of 82,341 cases were diagnosed, of which 77,892 patients were discharged, and 3,342 died as of april 15. since the early stages of the outbreak, the disease has spread to most countries in the world. as of april 15, 2020, more than 1,900,000 people have been infected and over 120,000 people have died worldwide (3) . the situation is likely to worsen with the rapid escalation and global spread of infection (4) . the symptoms for covid-19 vary from cough and fever to dyspnea, which can be difficult to identify. approximately 20% of the patients are estimated to develop severe illness, with overall mortality around 2.3% (5) . given that there are no drugs that have been proven to be clinically effective in targeting the sars-cov-2 directly, it is particularly important to identify the risk factors associated with disease progression and mortality (6, 7) . in this study, we explored the potential host risk factors associated with death in a retrospective cohort of 245 laboratoryconfirmed covid-19 patients admitted to the two appointed hospitals in wuhan. we present a detailed review of the medical information of each patient to clarify the clinical manifestations, laboratory test results, and outcomes to better understand the disease progression and prognosis. this multiple center retrospective study was approved by the institutional ethics board of the zhongnan hospital of wuhan university (no. 2020015) and the central hospital of wuhan (no. 2020072). oral informed consent was obtained from patients before data collection with their privacy rights protected. according to the seventh interim guidance of diagnosis and treatment of covid-19 published by the chinese national health commission on march 3, 2020 (8), patients with radiological characteristics of viral pneumonia were recognized as suspected cases. meanwhile, patients who tested positive with the real-time reverse-transcription-polymerase-chain-reaction (rt-pcr) test for sars-cov-2 or showed high-level homology with sars-cov-2 detected through gene sequencing were diagnosed as confirmed cases. therefore, patients who were negative on repeated rt-pcr test and those without clear outcomes within the observation cut-off time were excluded from the study. ultimately, we enrolled a total of 245 patients who were admitted to zhongnan hospital of wuhan university and the central hospital of wuhan between december 26, 2019, and february 15, 2020. all the patients were followed up until march 7, 2020. we collected data on the demographic, clinical, laboratory, and radiological characteristics, as well as treatment and clinical outcomes of the included patients. all the information was acquired from their electronic records and independently checked by three participants (sw, sc, and yh) to verify data accuracy. the demographic features included gender (male or female), age at diagnosis, comorbidities, symptoms, and time from onset to admission. laboratory tests included routine blood tests, blood coagulation tests, and tests for renal and liver functions, creatine kinase, infection-related biomarkers, brain natriuretic peptide (bnp), and rt-pcr analysis for sars-cov-2. the radiographic examination included chest ct or x-ray. clinical management and outcomes data included information on therapies, and clinical outcomes until the end of the follow-up period, time from onset to a negative rt-pcr result, and changes in chest x-rays and ct scans. the baseline characteristics of survivors and non-survivors were compared. categorical and continuous variables were presented as n (%) and median (iqr), respectively. the chi-square test or fisher's exact test were performed for categorical variables, and the mann-whitney u-test was used for continuous variables. univariable and multivariable cox regression analyses were applied to investigate the risk factors associated with in-hospital deaths. candidate factors for the multivariable analysis were chosen on the basis of the previous findings and findings of the univariable analysis. for laboratory results, we considered the normal ranges used in the zhongnan hospital of wuhan university as the reference. all data analyses were performed using spss (version 26.0). the 245 laboratory-confirmed covid-19 patients were divided into survivor (n = 222) and non-survivor (n = 23) groups. the demographic characteristics and symptoms of all the patients are shown in table 1 . the median age of all patients was 54 [interquartile range (iqr): 37-64] years, while that of patients in the survivor group was 52 years. the median age of the nonsurvivor group was 76 years. the proportion of men (48.2%) and women (51.8%) was comparable across the whole cohort. female patients accounted for a higher percentage (55.0%) of the survivor group, while male patients accounted for the majority (78.3%) of the non-survivor group. about half the patients (n = 122) had underlying diseases including hypertension, diabetes, chronic obstructive lung disease, cardiovascular disease (cvd), carcinoma, nervous system disease, and hepatic disease. hypertension was the most common comorbidity in the nonsurvivor group, followed by cvd. the most common symptoms on admission were fever and cough, followed by fatigue and expectoration ( table 1 ). the median time from the onset to admission was 6 (iqr: 3-8.5) days. table 2 summarizes the laboratory results of the study population. on admission, 168 (73.0%) patients had lymphocyte counts below the normal range, while 60 (26.0%) of them had it within the normal range. the non-survivor group had higher counts of white blood cells (median value: 6.88 vs. 4.19) and neutrophils (5.83 vs. 2.60) compared to the survivor group while the latter had lower counts of lymphocytes (0.85 vs. 0.91) and platelets (157.00 vs. 166.50). compared to the survivor group, the non-survivor group had three times higher levels of d-dimer as well as higher baseline levels of alanine aminotransferase (alt), aspartate transaminase (ast), total bilirubin, serum creatine, all infection-related biomarkers and brain natriuretic peptide. based on chest x-rays and ct manifestations, 91.9% (159/173) of the patients the univariable analysis found higher odds of in-hospital death in patients with chronic obstructive lung disease, and cvd (table 4) . age, sex, lymphocyte counts, prothrombin time, levels of albumin, alt, sodium, myoglobin, c-reactive protein, and ribavirin were also significantly associated with death (p < 0.05) ( table 4 ). the multivariate regression analysis showed ( though the epidemiology of patients with covid-19 is widely studied and reported, the death-related risk factors and detailed clinical characteristics of the disease have not been well-described. in this study, we summarized the clinical characteristics of 245 patients diagnosed with covid-19 at two centers in wuhan. we also identified risk factors associated with covid-19-related deaths. these included older age, ddimer > 1,000 ng/l, platelets < 125 × 10 9 /l, and higher serum creatinine levels. in our study, 9.4% of the patients died of covid-19. while the average age of the total cohort was 54 years, that of the non-survivor group was 76 years. in another retrospective, multicenter study on covid-19 cases from wuhan (9), 54 (28.3%) of the patients died in hospital, the median age of in wuhan is significantly higher than that in other regions. it is probably because of the concentration of a large number of cases. it has been reported that older patients have a worse prognosis of the middle east respiratory syndrome (mers) and severe acute respiratory syndrome (sars) (11, 12) . previous studies have found that older age is related to stronger host innate responses to virus infection and stronger activation of the proinflammatory pathways, with a marked decline in cell-mediated as well as humoral immune functions (13, 14) . in addition to age factors, we also found d-dimer levels >1,000 ng/l, and platelet counts < 125 × 10 9 /l on admission were associated with fatal outcomes in covid-19 patients. high levels of d-dimer have been verified to be a significant prognostic factor in patients with suspected infection and sepsis (15) . increased d-dimer is distinctly associated to disseminated intravascular coagulation, which is considered as an early stage of diffuse pulmonary intravascular coagulopathy (16) . extensive thrombosis in small vessels and the microvasculature has been confirmed histologically as one of the important basic pathological changes of lung in hospitalized covid-19 patients (17) . platelets also play an equally important role as a consumable substance in the clotting process. therefore, the reduction of platelets may also affect the survival status of patients through the same way. as we all know, covid-19 has many similarities to sars. in a retrospective study, 20-45% of sars patients had thrombocytopenia (18) . there are 7(35%) of non-survivor patients had platelets counts below the normal range on admission. moreover, severe infections could lead to secondary thrombocytopenia characterized by a rapid decline in platelet count (19) . these conditions are associated with damages to the hematopoietic system and the lungs, in which mature megakaryocytes release platelets (20) . however, qu et al. (21) have reported that while covid-19 patients with significantly elevated platelet count during treatment were on an average hospitalized longer, the platelet count at admission was lower in severely ill patients (169.67 ± 48.95) compared to those who were not severely ill (192.26 ± 58.12). the initial increase in platelet count, followed by a decrease in severely ill patients, may be associated with the progression of covid-19. basal cvd did not show a significant association with covid-19-related mortality. coronary heart disease has been correlated with acute cardiac incidents and adverse outcomes in respiratory viral infections (22) (23) (24) . however, consistent with our findings, previous studies (9) have also verified that cvd did not play an independent role in multivariate regression analysis of covid-19-related mortality. this study has some limitations. first, laboratory tests such as hypersensitive troponin, creatine kinase, and serum ferritin were missing because the study was retrospective. at the same time, because many cases were hospitalized in the early stage of the epidemic, there are also many missing data of viral nucleic acid test. second, the outcomes were evaluated at the end of the follow-up period instead of at a fixed time point during the course of the disease. finally, the sample size was small. hence, the interpretation of our results might be limited. however, by including patients from two appointed hospitals for covid-19, we believe the object of our study is representative of the total patient population. although wuhan achieved victory over covid-19 through hard work, this new coronary pneumonia is now a worldwide disease. the virus can be eliminated only if all countries take appropriate measures. the medical workers in wuhan have accumulated experience fighting this epidemic, and have no reservations in providing advice to colleagues in need. we are also committed to passing on our knowledge and expertise to other countries currently fighting covid-19. in conclusion, almost 9.4% of our study population died of covid-19. older age, elevated d-dimer levels, and thrombocytopenia on admission were independent risk factors for death. more studies on the risk factors associated with covid-19-related death are needed to control disease progression and to improve its treatment. a novel coronavirus from patients with pneumonia in china national health commission of the people's republic of china director-general's opening remarks at the mission briefing on covid-19 novel coronavirus pneumonia emergency response epidemiology host susceptibility to severe covid-19 and establishment of a host risk score: findings of 487 cases outside wuhan national health commission of the people's republic of china. guidelines for the diagnosis and treatment of covid-19 clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study china medical treatment expert group for, clinical characteristics of coronavirus disease 2019 in china princess margaret hospital, outcomes and prognostic factors in 267 patients with severe acute respiratory syndrome in hong kong clinical predictors of mortality of middle east respiratory syndrome coronavirus (mers-cov) infection: a cohort study exacerbated innate host response to sars-cov in aged nonhuman primates the immunopathogenesis of sepsis in elderly patients d-dimer is a significant prognostic factor in patients with suspected infection and sepsis covid-19 mortality in patients on anticoagulants and antiplatelet agents comparison of clinical and pathological features between severe acute respiratory syndrome and coronavirus disease the effect of sars coronavirus on blood system: its clinical findings and the pathophysiologic hypothesis recurrent acute thrombocytopenia in the hospitalized patient: sepsis, dic, hit, or antibiotic-induced thrombocytopenia proteomic analysis reveals platelet factor 4 and beta-thromboglobulin as prognostic markers in severe acute respiratory syndrome platelet-to-lymphocyte ratio is associated with prognosis in patients with coronavirus disease-19 association between influenza vaccination and cardiovascular outcomes in high-risk patients: a meta-analysis acute pneumonia and the cardiovascular system community-acquired pneumonia requiring admission to an intensive care unit: a descriptive study the raw data supporting the conclusions of this article will be made available by the authors, without undue reservation. the studies involving human participants were reviewed and approved by zhongnan hospital of wuhan university (no. 2020015) and the central hospital of wuhan (no. 2020072).written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements. lg, zl, and bc: conceptualization. sw, yh, wl, sc, ml, wzh, dc, lz, and mwa: data collection and processing. bc, mt, and hx: interpretation. all authors: wrote-review and editing. the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright © 2020 li, cheng, zeng, chen, tu, wu, tong, wang, huang, long, zhou, chen, zhou, wang, xu, deng, liu and guo. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord-354717-4vrqzbof authors: linton, natalie m.; kobayashi, tetsuro; yang, yichi; hayashi, katsuma; akhmetzhanov, andrei r.; jung, sung-mok; yuan, baoyin; kinoshita, ryo; nishiura, hiroshi title: incubation period and other epidemiological characteristics of 2019 novel coronavirus infections with right truncation: a statistical analysis of publicly available case data date: 2020-02-17 journal: j clin med doi: 10.3390/jcm9020538 sha: doc_id: 354717 cord_uid: 4vrqzbof the geographic spread of 2019 novel coronavirus (covid-19) infections from the epicenter of wuhan, china, has provided an opportunity to study the natural history of the recently emerged virus. using publicly available event-date data from the ongoing epidemic, the present study investigated the incubation period and other time intervals that govern the epidemiological dynamics of covid-19 infections. our results show that the incubation period falls within the range of 2–14 days with 95% confidence and has a mean of around 5 days when approximated using the best-fit lognormal distribution. the mean time from illness onset to hospital admission (for treatment and/or isolation) was estimated at 3–4 days without truncation and at 5–9 days when right truncated. based on the 95th percentile estimate of the incubation period, we recommend that the length of quarantine should be at least 14 days. the median time delay of 13 days from illness onset to death (17 days with right truncation) should be considered when estimating the covid-19 case fatality risk. as of 31 january 2020, mainland china reported 11,791 confirmed cases of novel coronavirus infections, causing 259 deaths [1] . initially, these infections were thought to result from zoonotic (animal-to-human) transmission; however, recently published evidence [2] and the exponential growth of case incidence show compelling evidence of human-to-human secondary transmission fueled by travel, with many cases detected in other parts of the world [3] . this geographic expansion beyond the initial epicenter of wuhan provides an opportunity to study the natural history of covid-19 infection, as these migration events limit the risk of infection to the time during which an individual traveled to an area where exposure could occur [4] . the incubation period is defined as the time from infection to illness onset. knowledge of the incubation period of a directly transmitted infectious disease is critical to determine the time period required for monitoring and restricting the movement of healthy individuals (i.e., the quarantine period) [5, 6] . the incubation period also aids in understanding the relative infectiousness of covid-19 and can be used to estimate the epidemic size [7] . time-delay distributions including dates of hospital admission (for treatment and/or isolation) and death also inform the temporal dynamics of epidemics. a published clinical study on the covid-19 epidemic has already shown that the average time delay from illness onset to hospital admission is approximately 7 days [8] , but this distribution has yet to be explicitly estimated. the time from hospital admission to death is also critical to the avoidance of underestimation when calculating case fatality risk [9] . using publicly available data from the ongoing epidemic with known case event dates, the present study aimed to estimate the incubation period and other time intervals that govern the interpretation of epidemiological dynamics of covid-19 infections. we retrieved information on cases with confirmed covid-19 infection and diagnosis outside of the epicenter of wuhan, china, based on official reports from governmental institutes, as well as reports on deceased cases from both in and outside of wuhan. we aggregated the data directly from government websites or from news sites that quoted government statements. the data were collected in real time, and thus may have been updated as more details on cases became available. the arranged data include a selection of cases reported through 31 january 2020 and are available as supplementary tables s1 and s2 . specifically, we collected the dates of exposure (entry and/or exit from wuhan or dates of close contact with a wuhan resident/known epidemic case), illness onset, earliest healthcare seeking related to infection, hospital admission (for treatment and/or isolation), and death. cases included both residents from other locations who travelled to wuhan, as well as individuals who lived, worked, or studied in wuhan (hereafter: wuhan residents) but who were diagnosed outside of wuhan and reported by the governments of the locations where their infection was detected. we thus estimated the incubation period by (i) excluding wuhan residents and (ii) including wuhan residents. the former may be more precise in defining the interval of exposure, but the sample size is greater for the latter. more detailed information about the criteria used for the estimation of each defined time interval and the data used are described in supplementary text s1. we used the dates of three critical points in the course of infection-illness onset, hospital admission, and death-to calculate four time intervals: the time from (a) exposure to illness onset (i.e., the incubation period), (b) illness onset to hospital admission, (c) illness onset to death, and (d) hospital admission to death. we used a doubly interval-censored [10] likelihood function to estimate the parameter values for these intervals, written as: here, in the case of (a) g(.) is the probability density function (pdf) of exposure following a uniform distribution, and f (.) is the pdf of the incubation period independent of g(.). d represents a dataset among all observed cases i, where exposure and symptom onset fall within the lower and upper bounds (e l , e r ) and (s l , s r ). we fit the pdf f (.) to lognormal, weibull, and gamma distributions. to address the selection bias in the dataset due to the continued growth of the outbreak (i.e., cases with shorter incubation periods are more likely to be included in the dataset), we also accounted for right truncation using the formula: here, r is the exponential growth rate (estimated at 0.14 [11] ), t is the latest time of observation (31 january 2020), and f(.) is the cumulative density function of f (.). in both cases, we used bayesian methods to infer parameter estimates and obtain credible intervals. we selected the best fit model by using the widely applicable information criterion (waic). we also verified that the bayesian estimates were in line with pointwise estimates derived by maximum likelihood estimation (mle). as the formulation of the likelihood with right truncation (1)(2) contained the function f and was dependent on both the time interval (s − e) and time of exposure e, we generalized a previously obtained result for doubly interval-censored likelihood with f (s − e, e) ≡ f (s − e) [10] . the data were processed using r version 3.6.2 [12] , mle was computed using julia version 1.3 [13] , and the markov chain monte carlo (mcmc) simulations were performed in stan (cmdstan version 2.22.1 [14] ). all code is freely available at the github repository: http://github.com/aakhmetz/ wuhanincubationperiod2020. the ratio of male to female cases among living cases resembled [2] , at 58%, with most 30-59 years of age (information missing for 9 cases). the deceased cases were more predominantly male (70%) and older (85% were 60 years of age or older). table 1 shows estimates for the various time intervals without right truncation. for the incubation period estimates, the lognormal distribution provided the best fit to the data, both when excluding and including wuhan residents. the mean incubation period was estimated at 5.0 days (95% credible interval [ci]: 4.2, 6.0) when excluding wuhan residents (n = 52) and 5.6 days (95% ci: 5.0, 6.3) when including wuhan residents (n = 158). the median time from illness onset to hospital admission was estimated at 3.3 days (95% ci: 2.7, 4.0) among living cases and 6.5 days (95% ci: 5.2, 8.0) among deceased cases using the gamma distribution, which provided the best fit for both sets of data. figure 1a shows the corresponding pdfs. data from the time from illness onset and hospital admission to death best fit lognormal and weibull distributions, respectively, as presented in figure 1b , c. the mean time from illness onset to death was 15.0 days (95% ci: 12.8, 17.5) and from hospital admission to death was 8.8 days (95% ci: 7.2, 10.8). table 2 shows estimates for the fit of the lognormal distribution for each interval when accounting for right truncation. the mean incubation period was 5.6 days (95% ci: 4.4, 7.4) when excluding wuhan residents-slightly larger than the estimate without right truncation. the mean estimate for illness onset to hospital admission was 9.7 days (95% ci: 5.4, 17.0) for living cases and 6.6 days (95% ci: 5.2, 8.8) for deceased cases, with the former nearly 2.5 times the length of its untruncated version. illness onset to death and hospital admission to death were likewise longer than their non-truncated counterparts, at 20.2 days (95% ci: 15.1, 29.5) and 13.0 days (95% ci: 8.7, 20.9), respectively. figure 2 shows the cumulative distribution function of the incubation period with and without right truncation. the 5th and 95th percentiles are shown in addition to the median. the 95th percentiles were estimated at 10.6 days (95% ci: 8.5, 14.1) and 10.8 days (95% ci: 9.3, 12.9) for non-truncated data excluding and including wuhan residents and 12.3 days (95% ci: 9.1, 19.8) when applying right truncation and excluding wuhan residents. the respective median values for these cdfs were 4.3 days (95% ci: 3.5, 5.1), 5.0 days (95% ci: 4.4, 5.6), and 4.6 days (95% ci: 3.7, 5.7). the present study advances the public discussion on covid-19 infections by presenting explicit estimations of the incubation period and other epidemiologic characteristics using publicly available data. our estimated mean incubation period of approximately 5 days is comparable to known mean values of the incubation period for severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) [9, [15] [16] [17] , as well as other recent estimates of the incubation period for covid-19 [17] . in addition to empirically showing the comparability of covid-19 to other disease-causing coronaviruses, the present study has also shown that the 95th percentile of the incubation period is around 10-14 days, indicating that a 14-day quarantine period would largely ensure the absence of disease among healthy exposed individuals. wuhan residents have a less precisely defined exposure period compared to travelers and secondary cases from known human to human transmission events. however, our calculations have shown that adding more cases to the dataset even with uncertainty reduces both the variance the present study advances the public discussion on covid-19 infections by presenting explicit estimations of the incubation period and other epidemiologic characteristics using publicly available data. our estimated mean incubation period of approximately 5 days is comparable to known mean values of the incubation period for severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) [9, [15] [16] [17] , as well as other recent estimates of the incubation period for covid-19 [17] . in addition to empirically showing the comparability of covid-19 to other disease-causing coronaviruses, the present study has also shown that the 95th percentile of the incubation period is around 10-14 days, indicating that a 14-day quarantine period would largely ensure the absence of disease among healthy exposed individuals. wuhan residents have a less precisely defined exposure period compared to travelers and secondary cases from known human to human transmission events. however, our calculations have shown that adding more cases to the dataset even with uncertainty reduces both the variance the present study advances the public discussion on covid-19 infections by presenting explicit estimations of the incubation period and other epidemiologic characteristics using publicly available data. our estimated mean incubation period of approximately 5 days is comparable to known mean values of the incubation period for severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) [9, [15] [16] [17] , as well as other recent estimates of the incubation period for covid-19 [17] . in addition to empirically showing the comparability of covid-19 to other disease-causing coronaviruses, the present study has also shown that the 95th percentile of the incubation period is around 10-14 days, indicating that a 14-day quarantine period would largely ensure the absence of disease among healthy exposed individuals. wuhan residents have a less precisely defined exposure period compared to travelers and secondary cases from known human to human transmission events. however, our calculations have shown that adding more cases to the dataset even with uncertainty reduces both the variance of the estimates and selection bias, improving the fit of the distribution mean. our estimates are in agreement with the report of li et al. [2] . a recent study by backer et al. [17] noted a similar finding in their analysis of the incubation period for 88 cases (including 63 wuhan residents). however, the estimates of backer et al. for the model that included wuhan residents were subject to overestimation as the lower bounds for wuhan residents-who had unknown left exposure dates-were fixed in their analysis. in contrast, we considered the left exposure dates for wuhan residents as parameters to be fitted-see [14] for details. notably, our results demonstrated the overall benefit of using additional case data, even when some of exposure values were not precisely known. the time from the illness onset to death is also comparable to sars [15] , and the 15-20-day mean delay indicates that a crude estimation of the ratio of the cumulative number of deaths to that of confirmed cases will tend to result in an underestimation of the case fatality risk, especially during the early stage of epidemic spread [18, 19] . during the sars epidemic in hong kong, 2003, the time from illness onset to hospital admission was shown to have shortened as a function of the calendar time, gradually reflecting the effects of contact tracing [9] . it remains to be seen if this will be the case for covid-19 as well. the time delay distribution between illness onset and hospital admission may also be negatively associated with the basic reproduction number, i.e., the average number of secondary cases generated by a single primary case in a fully susceptible population [18] . the median time from illness onset to hospital admission was approximately 4 days among cases not known to be deceased at the time of the case report, and 6 days among cases reported as deceased. the reasons for this difference are not altogether clear. however, the living cases include persons who were isolated-in some cases more for reducing transmission than for treatment purposes-while all deceased cases were admitted for treatment. in addition, deceased cases for whom information was available had onset dates closer to the beginning of the outbreak compared to the living cases, who mostly had onset in the latter two-thirds of january 2020. the time delay distributions from illness onset to hospital admission for cases reported later in the epidemic, when there was a more widespread recognition of the virus and a more prevalent social imperative for those with symptoms to seek healthcare, may differ from those of early cases [2] . several limitations of the present study exist. first, the dataset relies on publicly available information that is not uniformly distributed (i.e., collected from various sources), and therefore the availability of dates relevant to our analyses is limited to a small, selective sample that is not necessarily generalizable to all confirmed cases. moreover, given the novelty of the covid-19 pneumonia, it is possible that illness onset and other event data were handled differently between jurisdictions (e.g., was illness onset the date of fever or date of dyspnea?). second, our data include very coarse date intervals with some proxy dates used to determine the left and/or right hand dates of some intervals. third, as the sample size was limited, the variance is likely to be biased. fourth, we were not able to examine the heterogeneity of estimates by different attributes of cases (e.g., severity of disease) [16] . lastly, as we only have information on confirmed cases, there is a bias towards more severe disease-particularly for earlier cases. this study presents the estimates of epidemiological characteristics of covid-19 infections that are key parameter for studies on incidence, case fatality, and epidemic final size, among other possibilities [7, 11] . from the 95th percentile estimate of the incubation period we found that the length of quarantine should be at least 14 days, and we stress that the 17-24-day time delay from illness onset to death must be addressed when estimating covid-19 case fatality risk. this study was made possible only through open sharing of case data from china and other countries where cases were diagnosed. continued communication of dates and other details related to exposure and infection is crucial to furthering scientific understanding of the virus, the infections it causes, and preventive measures that can be used to contain and mitigate epidemic spread. supplementary materials: the following are available online at http://www.mdpi.com/2077-0383/9/2/538/s1, table s1 : event dates for exported cases included in the analysis, table s2 : event dates for deceased cases included in the analysis, text s1, estimation of the time interval distribution using doubly interval-censored likelihood, estimation of the time interval distributions using bayesian framework, and data cleaning rules implemented for the various time intervals. the authors declare no conflicts of interest. update on pneumonia of new coronavirus infection as of 21:00 on early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia european centre for disease prevention and control data estimates of shortand long-term incubation periods of plasmodium vivax malaria in the republic of korea new york city department of health and mental hygiene swine influenza investigation team. outbreak of 2009 pandemic influenza a (h1n1) at a new york city school determination of the appropriate quarantine period following smallpox exposure: an objective approach using the incubation period distribution the extent of transmission of novel coronavirus in wuhan, china, 2020 clinical features of patients infected with 2019 novel coronavirus in wuhan epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in hong kong estimating incubation period distributions with coarse data real time estimation of the risk of death from novel coronavirus (2019-ncov) infection: inference using exported cases r: a language and environment for statistical computing a fresh approach to numerical computing. siam rev stan modeling language users guide and reference manual, version 2.22.0 incubation periods of acute respiratory viral infections: a systematic review association between severity of mers-cov infection and incubation period the incubation period of 2019-ncov infections among travellers from wuhan, china. medrxiv 2020 who rapid pandemic assessment collaboration. pandemic potential of a strain of influenza a (h1n1): early findings methods for estimating the case fatality ratio for a novel, emerging infectious disease this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord-258748-nzynerfu authors: li, jinghua; wang, yijing; gilmour, stuart; wang, mengying; yoneoka, daisuke; wang, ying; you, xinyi; gu, jing; hao, chun; peng, liping; du, zhicheng; xu, dong roman; hao, yuantao title: estimation of the epidemic properties of the 2019 novel coronavirus: a mathematical modeling study date: 2020-02-20 journal: nan doi: 10.1101/2020.02.18.20024315 sha: doc_id: 258748 cord_uid: nzynerfu background the 2019 novel coronavirus (covid-19) emerged in wuhan, china in december 2019 and has been spreading rapidly in china. decisions about its pandemic threat and the appropriate level of public health response depend heavily on estimates of its basic reproduction number and assessments of interventions conducted in the early stages of the epidemic. methods we conducted a mathematical modeling study using five independent methods to assess the basic reproduction number (r0) of covid-19, using data on confirmed cases obtained from the china national health commission for the period 10th january to 8th february. we analyzed the data for the period before the closure of wuhan city (10th january to 23rd january) and the post-closure period (23rd january to 8th february) and for the whole period, to assess both the epidemic risk of the virus and the effectiveness of the closure of wuhan city on spread of covid-19. findings before the closure of wuhan city the basic reproduction number of covid-19 was 4.38 (95% ci: 3.63-5.13), dropping to 3.41 (95% ci: 3.16-3.65) after the closure of wuhan city. over the entire epidemic period covid-19 had a basic reproduction number of 3.39 (95% ci: 3.09-3.70), indicating it has a very high transmissibility. interpretation covid-19 is a highly transmissible virus with a very high risk of epidemic outbreak once it emerges in metropolitan areas. the closure of wuhan city was effective in reducing the severity of the epidemic, but even after closure of the city and the subsequent expansion of that closure to other parts of hubei the virus remained extremely infectious. emergency planners in other cities should consider this high infectiousness when considering responses to this virus. in december 2019 a novel coronavirus outbreak began in wuhan, hubei province, in china. as of 9 th february 37,558 cases of the virus had been confirmed globally, of which 37,251 were confirmed in china, with 813 deaths. 1 on 30 th january the who declared the novel coronavirus (covid-19) a public health emergency of international concern, 2 and on 23 rd january the hubei provincial government closed the city of wuhan, 3 followed by the closure of a wider network of cities in hubei on 24 th january, 4 to prevent its spread. although the number of cases outside of china remains small, mathematical modeling has identified the risk of spread of the disease to population centres and transit hubs in other countries, 5 with the possibility that the covid-19 outbreak could become a global pandemic. in the beginning stages of an epidemic, mathematical modeling is essential to understand the dynamics of the new disease, and to assess the organism's infectiousness and rapidity of spread. this is primarily achieved by calculation of the basic reproduction number, denoted as " , which measures the number of secondary cases that can be expected to be generated from a single case of the disease. 6 initial research from the first weeks of the covid-19 outbreak estimated the basic reproduction number to be between 2.20 and 3.58, indicating large uncertainty in estimates of its infectiousness. 7, 8 other unpublished estimates also placed the value of " within this range, 9 with wide uncertainty. 5 all of these estimates of the basic reproduction number were based on data to the end of january, and did not use a long series of data from the period after the closure of wuhan city. the data series for these reports also did not include significant periods of time after the chinese new year (24 th january, 2020), when a large number of people return to their home towns from large cities, with the attendant risk of significant spread of the disease. wuhan city has a population of 11 million people 10 , but during the chinese new year as many as 5 million residents leave the city, and 70% of those who leave travel within hubei province 11 , with the risk of significant spread of the disease within china, and especially across hubei province, during the chinese new year period. in this study we used data from the national health commission of the people's republic of china 12 (nhc) for the period from the 10 th january to the 8 th february to estimate the basic reproduction number of covid-19 using five mathematical modeling methods conducted independently. we used these modeling methods to estimate the basic reproduction number both before and after the closure of wuhan city, and across the whole time period of the epidemic. based on the results of these analyses we make recommendations for future control of the virus, and assess the future pandemic risk due to this new disease. data was obtained from the nhc for the period 10 th january to 8 th february, 2020. the nhc is a cabinet-level executive department under the state council of china which is responsible for public health, medical services and health emergencies in china. data from before the 10 th january was not included in this analysis because cases identified before 10 th january were based on symptomatic diagnosis and no standardized testing method was available. although the nhc provides information on suspected and confirmed cases, only data from confirmed cases was used in this analysis, to avoid confusion of routine seasonal influenza cases with ncov. 13 confirmed cases were analysed using by applying four different estimation techniques, to allow for different assumptions about epidemic growth and the epidemiology of the disease: • exponential growth (eg), which assumes an exponential growth curve to the virus and estimates the basic reproduction number from the lotka-euler equation 14 • maximum likelihood method (ml), in which the likelihood of the cases is expressed directly in terms of " on the assumption of a simple sir model structure 15 • sequential bayesian method (sb), in which the posterior probability distribution of the basic reproduction number is estimated sequentially using the posterior at the previous time point as the new prior 16 • time-dependent reproduction numbers (td), in which the basic reproduction number at any time point is estimated as an average of accumulated estimates at previous time points 17 these methods were implemented using the r0 package in r. 18 all these models require no assumption about recovery time, but in some cases require an assumption about the generation time of the epidemic. all methods were applied to the data for the whole period (january 10 th to february 8 th ), to the period only before the closure (january 10 th to january 23 rd ), and to only the period after the closure of wuhan city (january 23 rd to february 8 th ) because some of these methods are driven by a suceptible-infectious-recovered (sir) model, but an asymptomatic latent phase had been identified in the early progress of the disease, we also estimated the basic reproduction number using a standard susceptible-exposed-infectious-recovered (seir) model. an analytic expression for the basic reproduction number was obtained from the model using next generation matrices, 19 and predictions of cumulative cases were fitted to the data on national cases using maximum likelihood estimation to identify the optimal value of " . 20 a metropolis-hastings monte carlo sampling method 21 was used to estimate a credible interval for the basic reproduction number. in this model the latent phase was fixed to last 5.2 days, 8 and the recovery period was fixed at 7 days. although the biological recovery period of the disease has not been clearly established, the period from onset of symptoms to isolation in specialist hospitals was assumed to be 7 days, and the recovery compartment of the seir model acts as a proxy for isolation in these models. all mh estimates used 20,000 monte carlo iterations with a burn-in period of 5,000 iterations and a normally distributed proposal distribution. because all five modeling methods use different assumptions and tools and are likely to produce widely varying estimates of the basic reproduction number based on different aspects of the epidemic process, we combined all five estimates to produce an overall value for the basic reproduction number. we calculated a weighted average of the five basic reproduction numbers by calculating weights from a poisson loss function, 22 which is similar to a poisson likelihood but which was not used for estimation of parameters in any of the models. we also estimated a weighted standard error from the models. where standard errors do not overlap point estimates in the pre-and post-closure periods, we conclude there is a significant difference in the epidemic process between the periods. finally, we estimated the predicted epidemic trend from all models in each period, and plotted these against the observed number of cases for each period. mathematical details of the models are presented in the supplementary appendix. all results are presented as values of the basic reproduction number with its 95% confidence interval. for the mh method the inter-quartile range of the posterior distribution of " is presented. the funders had no involvement in study design, data collection, analysis or interpretation of the data, had no influence on the writing of the report or the decision to submit for publication. by february 8 th there were 37,198 confirmed cases nationally, with 27,100 of these cases in hubei (72.9% of all cases), and 14,982 in wuhan (40.2% of all cases). all models applied to these data estimated the basic reproduction number effectively. basic reproduction numbers for all fives methods for the entire time period, the pre-closure period and the post-closure period, are shown in table 1 . the best-fitting method in the entire period was the method based on time-dependent reproduction numbers, while the pre-closure and post-closure period were best fitted by the exponential growth model. the weighted average estimate of the basic reproduction number shows that the epidemic slowed down after the closure of wuhan city, dropping from 4.38 (95% ci 3.63 -5.13) before the closure to 3.41 (95% ci 3.16 -3.65) after. the 95% confidence intervals for the exponential growth estimate of post-closure " do not overlap the point estimate for the pre-closure period, indicating that there was a significant reduction in the basic reproduction number after the closure of wuhan. figure 1 shows the model predictions from all five models plotted against the observed cases for the pre-closure period (top left panel), post-closure period (top right panel) and entire period (bottom panel). a similar figure, with only the best-fitting model shown, is given in supplementary figure s2 . from figure 1 it is clear that models that estimated low values for the basic reproduction number in the pre-closure period or the entire period, such as the sequential bayesian model, produced very poor predictions that under-estimated the epidemic, and the bestfitting models were those that identified basic reproduction numbers over 4 in the preclosure period, and over 3 in the entire epidemic period. this study estimated the basic reproduction number, " , for the 2019 novel coronavirus using confirmed cases from 10 th january -8 th february. we applied five methods to estimate " in order to ensure that our estimate was robust to differences in assumptions about epidemic processes, differences in assumed underlying parameters, and about the nature of the dynamics of the affected population. we estimated the basic reproduction number for the whole period to be 3.39 (95% ci: 3.09 -3.70), a very high number indicative of a very fast rate of spread. we also estimated the basic reproduction number separately for the pre-closure period, finding that in the first 13 days of available high-quality data on the epidemic that the basic reproduction number was 4.38 (95% ci: 3.63 -5.13), a very high number indicative of a highly infectious disease. compared to this, we calculated the postclosure value of " to be 3.41 (95% ci: 3.16 -3.65), still a very high number but significantly lower than that observed in the earlier days of the epidemic. this lower basic reproduction number, and the recent apparent reduction in numbers of new infections, justifies the decision to close wuhan city, and also shows the potentially high impact of self-quarantine and voluntary exclusion methods. a separate study (not published) conducted by one of the study authors found that 25% of students in guangdong did not leave their home in the chinese new year period, 90% increased their handwashing frequency, and over 80% used a mask when moving in public places. these voluntary measures, combined with the closure of wuhan city, may have averted the spread of this disease and reduced its ability to reproduce through social changes. the reduction in infectiousness is particularly striking given the huge movement of people that typically occurs during chinese new year, and the risk of exposure in public transport and family gatherings at this time. a striking feature of our analysis is the very high value of the basic reproduction number we identified in the period of time up to the closure of wuhan city. three of our modeling methods -including the best-fitting method based on a poisson loss function -identified a value of " greater than 5, with some possibility of a value over 6. basic reproduction numbers in the 5-7 range are consistent with extremely contagious diseases such as mumps and smallpox, and indicate a disease with a very high risk of becoming a global pandemic. this finding has significant implications for cities like singapore, japan and london which are beginning to experience the first signs of spread of the disease without importation. in light of the epidemic threat identified here, these cities should consider implementing more aggressive prevention policies as necessary, while respecting human rights and the dignity of affected individuals and of those who might be disadvantaged by stricter quarantine and control mechanisms. previous studies 5,7-9 found lower values for the basic reproduction number. this variation may have arisen for two reasons. first, the empirical data that previous studies used were collected before 25 th jan, 2020. testing protocols and diagnostic tools changed during the early period of the study 23 , and the number of diagnosed cases collected before 15 th january were considered underestimated and less reliable. this would flatten the epidemic curve in early studies, and the estimation of r0 based on these data may be underestimated and have larger confidence intervals. second, previous studies only estimated the r0 based on a single method, and these estimates may have been affected by the implicit assumptions in these models. for example, a previous paper using the assumption of exponential growth found a value of " of 2.68 (95% credible interval 2.47 -2.86) 5 using an seir model with metropolis-hastings mcmc estimates of uncertainty, but our modeling has shown that this method likely underestimated the basic reproduction number during the pre-closure period. our model avoids the limitations of specific modeling choices by combining several methods with a poisson loss weight, using the most current and accurate case diagnosis. through this approach we calculate a more robust estimate than previous studies, and find a higher value of " . ours is also the first study to compare the pre-and post-closure periods in the data, and thus the first study to make a judgment about the effectiveness of this strategy. given the high risk of epidemic from covid-19, it is important to assess the value of this strategy before the disease takes hold in another global city. this study has several limitations. it was based on confirmed cases, and by excluding suspected cases or mild cases may have under-estimated the rate of spread of the disease. we did not estimate the values of the parameters defining the transition rate from exposed to infectious, or infected to recovered, but fixed them at previously published values. this was a necessary decision because the clinical features of the disease are not yet fully understood, and may affect estimates. however, our intuition after fitting these models is that the maximum likelihood estimate of the force of infection naturally adjusts to fit the value of the recovery rate, and produces a broadly similar value of the basic reproduction number as a result. furthermore, to adjust for the still-arbitrary nature of these estimates of key parameters, we used some methods that do not depend on any assumptions about these aspects of the disease process. another limitation of this study is the uncertainty introduced by the use of multiple modeling methods, which we combined with a weighted average. however, we believe that by presenting varying methods with different assumptions along with a weighted average, we enable researchers and policy-makers to make judgements about the dangers of the epidemic without relying on any particular set of assumptions about a disease that is not yet well understood. our results show that the 2019 novel coronavirus is an extremely rapidly spreading and dangerous infectious disease, with the potential to infect a very large proportion of the population very rapidly if not contained. extreme epidemic prevention measures, including city closures and wide-scale self-quarantine, may be necessary simply to reduce the pace of the epidemic, and even these extreme measures may not be sufficient to prevent pandemic. city officials, public health planners, policy-makers and governments in countries that are beginning to see the spread of this disease domestically need to act quickly, effectively and decisively, as the government of china did, to prevent a serious global pandemic. yh and jl conceived of the study. jl, sg, yjw, mw, dy, xy and yw conducted data analysis. sg, yjw, mw, dy and jl wrote the first draft of the paper. jl, jg, ch, zd and lp collected data. all authors offered scientific input and edited all drafts of the paper. the authors have no conflict of interests to declare. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024315 doi: medrxiv preprint international health regulations emergency committee. statement on the second meeting of the international health regulations (2005) emergency committee regarding the outbreak of novel coronavirus (2019-ncov) wuhan novel coronavirus pneumonia infection response command centre. wuhan city novel coronavirus pneumonia infection prevention and control command centre notice number 2 suspension of public transport in 8 regions of hubei province nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study an introduction to infectious disease modelling preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia report 3: transmissibility of national health commission of the people's republic of china. efforts to prevent and control the 2019-ncov epidemic. daily briefing epidemiological features and trends of influenza incidence in mainland china: a population-based surveillance study from how generation intervals shape the relationship between growth rates and reproductive numbers a likelihood-based method for real-time estimation of the serial interval and reproductive number of an epidemic real time bayesian estimation of the epidemic potential of emerging infectious diseases different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures the r0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks the construction of next-generation matrices for compartmental epidemic models estimating transmission intensity for a measles epidemic in niamey, niger: lessons for intervention understanding the hastings algorithm generalized linear models world health organization. laboratory testing for 2019 novel coronavirus (2019-ncov) in suspected human cases: : interim guidance key: cord-341135-gmi1ewc2 authors: kucharski, adam j; russell, timothy w; diamond, charlie; liu, yang; edmunds, john; funk, sebastian; eggo, rosalind m title: early dynamics of transmission and control of covid-19: a mathematical modelling study date: 2020-02-02 journal: nan doi: 10.1101/2020.01.31.20019901 sha: doc_id: 341135 cord_uid: gmi1ewc2 background: an outbreak of the novel coronavirus sars-cov-2 has led to 46,997 confirmed cases as of 13th february 2020. understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas. methods: we combined a stochastic transmission model with data on cases of novel coronavirus disease (covid-19) in wuhan and international cases that originated in wuhan to estimate how transmission had varied over time during january and february 2020. based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas. findings: we estimated that the median daily reproduction number, rt , declined from 2.35 (95% ci: 1.15-4.77) one week before travel restrictions were introduced on 23rd january to 1.05 (95% ci: 0.413-2.39) one week after. based on our estimates of rt,we calculated that in locations with similar transmission potential as wuhan in early january, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population. interpretation: our results show that covid-19 transmission likely declined in wuhan during late january 2020, coinciding with the introduction of control measures. as more cases arrive in international locations with similar transmission potential to wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually. as of 13 th february 2020, an outbreak of covid-19 has resulted in 46,997 confirmed cases (1) . the outbreak was first identified in wuhan, china, in december 2019, with the majority of early cases being reported in the city. the majority of internationally exported cases reported to date have a travel history to wuhan (2) . in the early stages of a new infectious disease outbreak, it is crucial to understand the transmission dynamics of the infection. in particular, estimation of changes in transmission over time can provide insights into the current epidemiological situation (3) and identify whether outbreak control measures are having a measurable effect (4, 5) . such analysis can inform predictions about potential future growth (6) , help estimate risk to other countries (7) , and guide the design of alternative interventions (8) . there are several challenges to such analysis, however, particularly in real-time. there can be a delay to symptom appearance resulting from the incubation period and delay to confirmation of cases resulting from detection and testing capacity (9) . modelling approaches can account for such delays and uncertainty, by explicitly incorporating delays resulting from the natural history of infection and reporting processes (10) . in addition, individual data sources may be biased, incomplete, or only capture certain aspects of the outbreak dynamics. evidence synthesis approaches, which fit to multiple data sources rather than a single dataset (or data point) can enable more robust estimation of the underlying dynamics of transmission from noisy data (11, 12) . combining a mathematical model of sars-cov-2 transmission with four datasets from within and outside wuhan, we estimated how transmission in wuhan varied between december and february 2020. we then used these estimates to assess the potential for sustained human-to-human transmission to occur in locations outside wuhan if cases are introduced. evidence before this study: we searched pubmed, biorxiv and medrxiv for articles published up to 10 th february 2020 using the keywords "2019-ncov", "novel coronavirus", "covid-19", "sars-cov-2" and "reproduction number", "r0", "transmission". we found several estimates of the basic reproduction number, r 0 , including average exponential growth rate estimates based on inferred or observed cases at a recent time point (13, 14) and early growth of the outbreak in china (15, 16) . however, we identified no estimates of how r 0 had changed in wuhan since control measures were introduced in late january, or estimates that jointly fitted to data within wuhan with international exported cases and evacuation flights. added value of this study: our study combines available evidence from multiple data sources, reducing the dependency of our estimates on a single time point or dataset. we estimate how transmission has varied over time, identify a decline in the reproduction number in late january to near 1, coinciding with the introduction of large scale control measures, and show the potential implications of estimated transmission for outbreak risk new locations. implications of all the available evidence: covid-19 is currently exhibiting sustained transmission in china. this creates a substantial risk of outbreaks in other countries, although if sars-cov-2 has mers-cov or sars-cov-like variability in . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.01.31.20019901 doi: medrxiv preprint transmission at the individual-level, multiple introductions may be required before an outbreak takes hold. to estimate the early dynamics of transmission in wuhan, we fitted a stochastic transmission dynamic model (17) to multiple publicly available datasets on cases in wuhan and internationally exported cases from wuhan. the four datasets we fitted to were: daily number of new internationally exported cases (or lack thereof), by date of onset, as of 26th january 2020; daily number of new cases in wuhan with no market exposure, by date of onset, between 1st december 2019 and 1st january 2020; daily number of new cases in china, by date of onset, between 29th december 2019 and 23 rd january 2020; proportion of infected passengers on evacuation flights between 29 th january and 4 th february 2020. we used an additional two datasets for comparison with model outputs: daily number of new exported cases from wuhan (or lack thereof) in countries with high connectivity to wuhan (i.e. top 20 most at risk), by date of confirmation, as of 10th february 2020; data on new confirmed cases reported in wuhan between 16 th january and 11 th february 2020 (full details in the appendix). in the model, individuals were divided into four infection classes ( figure 1 ): susceptible, exposed (but not yet infectious), infectious, and removed (i.e. isolated, recovered or otherwise no longer infectious). the model accounted for delays in symptom onset and reporting, as well as uncertainty in case observation (see appendix for full model details). the incubation period was assumed to be erlang distributed with mean 5.2 days (16) and delay from onset-to-isolation erlang distributed with mean 2.9 days (2,15). the delay from onset-to-reporting was assumed to be exponentially distributed with mean 6.1 days (2). once exposed to infection, a proportion of individuals travelled internationally and we assumed that the probability of cases being exported from wuhan to a specific other country depended on the number of cases in wuhan, the number of outbound travellers (assumed to be 3300 per day before travel restrictions were introduced on 23rd january 2020 and zero after), the relative connectivity of different countries (18) , and the relative probability of reporting a case outside wuhan, to account for differences in clinical case definition, detection and reporting within wuhan and internationally. we considered the 20 countries outside china most at risk of exported cases in the analysis. transmission was modelled as a geometric random walk process, and we used sequential monte carlo to infer the transmission rate over time, as well as the resulting number of cases and the time-varying basic reproduction number, r t , defined here as the average number of secondary cases generated by a typical infectious individual on each day in a full susceptible population. the model had three unknown parameters, which we estimated: magnitude of temporal variability in transmission, proportion of cases that would eventually be detectable, and relative probability of reporting a confirmed case within wuhan compared to an internationally exported case originated in wuhan. we assumed the outbreak started with a single infectious case on 22 nd november 2019 and the entire population was initially susceptible. once we had estimated r t , we used a branching process with a negative binomial offspring distribution to calculate the probability an introduced case would cause a large outbreak. we also conducted sensitivity analysis on . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.31.20019901 doi: medrxiv preprint assumptions about the initial number of cases, connectivity between countries and proportion of cases that were infectious before showing symptoms. more details of methodology, sensitivity analysis, data and code availability are provided in the appendix. the sponsor of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. the corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication we estimated that the daily reproduction number, r t , varied during january 2020, with median values ranging from 1.6-2.6 between 1st january 2020 and the introduction of travel restrictions on 23rd january (figure 2a ). we estimated a decline in r t in late january, from 2.35 (95% ci: 1.15-4.77) on 16 th of january, one week before the restrictions, to 1.05 (95% ci: 0.413-2.39) on 31 st january. the model reproduced the observed temporal trend of cases within wuhan and cases exported internationally, capturing all of the dynamics reflected by these different data streams ( figure 2b -d). our results suggested there were around tenfold more symptomatic cases in wuhan in late january than were reported as confirmed cases ( figure 2e ), but the model not predict the slowdown in cases that was observed in early february. the model could also reproduce the pattern of confirmed exported cases from wuhan, which was not explicitly used in the model fitting ( figure 2f ). we found that confirmed and estimated exported cases among the twenty countries most connected to china were generally in good correspondence, with the usa and australia as notable outliers, having had more confirmed cases reported with a travel history to wuhan than would be expected in the model ( figure 2g ). we estimated that 100% (95% ci: 51-100%) of cases would be eventually had detectable symptoms, implying that most infections that were exported internationally from wuhan in late january were eventually detected. to examine the potential for new outbreaks to establish in locations outside of wuhan, we used our estimates of the reproduction number to simulate new outbreaks with potential individual-level variation in transmission (i.e. 'superspreading events') (13, 19, 20) . such variation increases the fragility of transmission chains, making it less likely that an outbreak will take off following a single introduction; if transmission is more homogeneous, with all infectious individuals generating a similar number of secondary cases, it is more likely than an outbreak will establish (19) . based on the median reproduction number estimated during january before travel restrictions were introduced, we estimated that a single introduction of 2019-ncov with sars-like or mers-like individual-level variation in transmission would have a 20-28% probability of causing a large outbreak ( figure 3a ). assuming sars-like variation and wuhan-like transmission, we estimated that once four or more infections have been introduced into a new location, there is an over 50% chance that an outbreak will occur ( figure 3b ). . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.31.20019901 doi: medrxiv preprint combining a mathematical model with multiple datasets, we found that the median daily reproduction number, r t , of sars-cov-2 in wuhan likely varied between 1.6-2.6 in january 2020 prior to travel restrictions being introduced. we also estimated that transmission declined by around half in the two weeks spanning the introduction of restrictions. the estimated fluctuations in r t were driven by the rise and fall in number of cases both in wuhan and internationally, as well as prevalence on evacuation flights ( figures 2b-d) . such fluctuations could be the result of changes in behaviour in the population at risk, or specific superspreading events that inflated the average estimate of transmission (13, 19, 20) . we found some evidence of reduction in r t in the days prior to the introduction of travel restrictions in wuhan, which may have been reflected outbreak control efforts or growing awareness of sars-cov-2 during this period. the uncertainty in our estimates for r t following the decline in early february ( figure 2a ) results from limited data sources to inform changes in transmission during this period. comparing model predictions to observed confirmed cases reported in wuhan during late january and early february, we found that the model predicts ten-fold higher cases than have been reported; the model also does not predict the recent slowdown in cases, suggesting a potential change in reporting rather than a genuine slowdown in transmission in early february. our estimates for international cases in specific countries were broadly consistent with the number of subsequently confirmed exported cases outside of wuhan. however, there were notably more cases exported to france, us, and australia compared to what our model predicted. this may be the result of increased surveillance and detected as awareness of sars-cov-2 grew in late january, which would suggest earlier exported cases may have missed; it may also be the result of increased travel out of wuhan immediately prior to travel restrictions being introduced on 23rd january. based our on estimated reproduction number, and published estimates of individuallevel variation in transmission for sars and mers-cov, we found that a single case introduced to a new location would not necessarily lead to an outbreak. even if the reproduction number is as high as it has been in wuhan in early january, it may take several introductions for an outbreak to establish; this is because high individual-level variation in transmission makes new chains of transmission more fragile, and hence less likely that a single infection will generate out outbreak. this highlights the importance of rapid case identification, and subsequent isolation and other control measures to reduce the chance of onward chains of transmission (21) . our analysis highlights the value of combining multiple data sources in analysis of covid-19. for example, the rapid growth of confirmed cases globally during late january 2020, with case totals in some instances apparently doubling every day or so, would have had the effect of inflating r t estimates to implausibly large values if only these recent data points were used in analysis. our results also have implications for the estimation of transmission dynamics using the number of exported cases from a specific area (22) . once extensive restrictions are introduced, as they were in wuhan, the signal from such data gets substantially weaker. if restrictions and subsequent delays in detection of cases is not accounted for, it could lead to artificially low . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.31.20019901 doi: medrxiv preprint estimates of r t or inferred case totals from the apparently declining numbers of exported cases. our model estimates benefitted from the availability of testing data from evacuation flights, which allowed us to estimate current prevalence. having such information for other settings, either through widespread testing or serological surveillance, will be valuable to reduce reliance on case reports alone. there are several other limitations to our analysis. we used plausible biological parameters for sars-cov-2 based on current evidence, but these values may be refined as more comprehensive data become available. however, by fitting to multiple datasets to infer model parameters, and performing sensitivity analyses on key areas of uncertainty, we have attempted to make the best possible use of the available evidence about sars-cov-2 transmission dynamics. further, we used publicly available connectivity and risk estimates based on international travel data to predict the number of exported cases into each country. these estimates have shown good correspondence with the distribution of exported cases to date (23) , and are similar to another risk assessment for covid-19 with different data (24) . we also assumed that the latent period is equal to the incubation period (i.e. individuals become infectious and symptomatic at the same time) and all infected individuals will eventually become symptomatic. however, there is evidence that transmission of sars-cov-2 can occur with limited reported symptoms (25) . we therefore conducted a sensitivity analysis in which transmission could occur in the second half of the incubation period, but this did not change our overall conclusions (appendix, page 7). we also explored having a larger initial spillover event and also using different sources for flight connectivity data, neither of which changed the conclusions of the analysis. in our analysis of new outbreaks, we also used estimates of individual-level variation in transmission for sars and mers-cov to illustrate potential dynamics. however, it remains unclear what the precise extent of such variation is for sars-cov-2 (13); if transmission were more homogenous than sars of mers-cov, it would increase the risk of outbreaks following introduced cases. as more data becomes available, it will be possible to refine these estimates, and therefore we made an online tool so users can explore these risk estimates if new data become available (appendix, page 4) our results demonstrate that there was likely substantial variation in sars-cov-2 transmission over time, and suggest a decline in transmission in wuhan in late january around the time that control measures were introduced. if covid-19 transmission establishes outside of wuhan, understanding the effectiveness of control measures in different settings will be crucial for understanding the likely dynamics of the outbreak, and the likelihood that transmission can eventually be contained. interpreted the findings, contributed to writing the manuscript and approved the final version for submission. figure 1 : model structure. the population is divided into four classes: susceptible, exposed (and not yet symptomatic), infectious (and symptomatic), removed (i.e. isolated, recovered, or otherwise non-infectious). a fraction of exposed individuals subsequently travel and are eventually detected in their destination country. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . cc-by 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint world health organisation. coronavirus disease 2019 (covid-19) ncov-2019 data working group. epidemiological data from the ncov-2019 outbreak: early descriptions from publicly available data. 2020. xx add link xx temporal changes in ebola transmission in sierra leone and implications for control requirements: a real-time modelling study the impact of control strategies and behavioural changes on the elimination of ebola from lofa county transmission dynamics of the etiological agent of sars in hong kong: impact of public health interventions the rapidd ebola forecasting challenge: synthesis and lessons learnt delaying the international spread of pandemic influenza. sepulveda-amor j, editor evaluation of the benefits and risks of introducing ebola community care centers who ebola response team. ebola virus disease in west africa -the first 9 months of the epidemic and forward projections early epidemiological assessment of the virulence of emerging infectious diseases: a case study of an influenza pandemic evidence synthesis for stochastic epidemic models assessing optimal target populations for influenza vaccination programmes: an evidence synthesis and modelling study pattern of early human-to-human transmission of wuhan transmission dynamics of 2019 novel coronavirus (2019-ncov) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia capturing the time-varying drivers of an epidemic using stochastic dynamical systems situation report mainland china superspreading and the effect of individual variation on disease emergence the role of superspreading in middle east respiratory syndrome coronavirus (mers-cov) transmission. eurosurveillance [internet feasibility of controlling 2019-ncov outbreaks by isolation of cases and contacts. medrxiv report 2: estimating the potential total number of novel coronavirus cases in wuhan city novel coronavirus (2019-ncov) early-stage importation risk to europe preliminary risk analysis of 2019 novel coronavirus spread within and beyond china transmission of 2019-ncov infection from an asymptomatic contact in germany we would like to thank motoi suzuki for his help in identifying the flight evacuation data sources. the authors have no conflicts of interest to declare. key: cord-335460-g8rsiiy7 authors: wu, yu-ping; cao, jin-ming; chen, tian-wu; li, rui; liu, feng-jun; zeng, yue; zhang, xiao-ming; mu, qi-wen; li, hong-jun title: ct manifestations of the coronavirus disease 2019 of imported infection versus second-generation infection in patients outside the original district (wuhan, china) of this disease: an observational study date: 2020-05-22 journal: medicine (baltimore) doi: 10.1097/md.0000000000020370 sha: doc_id: 335460 cord_uid: g8rsiiy7 to explore the discrepancy in computed tomography (ct) manifestations of the coronavirus disease 2019 (covid-19) in patients outside the original district (wuhan, china) between cases with imported infection and second-generation infection, 22 patients with covid-19 from 2 hospitals in nanchong, china, 938 km away from the original district (wuhan, china) of this disease were enrolled. all patients underwent initial and follow-up ct after admission during the treatment, and were divided into 2 groups. group a and b were composed of 15 patients with a history of exposure to the original district (wuhan, china) in short-term (i.e., imported infection), and 7 with a close contact with the patients with confirmed covid-19 or with the healthy individuals from the original district (i.e., second-generation infection), respectively. initial ct features including extent score and density score between groups were statistically compared. we found that all patients in group a and 3 of 7 patients in group b had abnormal ct findings while 4 of 7 patients in group b had not. patients with abnormal ct findings were more frequent in group a than in group b (p < .05). on initial ct, pure ground glass opacity (ggo), and ggo with consolidation and/or other abnormalities were found in 20% (3/15) and 80% (12/15) patients in group a, respectively, while 1 (14.3%), 2 (28.6%), and 4 (57.1%) had pure ggos, ggo with focal consolidation, and normal ct appearances in group b, respectively. patients with extent and density scores of ≥5 were more frequent in group a than in group b (all p-values < .01). additionally, 3 of 4 (75%) patients with normal initial ct findings had focal pure ggo lesions on follow-up. in conclusion, covid-19 in patients with a history of exposure to the original district can be severer than with the second-generation infection on ct. in late december 2019, several medical institutions in wuhan admitted a cluster of patients with pneumonia of unexplained etiology. [1] [2] an unknown novel coronavirus, which was temporarily named as the 2019 novel coronavirus (2019-ncov), was identified as the pathogen. [3] subsequently, the pneumonia caused by the 2019-ncov has been officially named by the world health organization as the coronavirus disease 2019 . [4] accompanied with the arrival of the chinese spring festival travel rush, the 2019-ncov spread rapidly all over china. [5] as of february 17, 2020, a total of 72,436 patients with confirmed covid-19 including 42,752 (59.0%) in wuhan have been reported in china. [6] [7] of these, 11,741 and 1868 cases were severe and death cases, respectively. furthermore, most of severe (9222, 78.5%) and death (1381, 73.9%) population were from wuhan, china, the original district of this disease. the rate of severity and mortality in covid-19 patients from wuhan were significantly higher than that in other regions outside wuhan, suggesting patients infected in the original district (wuhan, china) of this disease may have more rapid aggravation. to detect covid-19, viral nucleic acid detection using realtime polymerase chain reaction (rt-pcr) remains the standard of reference. [8] however, several defects such as immature development of nucleic acid detection technology, variation in detection rate from different manufacturers, false negative caused by low patient viral load or improper clinical sampling may cause low efficiency of detection and limit its clinical application. [8] as a promising method recommended by chinese society of radiology, [9] computed tomography (ct) plays an essential role in diagnosis and monitoring treatment responses in covid-19. multifocal bilateral ground glass opacity (ggo) as an indicator of early disease stage, and patchy consolidations as a marker of the disease progression are the most common patterns of ct abnormalities. [9] [10] [11] based on above-mentioned typical ct findings, the severity of covid-19 could be staged into early, progression, severe, and dissipation stage which embodied in the consensus of chinese society of radiology. [9] as for the patients outside the original district (wuhan, china) of this disease, the infection routes included an exposure history of the original district (wuhan, china) in short term (i.e., imported infection), and a close contact with the infected individuals exposed to the original district recently (i.e., secondgeneration infection). to the best of our knowledge, there were no reports focusing on the discrimination in severity of the covid-19 between patients outside the original district (wuhan, china) according to different routes of infection. thus, the purpose of our research was to determine the discrepancy in ct manifestations of covid-19 in patients outside the original district (wuhan, china) between cases with imported infection and with second-generation infection, aiming to help clinicians outside the original district formulate more accurate and effective prevention and treatment measures. the institutional ethics committee of the affiliated hospital of north sichuan medical college approved this study (approval number, 2020er007-1), and the written informed consent was obtained from each participant. from january 23 to february 17, 2020, 22 consecutive covid-19 patients derived from 2 designated hospitals in nanchong, china, 938 km away from the original district (wuhan, china) of this disease, were enrolled into our study. all patients had positive results for 2019-ncov detection via the initial rt-pcr after admission. patients were subsequently classified into 2 groups based on the following criteria: (1) patients with imported infection were enrolled into group a, and they had a history of travelling to/or living in the original district (wuhan, china) recently for less than 1 month. (2) in group b, patients had second-generation infection, and they were in the absence of exposure to the original district (wuhan, china) but were in close contact with the patients with confirmed covid-19, or with the healthy individuals from the original district (wuhan, china). the baseline data of the onset of symptoms are recorded in table 1 . all patients underwent initial thoracic ct examinations ( fig. 1a and fig. 2a ) after admission. the intervals between the initial ct scan and the onset of symptoms were 4.9 ± 3.9 days in group a and 10 ± 4.5 days in group b. it should be noted that 1 patient in group a, and 3 in group b were asymptomatic, and there was no interval between the initial ct scan and the onset of symptoms. all patients underwent follow-up ct scans ( fig. 1b and c, and fig. 2b ) and rt-pcr every 3 to 8 days during their hospitalization based on the severity of covid-19. but for the asymptomatic patients in group b, they received follow-up ct scans when their rt-pcr results were positive. in addition, all patients received relevant medical management during their hospitalization. thoracic non-contrast enhanced ct scans were performed in 17 patients with 16-row multidetector row ct system (uct 510, united imaging, shanghai, china), and in 5 patients with a 128row multidetector ct system (somatom definition flash, siemens healthcare systems, germany). each examination was performed in a breath-hold mode at full suspended inspiration. the scanning coverage was from the thoracic inlet to the middle level of the left kidney. scanning parameters for the uct 510 scanner were as follows: table 1 baseline clinical characteristics of the coronavirus disease 2019. the scanning parameters for somatom definition flash scanner were similar to those for the 16-multidetector row ct scanner except the tube current of 250 ma and detector collimation of 0.6 mm. data from 2 ct scanners were respectively transferred to the image processing workstation (somatom definition flash, siemens healthcare systems, germany). the window width and level were set to 350 hu and 40 hu for mediastinal window, and to 1000 hu and -700 for lung window, respectively. all image data were independently reviewed on above-mentioned workstation by 2 experienced radiologists (the first author with 1 year of experience in radiology and the co first author with 8 years of experience in radiology) blinded to epidemiologic and clinical information. in case of discrepancy between the 2 observers, a third radiologist (co corresponding author with 12 years of experience in radiology) reviewed the images for the final adjudication. before the previous radiologists reviewed the image data, a professor of radiology (the corresponding author with 22 years of experience in body radiology) trained them on how to review the image data. according to the expert consensus, [9] the initial ct manifestations in groups a and b were assessed based on the following features: (1) no abnormal finding (2) ggo (3) consolidation (4) other abnormalities (e.g., reticulation, and interlobular septal thickening) in order to assess the severity of the disease more accurately, we also devised a semi-quantitative scoring system to evaluate the extent and severity of disease in this study. as illustrated in tables 2 and 3 , the ct lesion extent and density scores were determined based on the anatomic distribution and density of lung lesions referencing to the reported semi-quantitative score system. [12] the extent score was assessed on lung window based on the extent of the 5 lung lobes involved by covid-19. the overall lung extent score was obtained by summing the 5 lobe scores. the density score was evaluated on lung window based on the percentages of consolidation and other abnormalities in each covid-19 lesion, and the overall lung density score was acquired by summing the 5 lobe scores. the score range for both lungs in each patient is from 0 (no detectable abnormality) to 20 (more than 75% of each lung lobe involved by covid-19 lesion and 100% of consolidation in each lesion). in order to assess the intra-observer variability of the above semi-quantitative measurements, the first author repeated the image data analysis 3 days later. the intra-observer variability was obtained by comparison of the 2 measurements by the first author. the inter-observer variability was accessed with the results by 2 independent double-blinded observers (the first author and the co-first author). all data were statistically analyzed by ibm spss statistics software (version 25.0 for windows; spss, chicago, il, usa). the normality of distribution was evaluated by shapiro-wilk test. continuous variables, expressed as the mean and standard deviation. the categorical variables were described in percentiles and compared using the chi-squared test or fisher exact test. both intra-observer and inter-observer variability were tested for ct score using interclass correlation coefficient (icc). the semi-quantitative extent and density scores of covid-19 lesions on initial ct were considered to be reproducible when the icc was greater than 0.75. [13] statistical difference was defined as p < .05 for all tests. (fig. 1a ) and 3 (42.9%) in group b had abnormal findings on initial ct while the remaining 4 (57.1%) patients had none abnormal ct findings. patients with abnormal ct findings were more frequent in group a than in group b (p < .05). pure ggos, and ggos with consolidation and/or other abnormalities were observed in 3 (20%) and 12 (80%) patients in group a, respectively. in group b, 1 (14.3%) and 2 (28.6%) patients had pure ggos and ggos with consolidation, respectively. among the previous 4 patients with normal image on initial ct scan, 3 cases (75%) developed into focal pure ggo on follow-up scans ( fig. 2a) . the mean intra-observer and inter-observer icc values were 0.96 (95%ci: 0.91-0.98) and 0.94 (95%ci: 0.86-0.97) for extent score, and 0.95 (95%ci: 0.90-0.98) and 0.93 (95%ci: 0.84-0.97) for density score, respectively. therefore, the average of the extent score and density score from the first author and the co first author's measurements was used for the subsequent statistical analysis. as demonstrated in table 4 , the mean extent score of lesions on ct in group a was 6.7, ranged from 1 to 17. in group b, the mean extent score of lesions on ct was 1.1, ranged from 0 to 4. in group a, 13 (86.7%) and 2 (13.3%) patients scored at least 5 and 10, respectively. except the 4 patients with a normal ct finding on initial scans, the remaining 3 patients in group b scored 1, 3, and 4 according to the extent scoring system. the extent of lung lobe involved by covid-19 lesions in group a was strikingly greater than that observed in group b (p < .001). as shown in table 4 , the mean density score of lesions in both lungs in group a (mean score, 10.1; range, 1-17) was significantly higher than that in group b (mean score, 1.3; range, 0-4). in group a, 14 and 11 patients scored at least 5 (93.3%) and 10 (73.3%), respectively. in contrast, none of patients in group b with abnormal ct findings on initial scans had lesion density score of more than 5 (p < .001), indicating that the covid-19 in second-generation infected patients could be milder when compared with those with imported infection. table 3 the density scoring system of the coronavirus disease 2019 on initial computed tomography. no abnormal findings 0 pure ggo 1 ggo with < 50% consolidation and/or other abnormalities 2 ggo with≥50% consolidation and/or other abnormalities 3 consolidation with other abnormalities without ggo 4 ggo = ground glass opacity. table 4 comparisons of patients between groups according to the extent and density scores of the coronavirus disease 2019 on initial computed tomography. lesion score group a (n = 15) group b (n = 7) extent score 0 0 4 (57.1) 1 1 (6.7) 1 (14. covid-19 is a new disease with high infectivity causing an enormous impact on public health. [14] the chinese spring festival travel rush has triggered massive population movements which gave rise to the confirmed cases of covid-19 outside the original district (wuhan, china) of this disease with imported infection, as well as cases with second-generation infection in succession. in order to better master the characteristics of covid-19 in patients outside the original district for appropriate treatment, we carried out our study to investigate the discrepancy in ct manifestations of this pneumonia in patients outside the original district (wuhan, china) between cases with imported infection and the second-generation infection. our study revealed that abnormal findings on initial ct scans can be found in each patient with imported infection but not patients with the second-generation infection. in patients with the second-generation infection, some patients could have abnormal initial ct appearances, and some could not. our findings can be explained by the following pathological mechanism. as reported, [15] [16] [17] rna virus is characterized by error-prone viral replication and recombination and usually generates progeny viruses with highly diverse genomes which might result in reduction of virulence and pathogenicity. we could presume that the 2019-ncov as a novel rna virus might have the similar characteristics of reduction of virulence and pathogenicity resulted from the error-prone viral replication and recombination. as shown in our study, ggo and consolidation could be the most common patterns of ct abnormalities of the confirmed covid-19 in patients with imported infection, which was consistent with the published reports. [9] [10] [11] as reported, [9] ggo and consolidation could respectively reflect the potential pathological abnormalities in different stages of the disease. seen mainly in the early stage of the disease, the underlying pathologic change of pure ggo can be small amount of exudation of fluid in alveolar cavity and interlobular interstitial edema. [10] consolidation lesions could be regarded as a marker of more severe phase, [11] reflecting a large amount of cell-rich or fibrous exudation accumulated in the alveolar cavity and pulmonary interstitium. [10] it is noteworthy that 3 cases of second-generation with normal finding on initial ct scan developed into focal ggos during follow-up ct, suggesting that the limitation of ct in the early detection of asymptomatic patients with the second-generation. the covid-19 case without abnormal manifestation on initial ct scan should be confirmed by 2019-ncov detection via rt-pcr together with a history of close contact with imported infection. moreover, we found that the discrepancies of extent and density scores obtained on the initial ct could exist between patients with imported infection and with the second-generation infection. in detail, the extent of lung lobe involved by covid-19 lesions in patients with imported infection was strikingly greater than that in patients with second-generation infection. the previous discrepancies of extent and density scores between groups can be explained as follows. on one hand, the virus load or the chance of being exposed to the virus in the environment in the original district (wuhan) could be much higher than any other district where there were much fewer covi-19 cases. on the other hand, ggos with consolidation or other abnormalities (i.e., reticular and/or interlobular septal thickening) involving multiple lobes could be more common in patients with imported infection than in patients with the second-generation infection, resulting in elevated ct density and extent scores in patients with imported infection when compared with patients with secondgeneration infection. our findings suggest that patients with imported infection might have more rapid progression of disease and increasing likelihood of mixed bacterial coinfection. [18] [19] based on the comparison of ct density score between groups, we can presume that the covid-19 in second-generation infected patients could be milder when compared to those with imported infection. our study had several limitations. for one thing, a larger sample size of covid-19 patients is required for further investigation, especially with an emphasis on asymptomatic second-generation patients. for another thing, the semi-quantitative scoring system of disease in this study was based on the typical ct manifestations applied in the expert consensus, [9] the other abnormal findings such as reticulation and interlobular septal thickening did not particularly evaluate, and further modification is required. the ct findings of covid-19 vary according to the routes of infection. patients with imported infection tend to have more severe ct manifestations, suggesting that ct could accurately evaluate the covid-19 in the population. cases with secondgeneration infection could be manifested as normal finding on the initial ct scan, but may progress to mild abnormalities on follow-up cts, indicating 2019-ncov detection via rt-pcr could be essential in the population with high risk of infection. we hope that our findings can help clinicians outside the original district (wuhan, china) of this disease formulate more accurate and effective prevention and treatment measures. early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china emerging coronaviruses: genome structure, replication, and pathogenesis novel coronavirus (sars-cov-2) epidemic: a veterinary perspective medicine (2020) 99:21 www.md-journal ct features of coronavirus disease 2019 (covid-19) pneumonia in 62 patients in wuhan, china novel coronavirus pneumonia emergency response epidemiology teamthe epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (2019-ncov infected) in china updated understanding of the outbreak of 2019 novel coronavirus (2019-ncov) in wuhan sensitivity of chest ct for covid-19: comparison to rt-pcr chinese society of radiologyradiological diagnosis of new coronavirus infected pneumonitis: expert recommendation from the chinese society of radiology a rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-ncov) infected pneumonia (standard version) emerging coronavirus 2019-ncov pneumonia ct imaging features of 2019 novel coronavirus (2019-ncov) intraclass correlations: uses in assessing rater reliability severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and coronavirus disease-2019 (covid-19): the epidemic and the challenges clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china mutational dynamics of the sars coronavirus in cell culture and human populations isolated in 2003 comparative full-length genome sequence analysis of 14 sars coronavirus isolates and common mutations associated with putative origins of infection radiographic and ct features of viral pneumonia viral infections of the lower respiratory tract: old viruses, new viruses, and the role of diagnosis key: cord-257556-lmws8eed authors: rafiq, danish; batool, asiya; bazaz, m. a. title: three months of covid‐19: a systematic review and meta‐analysis date: 2020-05-18 journal: rev med virol doi: 10.1002/rmv.2113 sha: doc_id: 257556 cord_uid: lmws8eed the pandemic of 2019 novel coronavirus (sars‐cov‐2019), reminiscent of the 2002‐sars‐cov outbreak, has completely isolated countries, disrupted health systems and partially paralyzed international trade and travel. in order to be better equipped to anticipate transmission of this virus to new regions, it is imperative to track the progress of the virus over time. this review analyses information on progression of the pandemic in the past 3 months and systematically discusses the characteristics of sars‐cov‐2019 virus including its epidemiologic, pathophysiologic, and clinical manifestations. furthermore, the review also encompasses some recently proposed conceptual models that estimate the spread of this disease based on the basic reproductive number for better prevention and control procedures. finally, we shed light on how the virus has endangered the global economy, impacting it both from the supply and demand side. the initial outbreak of the novel coronavirus in december 2019 was centered in wuhan, hubei province of the people's republic of china. [1] [2] [3] [4] [5] it was initially named as 2019 novel coronavirus, soon after the international committee of taxonomy of viruses (ictv) named the virus as sars-cov-2, 1 because of the previously identified variant-severe acute respiratory syndrome coronavirus (sars-cov). the clinical illness it causes is termed as coronavirus disease 2019 . 2 while several other human coronaviruses such as hcov-nl63, hcov-229e, hcov-oc43, and hcov-hku1 cause mild respiratory disease, others like the zoonotic middle east respiratory syndrome coronavirus (mers-cov) and sars-cov tend to have a higher fatality rate 6 (summarized in table 1 ). they bear a core shell with surface projections that make them resemble a crown. they were first described by tyrell and bynoe in 1966, from patients with the common cold. 9 four subfamilies of coronaviruses have so far been discovered; • alpha: originate from mammals, particularly bats, cause asymptomatic or mildly symptomatic infections • beta: originate from mammals, particularly bats, can cause severe disease and fatalities. sars-cov-2 belongs to the betacoronaviruses and is closely related to the sars-cov virus. 10, 11 sars-cov-2 is 96% identical to a bat coronavirus at the wholegenome level. 11 • gamma and delta: originate from pigs and birds the genome size of coronaviruses varies between 26 and 32 kb with four major structural genes encoding the membrane glycoprotein (m), spike protein (s), nucleocapsid protein (n), and a small membrane protein (sm) (figure 2 ). an additional membrane glycoprotein (he) occurs in the hcov-oc43 and hku1 beta-coronaviruses. 12 sars-cov-2019 has succeeded in transferring from bats to humans, presumably in the seafood market in wuhan, china. however, potential intermediate hosts remain to be identified and the precise route of transmission urgently needs to be clarified. because of the novelty of this virus, experts' understanding of exactly how it spreads is restricted. major respiratory outbreaks in last century it has also been suggested that the receptor-binding ability of sars-cov-2 is 10-20 times stronger than that of sars-cov. 15 the patients may move through different stages of illness: • replicative stage -the virus may take several days to replicate. initially, it evokes the first line of defence, that is, innate immune response, but this fails to contain the virus resulting in fairly mild symptoms due to direct viral cytopathic effect. • adaptive immunity stage -the innate immune response is eventually followed by the adaptive immune response which tends to decrease the titer of the virus. meanwhile, the inflammatory cytokines show augmented levels culminating in tissue damage and consequent clinical deterioration. this explains the sudden deterioration of the patients after being relatively fine for several days. 20 potentially clinical inferences can be drawn: • preliminary clinical symptoms are not essentially prognostic of future outcome. • antiviral therapies need to be given during the replicative stage to work optimally. • it is desirable to deploy any immunosuppressive therapies in the adaptive immune stage to blunt the immunopathologic response. the initial clinical sign of the covid-19 that allowed its case detection was pneumonia. while some reports suggest gastrointestinal symptoms associated with this disease, others describe asymptomatic infections, particularly among young children. 21 sars-cov-2019 may cause lower respiratory symptoms, upper respiratory symptoms, constitutional symptoms, and, less commonly, gastrointestinal symptoms. most patients show lower respiratory symptoms and constitutional symptoms (eg, cough and fever). • the incidence of fever is variable among studies (ranging from 43% to 98%). this may relate to different strains of virus or different levels of disease severity between several cohorts. regardless of the frequency, absence of fever in a patient does not exclude covid-19. • about 80% of patients may have lymphopenia. 22, 23 • mild thrombocytopenia is very common (but only rarely do platelet counts decline below 100). • lower platelet count is a marker of poor prognosis. 19 • also, up to 10% of patients can initially show gastrointestinal symptoms (eg, nausea and diarrhea), followed by dyspnea. 24 • some patients, especially the elderly, may have "silent hypoxemia" and respiratory failure without dyspnea. 25 • approximately, 2% of patients may develop pharyngitis or tonsil enlargement. 22 3 | transmission and management typical of respiratory viruses like influenza virus, sars-cov-2019 can spread through large droplets (with a transmission risk restricted tõ 6 ft from the patient). 26 the droplet containing viral particles (saliva or mucous droplets) can be ejected during coughing, sneezing, laughing, singing, breathing, and talking. if these droplets do not encounter anything along the way, they typically land on the ground or the floor. this transmission via large droplet can be reduced by using a normal surgical-style mask. this mode of transmission is usually overlooked, but it is very important. it works in four chains of reactions: there are currently no reports of intrauterine maternal-fetal transmission, but neonatal transmission can occur. 29 research thus far has revealed more than 30 agents including natural products, western medicines, and traditional chinese medicines with potential efficacy against covid-19. some promising results have been achieved which are summarized below and listed in table 2 , but formal randomized clinical trials will be required to prove efficacy and safety. lopinavir and ritonavir are protease inhibitors that work in conjunction to block viral replication. ritonavir, being a cyp3a inhibitor, reduces the metabolism of lopinavir, thus boosting its levels. a 4 ug/ml concentration of lopinavir was required for in vitro antiviral activity against sars while 1ug/mg of lopinavir was enough when used in combination with ribavirin. 30 both protease inhibitors appear to function synergistically with ribavirin. combination of all three drugs has been used previously on sars and mers. 30 recently, the combination of lopinavir/ritonavir has not proven impressive, suggesting that a cocktail of ribavirin/lopinavir/ritonavir might be required for efficacy. 20 nevertheless, lopinavir/ritonavir is advantageous over ribavirin because of its wide availability and an established toxicity profile. originally developed for ebola, this drug was the most obvious fit for sars-cov-2019 as it has already been tried out for ssrna viruses like sars and mers. 31 remdesivir is a prodrug whose phosphoramide is cleaved off to leave the active compound gs-44-1524 with a 5 0 oh. chloroquine, generally used for amebiasis and malaria, is currently being considered for treating covid-19 in view of its ability to interfere with the cellular receptor ace2. it also impairs the acidification of endosomes, thereby impeding virus trafficking inside cells. although chloroquine has been unsuccessful in treatment of sarsinfected mice, 37 recent reports from in vitro data show that chloroquine inhibits sars-cov-2 at a 50% inhibitory concentration of 1 um. this suggests the possibility of achieving therapeutic levels in humans. 38 it is worth mentioning that for sars, the 50% inhibitory concentration of chloroquine is near to 9 um, 39 several other potential drugs include bcr-abl kinase inhibitor imatinib and type-ii transmembrane serine protease (tmspss2) inhibitors. 44 imatinib inhibits the fusion of virions with the endosomal membrane and as such possesses anti-coronavirus activity. 45 ple. 47 the interpretation of the results is given in table 3 . the presence of sars-cov-2 viral proteins (antigens) in a sample from the respiratory tract of a person can also be detected within considering p as the total population, it is assumed that the susceptible population (s) is stably decreasing at a protection rate (α) and moving to compartment (s q ) that represents the quarantined individuals. those who are not quarantined and come in contact with infected persons belong to the compartment exposed (e) depending upon the transmission rate (β). an exposed individual, if protected from being infected (eg, by using protection of face mask or hand sanitizers) will move back to the susceptible (s) compartment at the safety rate (μ). the exposed individuals can get infected and move either to infectious and symptomatic (i) or infectious but not yet symptomatic/presymptomatic to (a) compartment depending upon the average latent time (γ − 1 1 ) and (γ −1 2 ), respectively. the infected individuals can be detected and then hospitalized at a rate δ. from compartment (h), the patients can also move to the compartment recovery (r) at cure rate λ(t) or die at mortality rate κ 1 (t). however, the recovered persons are added back to the susceptible compartment (s) at a rate θ. it is important to mention that a percentage of people, though less, die in presymptomatic phase before being hospitalized. they also add to the death compartment at rate κ 2 (t). the seir model described above can be modeled by a set of ordinary differential equations (odes) given as follows: these nonlinear coupled odes can be solved using an explicit/ implicit time stepping integrating scheme like the regular fourth-order runge-kutta scheme. 56 in the past 3 months, various mathematical models have estimated • later an updated estimation risk has been shown 59 that included calculating the time-dependent contact and diagnosis rates. from a period of january 1, 2020 to february 7, 2020. • the authors have argued that the estimation of r o mainly depends on the estimation technique involved and the modeling assumptions used. • both deterministic and stochastic models were included in the study. • the study showed that the maximum-likelihood (ml) value of basic reproductive number (r 0 ) was 2.28 at an early stage on the ship for the covid-19 outbreak. • it was shown that if (r 0 ) value was reduced by 25% and 50%, the • the value of (r 0 ) was estimated using the next-generation matrix approach which came out to be 2.30 for reservoir to person and 3.58 for person to person. of covid-19 is presented in this study along with some useful insights from these models. • also, a susceptible-exposed-infected (sei) model framework was presented, and auxiliary strategies were described to prevent the covid-19 outbreak. the study showed that exposure time plays a significant role in spreading the disease. • the data were used for estimation of basic reproduction number using a susceptible infected recovered dead (sird) framework. • the estimated average value of r 0 was~2.6 based on confirmed cases. the plot for the estimated value of the (r 0 ) obtained by the above-mentioned studies is shown in figure 4 . the plot shows a high reproductive number at the beginning of the outbreak in china with the maximum peak in mid-january 2020. however, with passage of time, social distancing, self-quarantine, health care measures, and governmental actions had a substantial effect in containing the outbreak which is evident from the estimates of the (r 0 ) in the months of february and march, 2020. it is pertinent to mention that the estimates of the basic reproductive number mentioned in the above studies can be poor due to insufficient data, and different estimation techniques can result in different forecasts. however, further collection of data with robust modeling can result in close estimates. viral spread has borne out experts' downside fears, with consequences of possible containment measures, disrupted supply chains, and spill overs from the real economy to monetary markets. 75 this overview provides the basic, biomedical, and translational research communities some key insights on covid-19. we believe that the focus of future studies still lies in the progress of effective drugs in general and development of sars-cov-2 vaccines in particular. while uncertainty lingers, credible, coordinated, and coherent policy responses would deliver the best chance at limiting the fallout from this human tragedy. time alone can tell how the virus is going to affect our lives, but future outbreaks of pathogens of zoonotic origin and viruses are likely to continue. as such, besides curbing this epidemic, efforts should be implemented to devise inclusive measures to avert future outbreaks of zoonotic origin. though the virus has reshaped the geopolitical globalization, multilateralism and integration of countries are indispensable. without a doubt, we must move toward policy making and greater coordination to combat the current health crisis. severe acute respiratory syndrome-related coronavirus: the species and its viruses-a statement of the coronavirus study group a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of 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forecasting of the covid-19 outbreak nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study modelling the epidemic trend of the 2019 novel coronavirus outbreak in china transmission dynamics of 2019 novel coronavirus (2019-ncov) novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions early transmissibility assessment of a novel coronavirus in wuhan estimating the effective reproduction number of the 2019-ncov in china preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data driven analysis in the early phase of the outbreak how to cite this article: rafiq d, batool a, bazaz ma. three months of covid-19: a systematic review and meta-analysis the authors declare no conflicts of interest. danish rafiq and asiya batool collected the data and wrote the manuscript, m. a. bazaz analyzed the data and helped in critical analysis and proof reading of the manuscript. not required. https://orcid.org/0000-0002-9232-4875 key: cord-351167-4gpq5syb authors: koenig, kristi l.; beÿ, christian k.; mcdonald, eric c. title: 2019-ncov: the identify-isolate-inform (3i) tool applied to a novel emerging coronavirus date: 2020-01-31 journal: west j emerg med doi: 10.5811/westjem.2020.1.46760 sha: doc_id: 351167 cord_uid: 4gpq5syb 2019 novel coronavirus (2019-ncov) is an emerging infectious disease closely related to mers-cov and sars-cov that was first reported in wuhan city, hubei province, china in december 2019. as of january 2020, cases of 2019-ncov are continuing to be reported in other eastern asian countries as well as in the united states, europe, australia, and numerous other countries. an unusually high volume of domestic and international travel corresponding to the beginning of the 2020 chinese new year complicated initial identification and containment of infected persons. due to the rapidly rising number of cases and reported deaths, all countries should be considered at risk of imported 2019-ncov. therefore, it is essential for prehospital, clinic, and emergency department personnel to be able to rapidly assess 2019-ncov risk and take immediate actions if indicated. the identify-isolate-inform (3i) tool, originally conceived for the initial detection and management of ebola virus and later adjusted for other infectious agents, can be adapted for any emerging infectious disease. this paper reports a modification of the 3i tool for use in the initial detection and management of patients under investigation for 2019-ncov. after initial assessment for symptoms and epidemiological risk factors, including travel to affected areas and exposure to confirmed 2019-ncov patients within 14 days, patients are classified in a risk-stratified system. upon confirmation of a suspected 2019-ncov case, affected persons must immediately be placed in airborne infection isolation and the appropriate public health agencies notified. this modified 3i tool will assist emergency and primary care clinicians, as well as out-of-hospital providers, in effectively managing persons with suspected or confirmed 2019-ncov. 2019 novel coronavirus (2019-ncov) is a novel respiratory disease first reported in wuhan, hubei province, china in december 2019. 1 chinese health officials were originally investigating a sudden increase in cases of pneumonia which were later determined to be linked to 2019-ncov. while most cases originated within mainland china, the disease spread to neighboring countries including taiwan, thailand, south korea, and japan, and later to the united states, europe, and australia. a near real-time updated tracking website for cases and locations worldwide, along with reported deaths is available. 2 chinese health authorities have sequenced 2019-ncov and freely shared its genetic profile online. 3, 4 additionally, on january 28, 2020, an australian laboratory reported growing the virus from a patient sample. as of january 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths. 2 these numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin. the what was the research question? investigators adapted the "identify, isolate, inform" (3i) tool for use in suspected cases of 2019-ncov. what was the major finding of the study? a novel 2019-ncov 3i tool is designed for frontline clinicians in the management of suspected patients. this 2019-ncov 3i adaptation will aid healthcare providers most likely to encounter the disease in the containment and effective treatment of patients. age distribution of these verified deaths is currently not available. one preliminary, small-scale study of 41 patients in wuhan china, reported 6 deaths (15% mortality) with a median age of 49.0 years. 5 additionally, transmission of the virus has reportedly occurred in healthcare facilities in wuhan city, raising concerns of spread to healthcare workers, as was seen during prior outbreaks of the novel coronaviruses, middle eastern respiratory syndrome (mers) and severe acute respiratory syndrome (sars). due to the dynamic nature of the outbreak, exposure criteria may change depending on where new cases of 2019-ncov are detected, the degree of transmissibility, and when additional information regarding the origin of the virus is discovered and reported. on january 15, 2020, the centers for disease control and prevention (cdc) confirmed the first known imported case of 2019-ncov in the us state of washington. the patient had recently returned from wuhan city, where he likely contracted the disease. chicago health authorities reported a second us case on january 24, 2020. this was quickly followed by additional imported cases reported in orange and los angeles counties, california on january 26, 2020. additional suspected cases continue to be evaluated. on january 30, 2020, the cdc reported the first local transmission in the us between members in a household. on the same day, the world health organization declared 2019-ncov to be a public health emergency of international concern (pheic). 6 on january 31, 2020, the us department of health and human services declared coronavirus a public health emergency. 7 healthy individuals and those with mild illness may be asymptomatic, while others may have more pronounced symptoms of fever or lower respiratory illness. upon identification of a suspected patient, that individual should immediately be isolated with airborne precautions. further workup and laboratory confirmation can then proceed. emergency physicians (eps), emergency medical services (ems) personnel, and other healthcare workers who encounter patients with suspected 2019-ncov infection must inform the appropriate authorities, including but not limited to hospital infection control and local or state public health agencies. healthcare workers must follow on-going developments related to the outbreak, especially new information concerning detection and management. 8, 9 the 3i tool outlined in this paper is consistent with current us cdc guidelines and can be applied in a variety of settings such as those in emergency departments, urgent-care clinics, physicians' offices, and prehospital settings. this paper will first briefly review 2019-ncov and then present the novel 2019-ncov 3i tool as modified from its initial conception for ebola virus disease 10,11 and later adapted for measles, 12 mers, 13 mumps, 14 zika virus disease, 15 hepatitis a, 16 pertussis, 17 and scabies. 18 coronavirus 2019-ncov infection commonly presents with signs and symptoms of pneumonia or as a nonspecific lower respiratory illness, with coughing or difficulty breathing accompanied by fever. 5, 19, 20 fever and cough constitute the most common presentations. however, patients may have other respiratory symptoms, sore throat, nasal congestion, malaise, myalgia, and headache. bilateral infiltrates may be seen on chest x-ray. severe cases may present with sepsis and even shock. conversely, some patients may present as only mildly ill or asymptomatic altogether. 21 to date, patients with underlying medical conditions and the elderly are more likely to become severely ill, require hospitalization, and ultimately die. 22 early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. the 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 in addition, the world health organization (who) has created its own interim case definition. 24 by definition, the main features of a novel virus, for example, how it is transmitted, will not be immediately known. however, as with the development of any 3i tool, it is essential to understand specific characteristics of the disease. in the case of a novel virus such as 2019-cov, this is challenging since information is rapidly evolving and the science is not yet fully understood. it is possible that the virus will undergo mutations over time that could substantially change its the identify-isolate-inform (3i) tool applied to a novel emerging coronavirus koenig et al. features. nevertheless, an appreciation of the key concepts that drive evidence-based management is beneficial (table 1) . management guidance will likely change over time. with the initial discovery of a new potential public health threat, it will likely be unclear how patients become sick. for example, rather than a contagion, there could be a contaminant or a toxin responsible for signs and symptoms. in this case, the possibility of an environmental toxin in the wuhan market was a consideration early on when limited to no human-tohuman transmission was reported. the mode of transmission has implications for the types of personal protective equipment (ppe) needed to protect healthcare providers in the prehospital, clinic, and hospital settings. 25 in addition, patients may need decontamination after exposure to certain toxins. 26 another important consideration for application of the 3i tool is whether the disease is contagious prior to symptom onset (like measles) or only after symptoms develop (like ebola). a january 30, 2020 letter to the new england journal of medicine describes a purported confirmed instance of transmission from an asymptomatic individual. researchers state that, before symptom onset, the primary case infected two individuals, one of which infected two additional colleagues. 27 subsequent investigation suggested that the source patient did have mild symptoms and had taken an antipyretic, calling this reported asymptomatic transmission into question. while quarantine may not be feasible and can have unintended consequences, 28, 29, 30 it is a public health tool that can be considered in cases when disease is transmissible before symptom onset. 30 conversely, if a disease is known not to be transmissible prior to symptom onset, asymptomatic exposed patients must be monitored, but do not require quarantine or isolation unless they develop symptoms. initially, it may be unclear whether an infectious agent occurred naturally or was deliberately or accidentally released. in this case, a bsl-4 laboratory studying coronaviruses was located approximately 32 kilometers away from the market where initial exposures were felt to occur. 31 recall that in 2001, the anthrax letter attacks were initially thought to be naturally occurring. once determined to be bioterrorism, management of the event was similar to that for a chemical exposure with a sudden impact, defined scene, and need for a rapid response and decontamination on site. this differed from the who's modeling predicting an aerosolized release that would result in an incubation period with 100,000 or more persons exposed rather than the 22 people who contracted anthrax in 2001. 32 by understanding the key features of a novel disease, healthcare workers can take evidence-based measures to protect themselves, optimize individual patient management, and prevent further disease spread. it is currently unclear how 2019-ncov is spread, but it is suspected to be transmitted through contact with infected respiratory secretions, like other known coronaviruses. there are instances of sustained human-to-human transmission across generations of cases, especially near the epicenter in wuhan city. 21 current evidence suggests that close contact with an infected person is a major factor in disease transmission. cdc defines "close contact" 33 as being in or within two meters of an area with a confirmed patient or being directly exposed to infectious secretions without appropriate ppe. healthcare facilities in china have reported spread from person to person. in addition, some mildly ill or potentially even asymptomatic patients may have a higher chance of spreading the disease to others as they may be less likely to seek medical care. 34 the possibility that patients may be infectious prior to symptom onset further compounds the difficulty of containing the virus and effectively preventing transmission. the current majority of 2019-ncov cases have been within china and its bordering countries. 2 persons with recent travel (within 14 days) to wuhan city or another region with widespread disease, or exposure to a patient under investigation, are considered to have an epidemiologic risk factor and should be assessed for signs and symptoms of a viral illness such as fever and respiratory symptoms. coronavirus is a zoonotic virus the identify-isolate-inform (3i) tool applied to a novel emerging coronavirus that is transmitted to humans via contact with infected animals. preliminary reports suggest the disease may have originated in a seafood and live animal market in wuhan city, but it is still unknown how or whether such transmission occurred. clinicians working with local public health departments must arrange to have specimens from patients under investigation (puis) sent to the cdc laboratory. at this time, the cdc has the only laboratory that can definitively test for 2019-ncov, though laboratory testing capacity is being rapidly expanded. polymerase chain reaction (pcr) assays conducted on samples from a patient's upper and lower respiratory tracts will be used to confirm potential cases. in addition, serum antibody titers can be analyzed for confirmation of infection or evidence of immunity. up-to-date information about the needed specimens and handling requirements to test for 2019-ncov are available on the cdc website. 35 like other related coronaviruses, patients with 2019-ncov frequently present with non-specific symptoms resembling that of influenza. physicians may consider differential diagnoses related to a wide variety of respiratory infections. in order to relate these symptoms to 2019-ncov, it is imperative that the identification of a potential exposure event (epidemiologic risk factor) within 14 days of symptom onset is made so that a more focused work-up for 2019-ncov can be completed. although the likelihood of coinfection of 2019-ncov and another respiratory virus is thought to be low, a positive finding of another respiratory pathogen does not exclude the diagnosis of 2019-ncov. many commercially available respiratory panels include "coronavirus" in the results, but neither a positive nor a negative finding on these panels should be used to include or exclude a diagnosis of 2019-ncov. supportive care with appropriate infection control is the mainstay of current cdc treatment guidelines for 2019-ncov. there are not yet any approved antiviral treatments for 2019-ncov. emergency use authorizations (eua) for compassionate use cases may be forthcoming from the us federal government for normally unapproved treatments. supportive treatment predominantly includes respiratory support, hydration, and antipyretics. general treatment for severe cases should focus on the preservation of vital organ function. in the future, antiviral medications may be available. if a secondary bacterial infection such as pneumonia develops, targeted antibiotics are indicated. prevention of 2019-ncov transmission, like any other infectious agent, involves minimizing risk of exposure. vaccines are under accelerated development and may be useful in the future for post-exposure prophylaxis. healthcare personnel are at increased risk and should practice standard, droplet, and airborne precautions when encountering an infected person, a pui, or any symptomatic close contacts. healthcare workers handling specimens should also adhere to cdc guidelines and should not attempt to perform any virus isolation or characterization. fever screening has been implemented at numerous airports, including major international hubs within asia and the us. the efficacy of this intervention is not well documented, however, as some infected persons may be afebrile and disease transmission might occur prior to symptom onset. 27 in addition, people can artificially lower their temperature readings, e.g., by applying ice to their foreheads. as outlined above, admission criteria for 2019-ncov are similar to that of other patients. if patients do not meet medical criteria for hospitalization, they may be discharged home with isolation precautions and continued observation. eps must notify local public health authorities so appropriate monitoring and community protective measures can be instituted. the identify-isolate-inform (3i) tool was initially developed for ebola virus disease 10,11 and later adapted for measles, 12 mers, 13 mumps, 14 zika virus disease, 15 hepatitis a, 16 pertussis, 17 and scabies. 18 this novel tool for suspected 2019-ncov patients ( figure 1 ) provides frontline clinicians with a simple algorithm to manage an emerging disease. identification of exposed patients with an epidemiologic risk factor within 14 days of symptom onset is a crucial first step. an automatic prompt in the electronic health record can be useful in assisting clinicians with early identification of patients at risk. case definitions promulgated by the who 24 and cdc 33 provide useful comprehensive definitions that have been incorporated into the 3i tool. the 2019-ncov tool provides an accurate, summarized algorithm to immediately, and effectively manage suspected patients until additional resources can be consulted. patients who do not have an exposure risk or any symptoms may be triaged normally. however, before making patient contact, providers must first apply the vital sign zero concept. 36 vital sign zero is a preliminary, non-contact assessment (i.e., performed prior to touching a patient to take traditional vital signs) to first determine whether specific ppe is indicated before the examination commences. by taking the additional time to complete this assessment, risk of exposure and further transmission can be minimized. while in the treatment facility should be started and maintained to assist with the possibility of contact tracing. following isolation, physicians should immediately inform the appropriate authorities. patients who do not meet medical criteria for admission can be isolated at home during the evaluation phase. 37 health department officials can help prevent transmission in isolated patients by providing in-home monitoring and implementing appropriate exposure-control measures. providers in the prehospital setting who have a high likelihood of encountering 2019-ncov patients, such as those near international ports of entry, should adhere to established exposure control guidelines. 38 along with appropriate ppe, providers should also carry thermometers to quantify any fever. in the us, providers should contact the appropriate cdc quarantine station upon isolation of infected or suspected patients, especially those from wuhan, china or other regions with widespread disease, who report symptoms in the last 14 days. as for other infectious diseases, assessing travel history is essential. dispatch protocols have been instituted to facilitate identification of callers to 911 or the country-equivalent emergency number prior to prehospital personnel arrival. 39 in addition, cdc has promulgated ems guidelines for prehospital ppe, transportation of puis, vehicle decontamination, and 911 public safety answering points (psaps) for 2019-ncov. 40 2019-ncov is an emerging infectious disease with rapidly evolving features, the full scope of which will be defined over time. prior outbreaks of coronaviruses can help inform needed actions in the short term to assist with both treatment of individual patients and prevention of global disease spread. this adaptation of the identify-isolate-inform tool serves as a resource for healthcare workers who need to make clear, rapid assessments when confronted with potential patients. the concise nature of the 2019-ncov 3i tool allows for the rapid and effective management of a novel disease by healthcare providers. 2019-ncov global cases global initiative on sharing all influenza data national center for biotechnology information genbank. 2019-ncov sequences clinical features of patients infected with 2019 novel coronavirus in wuhan, china the-second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov) secretary azar delivers remarks on declaration of public health emergency for 2019 novel coronavirus world health organization. disease outbreak news (dons) emerging infectious diseases: concepts in preparing for and responding to the next microbial threat inform: a 3-pronged approach to management of public health emergencies ebola virus disease: essential public health principles for clinicians identify-isolate-inform: a tool for initial detection and management of measles patients in the emergency department 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coronavirus (2019-ncov) coronavirus infections-more than just the common cold surveillance case definitions for human infection with novel coronavirus (ncov) int/internal-publications-detail/surveillance-case-definitions-for-humaninfection-withnovel-coronavirus-(ncov) health care facilities' "war on terrorism": a deliberate process for recommending personal protective equipment health care facility-based decontamination of victims exposed to chemical, biological, and radiological material transmission of 2019-ncov infection from an asymptomatic contact in germany health care worker quarantine for ebola: to eradicate the virus or alleviate fear? the quarantine conundrum: perspectives for the humanitarian community is there a case for quarantine? perspectives from sars to ebola inside china's pathogen lab preparedness for terrorism: managing nuclear, biological and chemical threats novel coronavirus interim guidance for healthcare professionals a novel coronavirus emerging in china -key questions for impact assessment novel coronavirus guidelines for clinical specimens ebola triage screening and public health: the new "vital sign zero novel coronavirus, wuhan, china implementing home care section 6: occupational exposure health issues novel coronavirus interim guidance for ems key: cord-328687-clr1e9p6 authors: zhou, fuling; li, jingfeng; lu, mengxin; ma, linlu; pan, yunbao; liu, xiaoyan; zhu, xiaobin; hu, chao; wu, sanyun; chen, liangjun; wang, yi; wei, yongchang; li, yirong; xu, haibo; wang, xinghuan; cai, lin title: tracing asymptomatic sars-cov-2 carriers among 3674 hospital staff:a cross-sectional survey date: 2020-09-15 journal: eclinicalmedicine doi: 10.1016/j.eclinm.2020.100510 sha: doc_id: 328687 cord_uid: clr1e9p6 background: asymptomatic carriers were positive for severe acute respiratory syndrome coronavirus 2 (sars-cov-2) without developing symptoms, which might be a potential source of infection outbreak. here, we aim to clarify the epidemiologic and influencing factors of asymptomatic carriers in the general population. methods: in our hospital, all hospital staff have received throat swab rt-pcr test, plasma covid-19 igm/igg antibodies test and chest ct examination. we analyzed the correlation between infection rates and gender, age, job position, work place and covid-19 knowledge training of the staff. after that, all asymptomatic staff were re-examined weekly for 3 weeks. findings: a total of 3764 hospital staff were included in this single-center cross-sectional study. among them, 126 hospital staff had abnormal findings, and the proportion of asymptomatic infection accounted for 0.76% (28/3674). there were 26 staff with igm+, 73 with igg+, and 40 with ground glass shadow of chest ct. of all staff with abnormal findings, the older they are, the more likely they are to be the staff with abnormal results, regardless of their gender. of 3674 hospital staff, the positive rate of labor staff is obviously higher than that of health care workers (hcws) and administrative staff (p<0.05). in the course of participating in the treatment of covid-19, there was no statistically significant difference in positive rates between high-risk departments and low-risk departments (p>0.05). the positive rate of hcws who participated in the covid-19 knowledge training was lower than those did not participate in early training (p <0.01). importantly, it was found that there was no statistical difference between the titers of igm antibody of asymptomatic infections and confirmed patients with covid-19 in recovery period (p>0.05). during 3 weeks follow-up, all asymptomatic patients did not present the development of clinical symptoms or radiographic abnormalities after active intervention in isolation point. interpretation: to ensure the safety of resumption of work, institutions should conduct covid-19 prevention training for staff and screening for asymptomatic patients, and take quarantine measures as soon as possible in areas with high density of population. funding: the key project for anti-2019 novel coronavirus pneumonia from the ministry of science and technology, china; wuhan emergency technology project of covid-19 epidemic, china. currently, novel coronavirus disease caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has become a global pandemic [1, 2, 3, 4] , which has been declared a global public health emergency by world health organization (who). in china, tens of thousands of medical workers participated in this battle against covid-19. while saving the lives of patients, thousands of medical workers were unfortunately infected with covid-19 [5−7] . our hospital, the zhongnan hospital of wuhan university in china, has also made great efforts to fight the epidemic, including setting up 2000 isolation beds in our hospital and taking over the management of three designated hospitals (wuhan no.7 hospital, the wuhan living room cabin hospital and wuhan leishenshan hospital), with a total of 5400 beds for emergency treatment of covid-19 patients. most of the medical staff in our hospital participated in the first-line battlefield of fighting against covid19. nosocomial infection is an important way of covid-19 transmission. studies have shown that asymptomatic cases have a similar viral load as symptomatic cases [8] , a higher contagion to transmission more frequently [9] . a study has been reported that the role of asymptomatic sars-cov-2 transmission in the propagation of a large superspreading event, which led to at least two further generations [10] . a mathematical model incorporating asymptomatic carriers indicated that asymptomatic individuals are major drivers for the growth of covid-19 pandemic [11] . cases without symptoms suggest silent chains of transmission [12−13] , it is needed to prevent spread of infection to vulnerable populations from asymptomatic carriers. therefore, it is particularly important to find, isolate, test, and treat every case to break the chains of covid-19 transmission. recently, in order to avoid further nosocomial infection, all staff without clinical symptoms in our hospital participated in the physical examination before resumption of ordinary job, including chest ct, throat swab rt-pcr test and plasma covid-19 igm/igg antibodies test. this study aims to analyze the examination results, understand the infection status of staff, track the infection related risk factors, as well as tracing of asymptomatic infection individual, so as to provide effective suggestions for other hospitals and non-medical institution in wuhan, ensuring scientific and safe return to work. screening of clinically asymptomatic, we enrolled hospital staff at zhongnan hospital of wuhan university in this cross-sectional study, from march 16, 2020, to march 25, 2020. inclusion criteria: hospital staff without clinical symptoms related to covid-19. exclusion criteria: hospital staff who had been infected sars-cov-2. the staff carries on the chest ct inspection, covid-19 igm/igg test for antibodies against sars-cov-2, and reverse transcription-polymerase chain reaction (rt-pcr) test for covid-19 nucleic acid using throat swabs samples. among them, the main outcome were igm/igg and rt-pcr test, the secondary outcome was chest computerized tomography (ct) result. all patients met the diagnostic criteria of "diagnosis and treatment scheme of novel coronavirus−infected pneumonia (tentative 7th edition)" formulated by the general office of the national health committee of china [14] . thereafter, asymptomatic staff were re-examined weekly for 3 weeks until april 16, 2020. in our study, asymptomatic carrier refers to patients who have mild or non-symptoms but with positive test for viral nucleic acid of sars-cov-2 or with positive test for serum specific igm antibody. four physicians (m.x.l., j.f.l., x.b.z. and c.h.) extracted the following data using data collection form from electronic medical records. the study was approved by the institutional ethics board at zhongnan hospital of wuhan university (no. 2020074) and all participants signed their consent. we define hospital staff as health care workers (hcws, including doctors and nurses), administrative staff and clinical support staff (including drug delivery workers, toll collectors, sterilizers, technician assistants, caregivers, pharmacists, drivers, feeders, registrars, auxiliary workers, hygienists, blood collectors, distribution workers, security guard, and logistics staff) according to different workplaces. all hcws without clinical symptoms distributed in 46 clinical medical technology departments during the treatment of covid-19. we divided the departments of hcws into high-risk departments (hrds) and low-risk departments (lrds). hrds included the department of anesthesiology, department of pneumology and critical care medicine, emergency center, intensive care unit and department of infectious disease; all other clinical departments were identified as lrds. during the epidemic, most hcws were trained on the prevention and control of the outbreak, and training content included to standardize the flow of medical personnel entering and leaving the isolation ward, strengthen the training of nurses in and out of isolation clothes/protective clothing, and strengthen the self-protection consciousness. clinical specimens' collection and rt-pcr test for sars-cov-2 were previously described [15] . in brief, oropharyngeal swabs were collected by trained nurses or physicians wearing proper personal protection equipment. the viral nucleic acid kit (daan gene biotechnologies) was used to extract nucleic acids from clinical samples according to the kit instructions. rt-pcr tests for sars-cov-2 were performed to detect the orf1ab gene (ncovorf1ab) and the n gene (ncov-np) according to the manufacturer's instructions [16] . orf1ab gene: forward primer ccctgtgggttttacacttaa; reverse primer acgattgtgcatcagctga; and the probe 5 0 -vicà àccgtctgcgg-tatgtggaaaggttatgg-bhq1−3 0 . n gene: forward primer ggggaacttctcctgctagaat; reverse primer cagacattttgctct-caagctg; and the probe 5 0 -fam-ttgctgctgcttgacagatt-tamra-3 0 . the diagnostic criteria for positive and negative rt-pcr results were based on the recommendation by the national institute for viral disease control and prevention (china) [17] . serum samples from these people were collected. serum igm and igg antibodies to sars-cov-2 were measured with covid-19 igm/igg chemiluminescence test kit (shenzhen yahuilong biotechnology co., ltd., china; product code: c86095m/c86095g). the test kit contained recombinant sars-cov-2 antigen (spike protein and nucleocapsid protein) labelled with magnetic beads, anti-human igm monoclonal antibody, and anti-human igg monoclonal antibody. test results were showed as relative light unit (rlu). the fully-automated chemiluminescence immunoassay analyzer automatically calculated serum covid-19 igm and igg levels (au/ml) by comparing rlu to the internal calibration curve, as rlu correlated well with serum covid-19 igm and igg levels. after 20 ml of serum was diluted at a ratio of 1:3, the color development of the test card was observed within 10 min. tests were performed on iflash 3000 automated analyzer and an igm or igg level ≥10.0 au/ml was designated as positive. the image data acquisition requires both lung window and mediastinal window images, and the image quality meets the evaluation requirements. the patient routinely takes the supine position with his arms raised above his head, and breathes quickly after holding a deep spiral. all radiologic images were reviewed by two radiologists continuous variables such as titers of covid-19 igm/igg antibodies were reported using mean and 95% confidence interval (ci) if normally distributed or median and interquartile if nonnormally distributed. categorical variables were described as frequency rates the funder had no role in the design and conduct of this study; collection, management, analysis, and interpretation of the data; preparation, review or approval of this manuscript; and decision to submit the manuscript for publication. the work flow diagram of 3674 hospital staff participated in the physical examination from zhongnan hospital of wuhan university were shown in the fig. 1 . of all hospital staff without clinical symptoms, there are 2406 health care workers (hcws, doctors or nurses), 505 administrative logistics staff and 763 labor staff. among all the hospital staff without clinical symptoms, 67.7% (2486/3674) are female, and 82.6% (3034/3674) with age ranging from 18 to 50 years old. (see table 1 ). a total of 126 hospital staff were accompanied by abnormal findings: 61 staff only had abnormal igg results (igg positivity), 37 only had abnormal chest ct images (ground glass shadow), and 28 were asymptomatic carriers (igm/nucleic acid positive). of the 3674 hospital staff, there is no statistical difference between the proportions of male staff and female staff with abnormal findings (p>0.05). however, the positive rate of physical examination results for staff of different ages is statistically significant (p<0.05). the older they are, the more likely they are to be the staff with abnormal results, regardless of their gender (see table 1 ). in fig. 2 , there were 126 hospital staff with abnormal findings. the percentage of covid-19 igm+/ igg+ positive was 0.27% (10/3674). there were 26 staff with igm+, 73 with igg+, and 40 with ground glass shadow of chest ct. (fig. 5 ). of these 126 staff, 2 cases were positive in the results of throat swab rt-pcr test, and their results of covid-19 igg antibody were also positive. according to the covid-19 diagnosis and treatment plan (tentative 7th edition) in china [18] , the number of asymptomatic infections reached 28, and the proportion of asymptomatic infection is 0.76% (28/3674) in zhongnan hospital of wuhan university. these asymptomatic infection carriers were isolated and followed up regularly, without medication administration. asymptomatic infections table 1 ). according to the tracking, no obvious infection transmission occurred in the later period. after 3 weeks follow-up, the positive nuclear acid in 2 patients became negative, of which one patient was discharged within 14 days after isolation, and the other patient was discharged 21 days after treatment. although rt-pcr tests were all negative after 3 weeks, it showed 2/28(7.14%) with igm+/igg+ and 12/28(42.86%) with igm+/igg-from igm/igg antibodies test. however, all staff with abnormal ct findings recovered with absorption of ground-glass shadow after 3 weeks follow-up (see fig. 1 ). however, there was no statistically significant difference in positive rates between high-risk departments and low-risk departments (p = 0.386). in addition, the positive rate of hcws who participated in the treatment of covid-19 was lower than those of not participate in early training (p <0.01) (see fig. 3 ), which showed that early training could help us to avoid getting infected. we compared the titers of covid-19 igm/igg antibodies of 28 asymptomatic infections and 126 staff with abnormal findings screened from 3674 asymptomatic staff with 69 random healthy individuals and 172 confirmed patients with covid-19 in recovery period at same time. it was found that there was no statistical difference between the titers of igm antibody of asymptomatic infections and confirmed patients with covid-19 in recovery period (p>0.05), but igm antibody of asymptomatic infections was statistically significant compared to that of the other two groups (p<0.05, see fig. 4a ). however, there was no significant difference between the titers of igg antibody of asymptomatic infections and the staff with abnormal findings (p>0.05), but igg antibody of asymptomatic infections was statistically significant compared with that of the other two groups (p<0.05, see fig. 4b ). in addition, it was found that there was no significant difference among different ages and different gender in the titers of igm/igg antibodies of asymptomatic infections and the staff with abnormal findings (p>0.05, see figure s1 ). the results showed that the titers of igm/igg antibodies test could help us to screen and identify asymptomatic infections. with the further understanding of the covid-19, china has quickly taken effective measures to prevent and control it [19−21] . the epidemic situation has been initially controlled in wuhan, china. in the next stage to promote the resumption of work and production in wuhan, the prevention and control of the epidemic should focus on screening asymptomatic individuals who may not only progress to symptomatic infection patients [22, 23] , but more importantly, are potential infectious sources [24] . our hospital had completed covid-19 screening of 3674 staff without clinical symptoms, the results showed the proportion of asymptomatic infected staff was 0.76%. the proportion of asymptomatic individuals was 0.79% in administrative staff and 1.18% in labor staff. considering the asymptomatic transmission, the high proportion of asymptomatic infected people is a huge hidden danger [25] , which may bring difficulties to the resumption of work and production. asymptomatic carriers have been reported in several studies, rivett l et al. [26] reported that 3% of 1032 asymptomatic hcws from a large uk teaching hospital tested positive for sars-cov-2, indicating that it is necessary to screen asymptomatic carriers among the hospital staff, which may be important to prevent the secondary outbreak of the epidemic. there are several suggestions to reduce covid-19 transmission risk in this study. firstly, given the high cost and the radiation damage to human body by ct scan, covid-19 igm/igg antibodies and nucleic acid is more suitable for scanning asymptomatic carriers in general population, especially in densely populated work areas in wuhan, which may be helpful to confirm asymptomatic infection as early as possible. meanwhile, our results found that after isolation of asymptomatic patients for 3 weeks, although the nucleic acid test has turned negative, half of the patients are still positive for igm+ (with virus status). it is very essential to take rapid identification, registration, reporting, surveillance and epidemiological tracking of asymptomatic infected individuals. secondly, it should make full consideration to the possibility of long-term epidemic prevention and control. in particular, priority should be given to screening populations that have migrated due to the need to resume work and production to prevent the occurrence of "import cases" between regions. we also need to formulate differentiated regional management measures, strengthen the management of asymptomatic infection cases, take strict isolation measures, focus on high risk groups and special places, and do a good job in the prevention and control of the epidemic in crowded and enclosed environment. only in this way, we can ensure the prevention and control work is effective and sustainable. the safety of medical institutions is the key to ensure the health of average citizen. in our study, the positive rate of hcws who participated in the training was lower than those of not participate in training. in the early stages of the outbreak, due to lack of protected awareness or personal protective equipment, some medical workers were infected after contacting covid-19 patients, which may become the infection source in the department [6] . it demonstrated that good protection awareness and protective measures are the key for selfprotection. therefore, it is necessary to promote protection knowledge among hcws, supervise the strict implementation of protection measures at the early stage of the outbreak, to ensure the safety of hcws and prevent the spread of the epidemic [27] . our findings have several important clinical and public health implications. in this single-center cross-sectional study, very few hospital staff had positive igm/igg tests. both serum igm and igg levels were higher in recovered confirmed patients than hospital staff (p<0.001 for both). it is possible that some people may live with sars-cov-2 for a long period of time. whether those people are still infectious warrant further studies. unlike severe acute respiratory syndrome (sars) [28] , herd immunity will not develop for sars-cov-2 in the general population and seasonal outbreaks in the next few years may still be possible [29] . importantly, there would be a big question mark for the success of a vaccine against sars-cov-2 [30] . in our study, most of the healthcare providers without a confirmed covid-19 diagnosis have been exposed to a highly contagious environment with the wildtype sars-cov-2 virus. these findings raise the concern if the inactivated virus, subunit, and recombinant vaccines currently under development will be able to induce effective immune protections against sars-cov-2. in our study, all asymptomatic patients did not present the development of clinical symptoms or radiographic abnormalities after 3 weeks follow-up. the positive nuclear acid in 2 patients became negative for 2 to 3 weeks after active intervention in isolation point. it is clear that highly effective contact tracing and case isolation is necessary to control the progression of covid-19. although the pcr test were all negative after 3 weeks, most of them showed positive igm antibody. asymptomatic infection still carries the sars-cov-2, which means the risk of transmission and present a new challenge to isolation. we need to do sars-cov-2 detection to figure out what's going on for asymptomatic population with epidemiological contact history. meanwhile, treatment of the underlying disease may also help stop transmission of covid-19. there are several limitations to our study. first, our study only included the results of one hospital in wuhan, which may not be sufficient to represent the situation of other hospitals, whether it is from other hospitals in wuhan or other regions of china. therefore, it has certain limitations for the promotion of the results. second, we did not explore the relationship between clinical indicators and asymptomatic infection. other studies would be designed to explore the correlation between clinical parameters and asymptomatic carriers in the future, to link the asymptomatic state with differences in biochemical, immune, viral load and other factors to provide deeper insights. our work underscores the need for measures to limit transmission by individuals who become ill. these findings can support evidencebased policy to combat the spread of covid-19, and prospective planning to mitigate future emerging pathogens. we declare no competing interests. a novel coronavirus from patients with pneumonia in china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding coronaviridae study group of the international committee on taxonomy of viruses. the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 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[diagnosis and treatment guideline for covid-19 sars-cov-2 turned positive in a discharged patient with covid-19 arouses concern regarding the present standards for discharge the outbreak of covid-19: an overview the origin, transmission and clinical therapies on coronavirus disease 2019 (covid-19) outbreak -an update on the status clinical characteristics of 24 asymptomatic infections with covid-19 screened among close contacts in nanjing asymptomatic novel coronavirus pneumonia patient outside wuhan: the value of ct images in the course of the disease alert for non-respiratory symptoms of coronavirus disease 2019 (covid-19) patients in epidemic period: a case report of familial cluster with three asymptomatic covid-19 patients asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (sars-cov-2): facts and myths screening of healthcare workers for sars-cov-2 highlights the role of asymptomatic carriage in covid-19 transmission how to train health personnel to protect themselves from sars-cov-2 (novel coronavirus) infection when caring for a patient or suspected case immune responses in covid-19 and potential vaccines: lessons learned from sars and mers epidemic potential impact of seasonal forcing on a sars-cov-2 pandemic progress and prospects on vaccine development against sars-cov-2. vaccines (basel) 2020 we acknowledge all hospital staff participated in the diagnosis and treatment of covid-19 patients in zhongnan hospital of wuhan university. the raw data used in the study will accessible on contacting the corresponding authors. supplementary material associated with this article can be found in the online version at doi:10.1016/j.eclinm.2020.100510. key: cord-345724-6u9q0ox9 authors: zhu, xiaolin; zhang, aiyin; xu, shuai; jia, pengfei; tan, xiaoyue; tian, jiaqi; wei, tao; quan, zhenxian; yu, jiali title: spatially explicit modeling of 2019-ncov epidemic trend based on mobile phone data in mainland china date: 2020-02-11 journal: nan doi: 10.1101/2020.02.09.20021360 sha: doc_id: 345724 cord_uid: 6u9q0ox9 ias of february 11, 2020, all prefecture-level cities in mainland china have reported confirmed cases of 2019 novel coronavirus (2019-ncov), but the city-level epidemical dynamics is unknown. the aim of this study is to model the current dynamics of 2019-ncov at city level and predict the trend in the next 30 days under three possible scenarios in mainland china. we developed a spatially explicit epidemic model to consider the unique characteristics of the virus transmission in individual cities. our model considered that the rate of virus transmission among local residents is different from those with wuhan travel history due to the self-isolation policy. we introduced a decay rate to quantify the effort of each city to gradually control the disease spreading. we used mobile phone data to obtain the number of individuals in each city who have travel history to wuhan. this city-level model was trained using confirmed cases up to february 10, 2020 and validated by new confirmed cases on february 11, 2020. we used the trained model to predict the future dynamics up to march 12, 2020 under different scenarios: the current trend maintained, control efforts expanded, and person-to-person contact increased due to work resuming. we estimated that the total infections in mainland china would be 72172, 54348, and 149774 by march 12, 2020 under each scenario respectively. under the current trend, all cities will show the peak point of daily new infections by february 21. this date can be advanced to february 14 with control efforts expanded or postponed to february 26 under pressure of work resuming. except wuhan that cannot eliminate the disease by march 12, our model predicts that 95.4%, 100%, and 75.7% cities will have no new infections by the end of february under three scenarios. the spatial pattern of our prediction could help the government allocate resources to cities that have a more serious epidemic in the next 30 days. wuhan, a large city with 14 million residents and a major air and train transportation hub of central china, identified a cluster of unexplained cases of pneumonia on december 29, 2019 1 . four patients were initially reported and all these initial cases were linked to the huanan seafood wholesale market 2 . chinese health authorities and scientists did immediate investigation and isolated a novel coronavirus from these patients by january 7, 2020, which is then named as 2019-ncov by the world health organization 3, 4 . 2019-ncov can cause acute respiratory diseases that progress to severe pneumonia 5 . the infection fatality risk is around 3% estimated from the data of early outbreak 3, 6 . information on new cases strongly indicates human-to-human spread 1, 7, 8 . infection of 2019-ncov quickly spread to other cities in china and other countries ( figure 1 ). it becomes an event of global health concern 9 . up to february 11, 2020, according to the reports published by the chinese center for disease control and prevention, all prefecturelevel cities of mainland china have confirmed cases and the total number reaches to 42667, of whom 1016 have died and 4242 recovered; 24 oversea countries have 398 confirmed cases (1 died). chinese government took great effort to control the spread of disease, including closing the public transportation from and to wuhan on january 23, extending the spring festival holiday, postponing the school-back day, and suspending all domestic and international group tours. unfortunately, many external factors bring a challenge to control virus spreading. first, it might be already late to stop the migration of infected cases. evidence suggests that wuhan is the center of 2019-ncov outbreak 1, 10 . however, around 5 million wuhan residents left wuhan in january 2020 due to the spring festival (january 24, 2020). it is very likely that a considerable number of infected cases have moved from wuhan to other cities before wuhan government implemented border control on january 23. second, it is highly possible that infected cases spread the virus to their family members or relatives 7 . a study based on 425 patients at the early stage of outbreak revealed that the time from infection to illness onset is 5.2 days 1 . as a result, presymptomatic cases who have left wuhan may not be isolated themselves from their family and relatives 11 . third, due to the sudden outbreak of virus, the preparation and resources for preventing virus transmission are limited. the protective equipment in many hospitals in wuhan was in short supply so that it is difficult to maintain strict personal hygiene. with the quick increase of infected cases, wuhan and other cities in hubei province have large pressure to isolate and give medical treatment to infected people. all above factors make preventing the spread of 2019-ncov even more difficult than the severe acute respiratory syndrome (sars), another coronavirus outbreak in china 17 years ago that caused more than 8000 infections and 800 deaths. projecting the epidemic trend of 2019-ncov outbreak is critical for the decision makers to allocate resources and take appropriate actions to control virus transmission. right after the outbreak, several studies have retrieved the epidemiological parameters and predicted the future situation [12] [13] [14] [15] . these studies used the reported cases at the early stage of outbreak and modeled epidemic dynamics in wuhan and nation-wide. a recent study 10 used air passenger data and social medium data to forecast the spread of 2019-ncov in wuhan and other major chinese cities. they estimated that 75815 individuals have been infected in greater wuhan as of january 25, 2020 and epidemics are already growing exponentially in major cities of china with a 1-2 weeks lag time behind wuhan outbreak. although these studies at the early stage of outbreak help us understand the key epidemiological characteristics of 2019-ncov, the fine-scale and updated epidemic trend in individual chinese cities remains unknown, which is more helpful for allocating medical resources to achieve the optimal result of preventing disease spreading. to model the updated fine-scale epidemic dynamics of all individual cities in mainland china, we proposed a spatially explicit approach. we first used mobile phone data to obtain the number of people who traveled from wuhan to each individual city. then we developed a new epidemiological model based the classic susceptible-infectious-recovered (sir) model to fit the dynamics of 2019-ncov at the city level. finally, we used this model to predict the trend under three possible scenarios: the current trend maintained, control efforts expanded, and person-toperson contact increased due to work/school resuming. we collected the daily data of confirmed cases of 2019-ncov pneumonia in 306 prefecture-level cities in mainland china up to february 11, 2020 (supplementary data table 1 ) from a platform reporting real-time statistics of 2019-ncov (https://ncov.dxy.cn/ncovh5/view/pneumonia). these daily reported data were used to train and validate our epidemic model. we employed china unicom mobile phone database (https://www.cubigdata.cn) to obtain the inter-city human mobility. china unicom is one of three largest mobile service providers in china. it has 0.32 billion users. considering that 2019-ncov emerged in wuhan around january 1, 2020 and wuhan implemented the quarantine on january 23, 2020, we collected the number of people who have wuhan travel history during january 1-24, 2020 in each city based on the mobile phone dataset ( figure 2 and supplementary data table 2 ). in addition, household registered population at 2017 year-end derived from census data was used to approximate the number of local residents in each city during 2020 spring festival (supplementary data table 2 ). a spatially explicit epidemic model our proposed model stems from the sir model, a classic approach to simulate epidemiological dynamics. we modified the sir structure based on the unique characteristics of the outbreak of 2019-ncov. first, in all cities other than wuhan, the initial infectious cases are most likely imported from wuhan 10 . second, many wuhan residents moved to other cities due to the spring festival and this mobility was closed after the quarantine on january 23. third, those people from wuhan have low contacts with local residents because chinese government required them to implement self-isolation. last, during the past 40 days, all cities took efforts to control the virus spreading, which slows down the daily increase of new infections ( figure 1 ). accordingly, in the modified sir model, the susceptible variable was divided into two groups: 1 , the number of local susceptible, and 2 , the number of susceptible with wuhan travel history. these wuhan-inbound groups ( 2 ), have transmission rate ( 2 ) different from transmission rate ( 1 ) of local residents ( 1 ) as chinese government took measures to reduce the person-to-person contacts. a decay rate a was introduced to tune the value of β in each day, accounting for the gradual impact of prevention interventions in each city. in our modified sir model, recovered population r was extended to include those cured, died, and isolated in hospital because they cannot transmit the virus. the differentiate equations of our modified sir model is as follows: where is the total local population derived from the census data, and represents the total population with wuhan travel history during january 1 to january 24, estimated from mobile phone data; i is the number of infections, and denote the daily transmission rate and daily recovery rate respectively. in our model, four variables need to be initialized: (1) initial number of infectious 0 , treated as a parameter to be estimated (see next section); (2) initial number of local susceptible 10 , equal to the total number of the local population of each city 10 = ; (3) initial number of susceptible traveling from wuhan 20 , equal to the population from wuhan excluding the initial infectious 20 = − 0 ; and (4) initial number of removed 0 , assuming no cured, hospitalized, or death at initial state 0 = 0. our modified sir model has four parameters: transmission rate 1 among local residents, 2 among people with wuhan travel history, decay rate a, and recovery rate . for , we assume that once an infected individual is hospitalized, the person will be segregated and therefore no longer infectious. according to a recent study using the first 425 patients 1 , the mean incubation period of 2019-ncov is 5.2 days, and the mean duration from illness onset to hospital admission is 9.1 days. we assume that the incubation period and duration from illness onset to first medical visit is similar with these 425 infected cases. therefore, the estimated infectious period is 5.2 + 9.1 = 14.3 days and equals 1/14.3 = 0.0699. for parameters 1 , 2 , and a, we used the daily cumulative confirmed cases up to february 10, 2020 to retrieve their optimal values to reflect the current dynamics in each city. we first estimated the optimal value of 2 and a of wuhan since its epidemic model only has one transmission rate 2 . then, the estimated 2 was used as a prior parameter for the estimation of 1 and a for individual prefecture-level cities. the nelder-mead algorithm 17 was employed to estimate parameters through minimizing the sum of squared differences between the simulated and actual daily cumulative confirmed cases. to better capture the current trend, the number of daily cumulative cases were also used to weight the samples in parameter retrieval. since the epidemic model is highly sensitive to the initial infectious number i0, and the reported initial infectious number often has large uncertainty, we treated the initial infectious number 0 as another parameter to be estimated together with 1 and 2 . specifically, we used daily cumulative confirmed cases of each city from january 25 to february 10, 2020 to retrieve the parameters and assumed january 20, 2020 as the start point when massive inter-city mobility happened before the spring festival. the goodness of model fitting was assessed by comparing the number from model simulation and reported cases. the trained model was further validated using the reported data on february 11, 2020. we predicted the epidemic dynamics in the next 30 days under three scenarios: the current trend maintained (scenario 1), control efforts expanded (scenario 2), person-to-person contacts increased due to work resuming (scenario 3). these three scenarios were designed by considering the joint effect of virus transmissibility and outbreak control 18, 19 and realized by manipulating model parameters from february 11, 2020 to march 12, 2020 (see an example in figure 3 ). decay rate reveals the effectiveness of government control and removal rate represents the promptness of medical treatment. therefore, scenario 1 keeps a value the same as the trained model. in scenario 2, we doubled the value of a to reflect more efforts in each city for controlling the disease. in scenario 3, the interference of work resuming was considered, so a short rebound was introduced to the transmission rate (i.e. changing a to -a during february 11-15 period). in all scenarios gradually increased from 1/14.3 to 1/9.8 in the 30 days to reflect the reduction of average diagnostic isolation time 20 . to examine the goodness of model fitting, we calculated r-squared and root mean square error (rmse) between the fitting result and confirmed cases in each city (see representative examples in figure 4 ). the median value of r-squared and rmse across all cities is 0.96 and 1.20 respectively, indicating that our model can well fit the current spreading trend. we examined the fitted models with r-squared less than 0.7 (26 out of 306 cities) and found that all these cities have very small number (1-3) of confirmed cases and the number does not change in the past several days. it is reasonable to assume that these cities have completely controlled the spreading and no new infected cases will emerge in the future. therefore, for these cities with r-squared less than 0.70, the 1 value of the city was set to zero. transmission rate 2 estimated using wuhan confirmed cases is 0.9, reflecting a high transmission around january 20. the transmission rate 1 , decay rate a, and initial infectious population 0 vary from city to city (supplementary data table 3 ). as the transmission rate among local residents in each city, 1 reflects the intensity of control measures adopted by each local government at the beginning of outbreak, as well as the awareness of citizens to take protective measures. for example, 1 in megacities such as beijing, shanghai, guangzhou and shenzhen are low ( figure 5 .a) which may attribute to higher health literacy of their citizens 21 , although they have intensive traffic and population mobility. decay rate a reflects the continuous effort input by each city to control the transmission of disease. it shows that decay rates of cities close to wuhan is generally lower than other cities ( figure 5 .b), suggesting the big challenge faced by these cities to control the disease spreading. to test the prediction capacity of our model, we used the reported confirmed cases on february 11 in all cites excluding wuhan because its high confirmed case leads to bias in assessment. we compared the predicted daily new infections on february 11 with the reported confirmed cases in the same day. the predicted values by our model well match the reported infected cases (rsquared: 0.86, rmse: 6.35, p < 0.0001, figure 6 author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.09.20021360 doi: medrxiv preprint we predicted daily infected cases of each city up to march 12, 2020 under three different scenarios (scenario 1 -the current trend maintained; scenario 2 -control efforts expanded; and scenario 3 -person-to-person contacts increased due to work resuming). our prediction shows that the whole mainland china will have 72172, 54348, and 149774 people infected up to march 12, 2020 under the above three scenarios respectively (supplementary data table 4 ). to provide an intuitive picture about epidemic dynamics in different scenarios, we showed in figure 7 the number of cumulative infections in each city on march 12. the infected people will mainly distribute in the central and eastern provinces, the number of western cities at a relatively low level under all scenarios. in scenario 3 (figure 7 .c), many cites have much larger number of infections than scenario 1 (figure 7 .a) and 2 (figure 7 .b), suggesting that work resuming will bring large challenge to control the disease timely. this difference is significant for those cities with largest number of infections by march 12 (figure 8) , such as wuhan and other cities in hubei province. to understand the specific attributes of epidemic dynamics under different scenarios, we investigated the temporal changes of daily new infections across all cities in mainland china. in figure 9 , we show the results in wuhan, hubei province excluding wuhan, other provinces, and four first-tier cities. compared with the scenario 1 where current trend is maintained, the daily new infections in scenario 2 reduces quickly in the second half of february. in scenario 3 where transmissibility rebounds after the public holiday in all cities, the peak of new infections will postpone ten days and the magnitude will be twice of that in scenarios 1 and 2. our simulation suggests that strict quarantine of inner-and inter-city population movement during february would have a significant effect on the suppression of virus spreading. table 4 ) suggests that the exponential growing of disease will stop and the spreading would be controlled gradually. under current trend, our model estimated that the number of new infections in 79.7% cities already reached the peak point before february 11 and in all other cities, it will reach the peak point by february 21. with the control effort expanded, all cities will have the peak point of new infections by february 14, one week earlier than current trend. however, the peak point of new infections will be greatly delayed under scenario 3 that a few cities in hubei province will show the peak point of new infections by february 26. the daily new infections decreasing to zero (figure 10 .d-f, supplementary data in this study, we modeled the updated epidemic trend of 2019-ncov for each individual city in mainland china and used the model to predict the future trend under three possible scenarios. 10 , the prediction of epidemic trend of all major cities would be similar to wuhan (see figure 4 in wu et al., 2020). our predictions of three future scenarios, namely the current trend maintained, control efforts expanded, person-to-person contacts increased due to work resuming, provide information for decision makers to allocate resources for controlling the disease spread. generally speaking, densely populated cities and cities in central china will face severe pressure to control the epidemic, since the number of infections keeps increasing in all three scenarios in the near future. by comparing predictions of three scenarios, it is obvious that reducing the transmissibility is a critical approach to reduce the daily new infections and controlling the magnitude of epidemics. fortunately, the latest number of confirmed diagnoses ( figure 1 ) and our prediction both show the slowing down of new infections in these days, indicating current control measures implemented by chinese government are effective, including controlling traffic between wuhan and other regions, isolating suspected patients, canceling mass gatherings, and requiring people to implement protective measures. however, once the spring festival travel rush returns as scenario 3 (most provinces planned to resume work on february 9), it will inevitably cause considerable growth in transmissibility and further re-increase of epidemics. in addition, current insufficient supply of protective equipment may exacerbate this situation. therefore, public health interventions should be performed continuously to obtain the best results of epidemic control. the following measures are recommended to implement continuously in the near future, such as, postponing work resuming, arranging work-from-home, and instructing enterprises to implement epidemic prevention measures. essentially, all measures are for reducing population mobility and person-to-person contact, and there is no panacea for all conditions, hence interventions in different regions should be adapted according to local epidemics. our modeling work has several limitations. first, due to the limited prior knowledge for this sudden 2019-ncov outbreak, the infection rate and recovery rate in this study are regarded as the same for different age groups, which may result in errors of predication for cities with different age structures. second, the model parameters were estimated using the reported confirmed cases that may be lower than the actual number of infections, so parameter estimation may not represent the real situation. third, besides transmission between wuhan and other cities, we do not consider other inter-city transmissions. although the chinese government strictly controlled the traffic between cities, the inter-city transmission may contribute to the epidemic dynamics in future days, especially during days of work resuming. author contributions: xz designed the experiments. pj, zq, and jy collected and processed data. az and sx analyzed data. all authors interpreted the results and wrote the manuscript. the authors declare no conflict of interest. data sharing: data obtained for this study will be available to others. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.09.20021360 doi: medrxiv preprint early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a novel coronavirus from patients with pneumonia in china a novel coronavirus outbreak of global health concern coronaviruses: genome structure, replication, and pathogenesis clinical features of patients infected with 2019 novel coronavirus in wuhan another decade, another coronavirus a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster pattern of early human-to-human transmission of wuhan the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study a novel coronavirus emerging in china -key questions for impact assessment modelling the epidemic trend of the 2019 novel coronavirus outbreak in china novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions transmission of 2019-ncov infection from an asymptomatic contact in germany a simplex method for function minimization epidemiology, transmission dynamics and control of sars: the 2002-2003 epidemic sars outbreaks in ontario, hong kong and singapore: the role of diagnosis and isolation as a control mechanism early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia assessment of the chinese resident health literacy scale in a population-based sample in south china key: cord-352509-qrzt4zva authors: chen, haohui; xu, weipan; paris, cecile; reeson, andrew; li, xun title: social distance and sars memory: impact on the public awareness of 2019 novel coronavirus (covid-19) outbreak date: 2020-03-16 journal: nan doi: 10.1101/2020.03.11.20033688 sha: doc_id: 352509 cord_uid: qrzt4zva this study examines publicly available online search data in china to investigate the spread of public awareness of the 2019 novel coronavirus (covid-19) outbreak. we found that cities that suffered from sars and have greater migration ties to the epicentre, wuhan, had earlier, stronger and more durable public awareness of the outbreak. our data indicate that forty-eight such cities developed awareness up to 19 days earlier than 255 comparable cities, giving them an opportunity to better prepare. this study suggests that it is important to consider memory of prior catastrophic events as they will influence the public response to emerging threats. public awareness is important in managing the spread of infectious diseases. individual actions, such as increased attention to hygiene and avoiding crowds, can reduce disease spread. awareness also supports rapid identification and treatment of new cases and facilitates collective responses, such as closures of schools or transit systems 1 . in the modern world, diseases can move faster than ever due to the growing movement of people between cities, regions and countries. however, digital technology means information can move even faster, providing an opportunity for individuals and communities to protect themselves ahead of the disease itself arriving. 2 this study considers the spread, and persistence, of public awareness of the novel wuhan coronavirus which emerged in late 2019. during the first few weeks of this outbreak there was little coverage from mainstream media outlets, providing an unusual opportunity to study the spread of awareness of an emerging disease via other channels. previous studies show that the spread of awareness is strongly related to the physical locations of individuals in a social network in relation to the unfolding events [2] [3] [4] , termed the social distance effect. in online social networks, people with more connections tend to receive earlier warnings of catastrophic events. for example, in hurricane sandy in the usa, twitter users with more followers had an awareness lead-time of up to 26 hours than less connected users 4 . moreover, the magnitude of awareness increases over decreasing distances to the epidemic centers. for example, public awareness in weibo, a chinese social media platform, was two orders of magnitude stronger for the h7n9 influenza outbreak that occurred in china than the middle east respiratory syndrome coronavirus (mers-cov) outbreak that occurred elsewhere 5 . experience of similar events, such as outbreaks of h5ni influenza in 2001, sars (severe acute respiratory syndrome) in 2003, h1n1 influenza in 2009 and ebola in 2014 is also likely to influence awareness. in china, the outbreak of sars between 2003 and 2004 caused a total of 7,429 reported cases and 685 deaths 6 , and had a lasting traumatic impact on survivors and communities 7, 8 . in this work, we set out to test whether public awareness of the new disease outbreak is related to social distance from the centre of the epidemic and past experience of the sars epidemic in 2003. the sars outbreak was 17 years ago, but its horror might still condition public awareness of lethal infectious diseases. to the best of our knowledge, few studies were carried out to understand how past severe outbreaks affect public awareness when a new outbreak occurs. this study estimates the post-sars effect, called sars memory effect, on the current outbreak. we use the continuing wuhan coronavirus outbreak as our case study to estimate the effects of social distance and sars memory on the spread of public awareness. in late 2019, a new coronavirus, designated as covid-19, was identified in wuhan, the capital of china's hubei province 9 . as of february 1st, 2020, the virus has caused approximately 11,184 cases and 258 deaths in 21 countries with the majority of cases in mainland china 10 . the first symptoms were reported on december 1st, 2019 11 , but there was no solid evidence of human-to-human transmission until january 10 th , 2020, when a patient, who did not travel to wuhan, became infected with the virus after several days of contact with four family members 12 . however, there was little information available to the public until an official announcement about human-to-human transmission of the virus on january 20 th , 2020 13 . wuhan city, long known as the "nine provinces" thoroughfare ("九省通衢"), is in the central part of china, serving as a major transportation hub transiting more than 120 million passengers every year 14 . the massive numbers of transits provided a perfect opportunity for the virus to spread. another feature is the timing of the outbreak, close to the spring festival travel season, chunyun ("春运"), which started on january 10 th , 2020. while the virus spread across almost all provinces, 16 cities had been locked down by january 23 rd , 2020 15 . accordingly, this study focuses on the time period between december 15 th , 2019 and jan 23 rd , 2020. seeking epidemic-related information online can provide an indicator of public awareness of this new disease. in this study, we use the baidu search index (bsi), available publicly at http://index.baidu.com, to measure the public awareness over time and locations (e.g., city). the total number of internet users using the baidu search engine reached 649 million in 2014, accounting for 47.9% of the national population 16 . bsi has been used to predict epidemic outbreak 17 , hiv/aids incidence 18 and tourism flows 19 , suggesting bsi can provide a representative proxy for public awareness. bsi provides a weighted index for each search term. in this study, we used the term "wuhan pneumonia" ("武汉肺 炎"), as the public has widely used. we also tried "novel coronavirus" ("新型冠状病毒") and "wuhan outbreak" ("武汉爆发"), but the former did not exhibit a search surge, and the latter was not indexed by baidu. due to the privacy concern, baidu masks daily readings that are below 57 as zero. therefore, we used the maximum bsi value of the search term "common cold" ("感冒") between dec 10 th and 31 th , 2019, to control the size effect for each city. we use the ljung-box test 20 to estimate whether or not the daily readings of "common cold" are stationary. as a result, the daily readings of 18 out of 364 cities were found to be non-stationary, so they were excluded from this study. the magnitude of public awareness of the wuhan outbreak over time and city ∈ {1, … , 346} can be represented as the earliest day the magnitude of public awareness exceeds the arbitrary thresholds ∈ {1.5, 2, 3, 4} is defined as the earliest warning day, ( ) , for city . we also define the starting day of chunyun as ℎ , indicating the onset day when it is likely the virus would reach all cities. as chunyun transited approximately 3 billion million passengers in 40 days in 2019 21 , crowded transport hubs create perfect opportunities for the virus to spread. therefore, the earlier the lead-time awareness, the better for infection control. the lead-time of awareness for city is thus defined as: awareness typically follows a cyclical process, called the unaware-aware-unaware (uau) process, as time passes. keeping the public at a high level of awareness could help mitigate the virus transmission process. therefore, we also measure the awareness retention rate as the average of magnitude from the next day of ( ) to the day of chunyun over the magnitude at ( ) . microblogs (e.g., weibo) and private social media (e.g., wechat) are the primary communication tools used by most chinese people 16 . while information flows cannot be observed directly, empirical studies show that social networks are influenced by long distance travel. 22 we therefore use migration flows as a proxy for long-distance information flows to be more specific, if workers born and raised in city a now work in city b, they are likely to relate information about an epidemic in city b back to friends and family in city a. this is particularly relevant in the chinese context, where migrant workers account for more than one-third of the working population 23 . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint proportional to the numbers of transit passengers at the corresponding city. the network does not include hong kong, macau and taiwan, as the baidu migration matrix does not include them. we use the migration flows extracted from the baidu migration matrix (bmm) to build a migration network (fig. 1) . we then compute the shortest steps between any city to wuhan, deriving the variable social distances for city as ∈ (1, 8) . wuhan and the cities located in hubei province have = 1, while cities located far away from wuhan tend to have larger values, e.g., = ℎ = 6. moreover, we added = = 1, based on the rationale that hong kong has more airline traffic flows to wuhan than shanghai 24 , which has = ℎ ℎ = 1. macau and taiwan both have frequent traffic flows to hong kong 24 , so we added = = 2 and = = 2. we collected all reported sars cases in mainland china, hong kong, taiwan and macau, and assign the numbers of cases to each city as , ∈ {1, … , 346}. the values range between zero (no reported cases) and 2,521 ( = ), with an average of 70.8 and a median of 4 cases in cities with at least one case reported. we then use the logarithm, as most cities reported zero cases of sars resulting in: we build three groups of regression models to estimate the effects of social distance and sars memory on public awareness measures δ , ( ) covid−19 and δ respectively. _ _ represents the gross domestic product (gdp) per capita for city . indicates whether or not city has sub-provincial or greater administrative power. sub-provincial cities are mostly capitals of the provinces in which they are located, or important cities designated by the central government. four cities, including beijing, shanghai, tianjin and chongqing, which are under direct control of the central government are also labelled as = 1. those sub-provincial and above cities have much better facilities and expertise for infection control than other cities 25 , so we assume residents could be more alert. is used to control the effects of administrative level. we also introduce euclidean distances as a control variable, denoted as . all data necessary to replicate the analysis is attached as s2 of the sm. the early warnings of the outbreak as early as dec 31 st , 2019, most of the cities (326 out of 346) have exhibited at least some awareness of the emerging wuhan outbreak (fig. 2b) . however, awareness then decreased until jan 19 th , 2020, one day before the chinese centre for disease control and prevention confirmed human-to-human transmissions of the novel coronavirus. since jan 20 th , 2020, overall awareness has increased by a magnitude of at least five, demonstrating significant awareness across all cities (fig. 2b ). awareness remained low as the epidemic spread, falling close to its lowest point on the starting day of chunyun (jan 10 th , 2020). considering cities that showed initial novel coronavirus awareness levels at least 1.5 times that of the search term "common cold", we found a total of 166 alert cities as early as dec 31 st , 2019 (48 cities at a tighter threshold of = 3.0 times, illustrated in fig. 2a ). however, awareness decreased significantly during chunyun. . cc-by 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 16, 2020. . the evolution of public awareness over time followed an unusual pattern. in a typical uau process, people are unaware of emerging catastrophic events until they are told by their social contacts. they remain aware during the event, and awareness then fades subsequently 2, 26 . however, during the wuhan outbreak, the public experienced a process as aware-unaware-aware, with public awareness declining during the early phase of the outbreak. dividing cities into two groups of equal size according to the numbers of reported sars cases, we found the cities that had been struck by sars to be more alert ( p < 0.05 ) during onset (2b). therefore, we believe the sars memory still conditions public awareness. we provide evidence of its effects at the end of this section. three features define the awareness advantage of alert cities, including early awareness, strong magnitude and high retention of awareness. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 16, 2020. . days and a median of -10 days. forty-eight cities emerge with early signals of public awareness, as early as dec 31 st , 2019, while for most others (255 cities), awareness is as late as jan 20 th , 2020 ( fig. 2a) . the cities of substantial lead-time advantage are those either closed to wuhan in terms of social distances or struck by the sars outbreak. for example, changchun in jilin province with 34 sars cases and far away from wuhan still achieved a ten days lead-time advantage. the cities that did not exhibit awareness, such as qaramay and heihe, are mainly located far away from wuhan and did not suffer from the sars outbreak. in terms of the magnitude of awareness, all 346 cities exhibit at least some awareness during the onset. the values of even though most of the cities exhibit at least some awareness as early as dec 31 st , 2019, only a few retain it over the following weeks as the virus began to spread. the retention rates, δ , range between zero and 137%, with an average of 54% and a median of 55%. eight cities lost awareness before chunyun, while four cities developed greater awareness. xilingol league in inner mongolia ranked 4 th , with a retention rate at 103%. xilingol is far away from wuhan in terms of social distance, but it was struck by sars. it is worth noting that a confirmed case of plague was reported in xilingol on nov 16 th , 2019, only 45 days before the wuhan outbreak. the effects of social distance and sars memory on the lead-time advantage are estimated according to eq. 4, controlled by euclidean distances, gdp per capita and the city's administrative level (table 1) . we found that, in model (3) in table 1, exhibits positive effects, while shows a negative association with awareness. that means cities of strong sars memory and which are closer to wuhan in terms of social distances develop early awareness. moreover, the interaction term * exhibits negative effects, indicating that the sars memory effect becomes stronger where cities are closer to wuhan in terms of social distances. while controlling the model with euclidean distances (model (5) in table 1 ), we found that sars memory effect becomes non-significant, but social distance and its interaction with sars memory hold. meanwhile, euclidean distances effect are non-significant, even though it exhibits negative effect alone in model (4) in table 1 . we further control the model with gdp per capita and administrative level (model (6) & (7) in table 1 ). model (6) is more favorable than model (7), because the former achieves slightly lower aic scores (akaike's information criteria) 27 at 1893.132 with fewer degrees of freedom (df = 8) than the latter (aic = 1894.160, df = 9). in model (6) in table 1 , we found that both social distance and euclidean distances exhibit negative effects, but the social distance effects decrease almost half compared to model (5) in table 1 . the sars memory effects hold. also, the interaction term * is still significant, which means cities of stronger sars memory will develop more lead-time advantage, particularly when they are closer to wuhan. gdp per capita and the binary variable exhibit significant positive effects on the lead-time advantage. lead-time δ ( = 3.0) . cc-by 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint note: *p**p***p<0.01 the effects of social distance and sars memory on the magnitude of awareness are estimated according to eq. 5 (table 2 ). similar to the findings in table 1 , memory positively affects public awareness in all models. social distances show a significant negative effect only in the models without controlling variables (model (1), (2) & (3) in table 2 ). however, the interaction term between social distances with sars memory show a significant negative effect. when we control by euclidean distances, gdp per capita and the administrative level (model (5) and (6) in table 2 ), those effects still hold. moreover, the effects of administrative level and development level both exhibit positive effects on the magnitude of awareness. we hypothesize that residents with better education (proxied by gdp per capita) better understand the danger of deadly infectious diseases and, accordingly, tend to seek up-to-date information online. magnitude of awareness at the earliest day of awareness: is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint note: *p**p***p<0.01 the effects of social distance and sars memory on retention of awareness are estimated according to eq. 6. unlike the results in tables 1 and 2 , we observe no effects from sars memory (model (6) in table 3 ). when we control euclidean distances, the development level and the administrative level, the explanatory power of the model is still relatively weak (adj. 2 = 0.104). it seems the decreasing awareness is a collective behavior that occurred simultaneously. interestingly, social distances have a significant effect while the euclidean distances do not. development level exhibits positive effects, which suggests residents of better educated cities could be more alert during the epidemic onset. however, administrative level shows a negative effect. it seems residents living in important cities (in terms of administrative power) lost interest in the infectious diseases before chunyun. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the wuhan coronavirus outbreak is still striking china, with thousands of cases and dozens of deaths reported every day. from this study, we found that the spread of public awareness varies markedly across chinese cities. through controlling for development, administrative levels, and euclidean distances, we observe cities that were struck by sars and have more migration to the epicentre, wuhan, showed earlier, stronger and more durable public awareness of the outbreak. moreover, 48 cities had developed public awareness as early as dec 31 st , 2019, with up to 19 days of lead-time advantage against some other 255 cities. the study suggests that memory of previous events, as well as social links to an emerging threat, may influence public behaviour. greater awareness could help slow the spread of a disease, for example through increased attention to hygiene, mask-wearing and reduced interpersonal contact. it might also facilitate collective responses such as enforced quarantine measures. however, in some circumstances enhanced awareness could have negative impacts, such as unnecessary panic or ostracism of groups perceived as being at greater risk of infection due to the lack of infection statistics, we cannot yet statistically estimate the effect of public awareness on the subsequent seriousness of the outbreak. we note that xilingol league in inner mongolia, which had relatively stronger and more durable public awareness, had fewer cases (two cases as reported at feb 7 th , 2020 10 ) than other cities in the same province (totally 50 cases, with an average of 4.55 cases per city 10 ). to the best of our knowledge, this study is the first to investigate how memory of previous catastrophic events, e.g., sars, and social distances could affect the spread of public awareness. further studies will be needed to understand whether this holds in other context, beyond the unusual and tragic circumstances of the noel coronavirus in wuhan. file s1: baidu search index data file s2: the data necessary to replicate the analysis of this study. . cc-by 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 16, 2020. . https://doi.org/10.1101/2020.03.11.20033688 doi: medrxiv preprint the effect of public health measures on the 1918 influenza pandemic in u dynamical interplay between awareness and epidemic spreading in multiplex networks rapid assessment of disaster damage using social media activity performance of social network sensors during hurricane sandy chinese social media reaction to the mers-cov and avian influenza a(h7n9) outbreaks responding to global infectious disease outbreaks: lessons from sars on the role of risk perception, communication and management psychological impact on sars survivors: critical review of the english language literature pandemic cities: biopolitical effects of changing infection control in post-sars hong kong what you need to know about the wuhan coronavirus a novel coronavirus from patients with pneumonia in china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster china coronavirus: cases surge as official admits human to human transmission wuhan urban and rural construction bureau -wuhan transits ranked no. 1, becoming the largest transit station in china and at least 15 other cities have been quarantined as china attempts to halt the spread of the coronavirus. that's about 50 million people on lockdown cnnic. china internet network information center the thirty-sixth statistics report of china internet development using baidu search index to predict dengue outbreak in china using the baidu search index to predict the incidence of hiv/aids in china the baidu index: uses in predicting tourism flows-a case study of the forbidden city approximately 3 billion passengers transited in the chunyun of 2019 -xinhuanet friendship and mobility: user movement in location-based social networks we thank dr. ross sparks from data61, csiro for helpful suggestions and advice on the methodologies. we also thank the anonymous reviewers for their valuable suggestions.funding: x.l. and w.x. were supported by the national natural science foundation of china, no. 41571118. the authors declare that they have no competing interests.author contributions: x.l., h.c., c.p. and a.r. conceived of the research question. h.c. and w.x. processed the baidu search index data. x.l. and w.x. collected the other meta data including sars cases and gdp per capita. h.c., x.l., w.x., a.r. and c.p. interpreted the result. h.c., x.l., w.x., a.r. and c.p. drafted the manuscript and compiled supplementary information. all authors edited the manuscript and supplementary information and aided in concept development.data and materials availability: all data needed to evaluate the conclusions in the paper are present in the paper and/or the supplementary materials. key: cord-261246-m40kwgcg authors: chen, nanshan; zhou, min; dong, xuan; qu, jieming; gong, fengyun; han, yang; qiu, yang; wang, jingli; liu, ying; wei, yuan; xia, jia'an; yu, ting; zhang, xinxin; zhang, li title: epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study date: 2020-01-30 journal: lancet doi: 10.1016/s0140-6736(20)30211-7 sha: doc_id: 261246 cord_uid: m40kwgcg background: in december, 2019, a pneumonia associated with the 2019 novel coronavirus (2019-ncov) emerged in wuhan, china. we aimed to further clarify the epidemiological and clinical characteristics of 2019-ncov pneumonia. methods: in this retrospective, single-centre study, we included all confirmed cases of 2019-ncov in wuhan jinyintan hospital from jan 1 to jan 20, 2020. cases were confirmed by real-time rt-pcr and were analysed for epidemiological, demographic, clinical, and radiological features and laboratory data. outcomes were followed up until jan 25, 2020. findings: of the 99 patients with 2019-ncov pneumonia, 49 (49%) had a history of exposure to the huanan seafood market. the average age of the patients was 55·5 years (sd 13·1), including 67 men and 32 women. 2019-ncov was detected in all patients by real-time rt-pcr. 50 (51%) patients had chronic diseases. patients had clinical manifestations of fever (82 [83%] patients), cough (81 [82%] patients), shortness of breath (31 [31%] patients), muscle ache (11 [11%] patients), confusion (nine [9%] patients), headache (eight [8%] patients), sore throat (five [5%] patients), rhinorrhoea (four [4%] patients), chest pain (two [2%] patients), diarrhoea (two [2%] patients), and nausea and vomiting (one [1%] patient). according to imaging examination, 74 (75%) patients showed bilateral pneumonia, 14 (14%) patients showed multiple mottling and ground-glass opacity, and one (1%) patient had pneumothorax. 17 (17%) patients developed acute respiratory distress syndrome and, among them, 11 (11%) patients worsened in a short period of time and died of multiple organ failure. interpretation: the 2019-ncov infection was of clustering onset, is more likely to affect older males with comorbidities, and can result in severe and even fatal respiratory diseases such as acute respiratory distress syndrome. in general, characteristics of patients who died were in line with the mulbsta score, an early warning model for predicting mortality in viral pneumonia. further investigation is needed to explore the applicability of the mulbsta score in predicting the risk of mortality in 2019-ncov infection. funding: national key r&d program of china. since dec 8, 2019, several cases of pneumonia of unknown aetiology have been reported in wuhan, hubei province, china. [1] [2] [3] most patients worked at or lived around the local huanan seafood wholesale market, where live animals were also on sale. in the early stages of this pneumonia, severe acute respiratory infection symptoms occurred, with some patients rapidly dev eloping acute respiratory distress syndrome (ards), acute respiratory failure, and other serious complications. on jan 7, a novel coronavirus was identified by the chinese center for disease control and prevention (cdc) from the throat swab sample of a patient, and was subsequently named 2019ncov by who. 4 coronaviruses can cause multiple system infections in various animals and mainly respiratory tract infections in humans, such as severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers). [5] [6] [7] most patients have mild symptoms and good prognosis. so far, a few patients with 2019ncov have developed severe pneumonia, pulmonary oedema, ards, or mul tiple organ failure and have died. all costs of 2019ncov treatment are covered by medical insurance in china. at present, information regarding the epidemiology and clinical features of pneumonia caused by 2019ncov is scarce. [1] [2] [3] in this study, we did a comprehensive exploration of the epidemiology and clinical features of 99 patients with confirmed 2019ncov pneumonia admitted to jinyintan hospital, wuhan, which admitted the first patients with 2019ncov to be reported on. for this retrospective, singlecentre study, we recruited patients from jan 1 to jan 20, 2020, at jinyintan hospital in wuhan, china. jinyintan hospital is a hospital for adults (ie, aged ≥14 years) specialising in infectious diseases. accord ing to the arrangements put in place by the chinese government, adult patients were admitted centrally to the hospital from the whole of wuhan without selectivity. all patients at jinyintan hospital who were diagnosed as having 2019ncov pneumonia according to who interim guidance were enrolled in this study. 4 all the data of included cases have been shared with who. the study was approved by jinyintan hospital ethics committee and written informed consent was obtained from patients involved before enrolment when data were collected retrospectively. we obtained epidemiological, demographic, clinical, laboratory, management, and outcome data from patients' medical records. clinical outcomes were followed up to jan 25, 2020. if data were missing from the records or clarification was needed, we obtained data by direct communication with attending doctors and other health care providers. all data were checked by two physicians (xd and yq). laboratory confirmation of 2019ncov was done in four different institutions: the chinese cdc, the chinese academy of medical science, academy of military medical sciences, and wuhan institute of virology, chinese academy of sciences. throatswab specimens from the upper respiratory tract that were obtained from all patients at admission were maintained in viraltransport medium. 2019ncov was confirmed by realtime rtpcr using the same protocol described previously. 3 rtpcr detection reagents were provided by the four institutions. other respiratory viruses including influenza a virus (h1n1, h3n2, h7n9), influenza b virus, respiratory syncytial virus, parainfluenza virus, adenovirus, sars coronavirus (sarscov), and mers coronavirus (merscov) were also examined with real time rtpcr sputum or endotracheal aspirates were obtained at admission for identification of possible causative bacteria or fungi. additionally, all patients were given chest xrays or chest ct. we describe epidemi ological data (ie, shortterm [occasional visits] and longterm [worked at or lived near] exposure to huanan seafood market); demographics; signs and symptoms on admission; comorbidity; labora tory results; coinfection with other respiratory pathogens; chest radiography and ct findings; treatment received for 2019ncov; and clinical outcomes. we present continuous measurements as mean (sd) if they are normally distributed or median (iqr) if they are not, and categorical variables as count (%). for laboratory results, we also assessed whether the mea surements were outside the normal range. we used spss (version 26.0) for all analyses. the funder of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. the corresponding authors had full access to all the data in the study and had final responsibility for the decision to submit for publication. 99 patients with 2019ncov were included in this study, two of whom were husband and wife. in total, 49 (49%) evidence before this study we searched pubmed on jan 25, 2020, for articles that describe the epidemiological and clinical characteristics of the 2019 novel coronavirus (2019-ncov) in wuhan, china, using the search terms "novel coronavirus" and "pneumonia" with no language or time restrictions. previously published research discussed the epidemiological and clinical characteristics of severe acute respiratory syndrome coronavirus or middle east respiratory syndrome coronavirus, and primary study for the evolution of the novel coronavirus from wuhan. the only report of clinical features of patients infected with 2019-ncov was published on jan 24, 2020, with 41 cases included. we have obtained data on 99 patients in wuhan, china, to further explore the epidemiology and clinical features of 2019-ncov. this study is, to our knowledge, the largest case series to date of 2019-ncov infections, with 99 patients who were transferred to jinyintan hospital from other hospitals all over wuhan, and provides further information on the demographic, clinical, epidemiological, and laboratory features of patients. it presents the latest status of 2019-ncov infection in china and is an extended investigation of the previous report, with 58 extra cases and more details on combined bacterial and fungal infections. in all patients admitted with medical comorbidities of 2019-ncov, a wide range of clinical manifestations can be seen and are associated with substantial outcomes. the 2019-ncov infection was of clustering onset, is more likely to affect older men with comorbidities, and could result in severe and even fatal respiratory diseases such as acute respiratory distress syndrome. early identification and timely treatment of critical cases of 2019-ncov are important. effective life support and active treatment of complications should be provided to effectively reduce the severity of patients' conditions and prevent the spread of this new coronavirus in china and worldwide. patients were clustered and had a history of exposure to the huanan seafood market. among them, there were 47 patients with longterm exposure history, most of whom were salesmen or market managers, and two patients with shortterm exposure history, who were shoppers. none of the patients were medical staff. most patients were men, with a mean age of 55·5 years (sd 13·1; table 1). 50 (51%) patients had chronic diseases, including cardiovascular and cerebro vascular diseases, endocrine system disease, digestive system disease, respiratory system disease, malignant tumour, and nervous system disease (table 1) . on admission, most patients had fever or cough and a third of patients had shortness of breath (table 2) . other symptoms included muscle ache, headache, confu sion, chest pain, and diarrhoea (table 2) . many patients presented with organ function damage, including 17 (17%) with ards, eight (8%) with acute respiratory injury, three (3%) with acute renal injury, four (4%) with septic shock, and one (1%) with venti latorassociated pneumonia (table 2) . on admission, leucocytes were below the normal range in nine (9%) patients and above the normal range in 24 (24%) patients ( (table 3) . platelets were below the normal range in 12 (12%) patients and above the normal range in four (4%). 43 patients had differing degrees of liver function abnormality, with alanine aminotransferase (alt) or aspartate aminotransferase (ast) above the normal range (table 3) ; one patient had severe liver function damage (alt 7590 u/l, ast 1445 u/l). most patients had abnormal myocardial zymogram, which showed the elevation of creatine kinase in 13 (13%) patients and the elevation of lactate dehy drogenase in 75 (76%) patients, one of whom also showed abnormal creatine kinase (6280 u/l) and lactate dehydrogenase (20 740 u/l). seven (7%) patients had different degrees of renal function damage, with elevated blood urea nitrogen or serum creatinine. regarding the infection index, procalcitonin was above the normal range in six (6%) patients. most patients had serum ferritin above the normal range (table 3 ). 73 patients were tested for creactive protein, most of whom had levels above the normal range (table 3 ). all patients were tested for nine respiratory pathogens and the nucleic acid of influenza viruses a and b. bacteria and fungi culture were done at the same time. we did not find other respiratory viruses in any of the patients. acinetobacter baumannii, klebsiella pneumoniae, and aspergillus flavus were all cultured in one patient. a baumannii turned out to be highly resistant to antibiotics. one case of fungal infection was diagnosed as candida glabrata and three cases of fungal infection were diagnosed as candida albicans. according to chest xray and ct, 74 (75%) patients showed bilateral pneumonia (75%) with just 25 (25%) procalcitonin (ng/ml; normal range 0·0-5·0) 0·5 (1·1) figure) . additionally, pneumothorax occurred in one (1%) patient. all patients were treated in isolation. 75 (76%) patients received antiviral treatment, including oseltamivir (75 mg every 12 h, orally), ganciclovir (0·25 g every 12 h, intra venously), and lopinavir and ritonavir tablets (500 mg twice daily, orally). the duration of antiviral treatment was 3-14 days (median 3 days [iqr 3-6]). most patients were given antibiotic treatment (table 2); 25 (25%) patients were treated with a single antibiotic and 45 (45%) patients were given combination therapy. the antibiotics used generally covered common patho gens and some atypical pathogens; when secondary bacterial infection occurred, medication was admin istered according to the results of bacterial culture and drug sensitivity. the antibiotics used were cephalo sporins, quinolones, carbapenems, tigecycline against methicillinresistant staphylococcus aureus, linezolid, and antifungal drugs. the duration of antibiotic treatment was 3-17 days (median 5 days [iqr [3] [4] [5] [6] [7] ). 19 (19%) patients were also treated with methylpred nisolone sodium succinate, methylprednisolone, and dexametha sone for 3-15 days (median 5 [3] [4] [5] [6] [7] ). 13 patients used noninvasive ventilator mechanical ventilation for 4-22 days (median 9 days [iqr 7-19]). four patients used an invasive ventilator to assist ventilation for 3-20 days (median 17 [12] [13] [14] [15] [16] [17] [18] [19] ). the ventilator adopted psimv mode, the inhaled oxygen concentration was 35-100%, and the positive end expiratory pressure was 6-12 cm h 2 o. all four patients were still using ventilators at data cutoff. moreover, nine (9%) patients received continuous blood purifi cation due to renal failure and three (3%) patients were treated with extracorporeal membrane oxygenation (ecmo; table 2). by the end of jan 25, 31 (31%) patients had been discharged and 11 (11%) patients had died; all other patients were still in hospital (table 1). the first two deaths were a 61yearold man (patient 1) and a 69yearold man (patient 2). they had no previous chronic underlying disease but had a long history of smoking. patient 1 was transferred to jinyintan hospital and diagnosed with severe pneumonia and ards. he was immediately admitted to the intensive care unit (icu) and given an intubated ventilatorassisted breathing therapy. later, the patient, having developed severe res piratory failure, heart failure, and sepsis, experienced a sudden cardiac arrest on the 11th day of admission and was declared dead. patient 2 had severe pneumonia and ards after admission. the patient was transferred to the icu and given ventilatorassisted breathing, and received anti infection and ecmo treatment after admission. the patient's hypoxaemia remained unresolved. on the ninth day of admission, the patient died of severe pneumonia, septic shock, and respiratory failure. the intervals 1 (1a) . the brightness of both lungs was diffusely decreased, showing a large area of patchy shadow with uneven density. tracheal intubation was seen in the trachea and the heart shadow outline was not clear. the catheter shadow was seen from the right axilla to the mediastinum. bilateral diaphragmatic surface and costal diaphragmatic angle were not clear, and chest x-ray on jan 2 showed worse status (1b). case 2: chest x-ray obtained on jan 6 (2a). the brightness of both lungs was decreased and multiple patchy shadows were observed; edges were blurred, and large ground-glass opacity and condensation shadows were mainly on the lower right lobe. tracheal intubation could be seen in the trachea. heart shadow roughly presents in the normal range. on the left side, the diaphragmatic surface is not clearly displayed. the right side of the diaphragmatic surface was light and smooth and rib phrenic angle was less sharp. chest x-ray on jan 10 showed worse status (2b). case 3: chest ct obtained on jan 1 (3a) showed mass shadows of high density in both lungs. bright bronchogram is seen in the lung tissue area of the lesion, which is also called bronchoinflation sign. chest ct on jan 15 showed improved status (3b). between the onset of symptoms and the use of ventilator assisted breathing in the two patients were 3 days and 10 days, respectively. the course of the disease and lung lesions progressed rapidly in both patients, with both developing multiple organ failure in a short time. the deaths of these two patients were consistent with the mulbsta score, an early warning model for predicting mortality in viral pneumonia. 8 of the remaining nine patients who died, eight patients had lymphopenia, seven had bilateral pneumonia, five were older than 60 years, three had hypertension, and one was a heavy smoker. this is an extended descriptive study on the epidemiology and clinical characteristics of the 2019ncov, including data on 99 patients who were transferred to jinyintan hospital from other hospitals across wuhan. it presents the latest status of the 2019ncov infection in china and adds details on combined bacterial and fungal infections. human coronavirus is one of the main pathogens of respiratory infection. the two highly pathogenic viruses, sarscov and merscov, cause severe res piratory syndrome in humans and four other human corona viruses (hcovoc43, hcov229e, hcovnl63, hcovhku1) induce mild upper respiratory disease. the major sarscov outbreak involving 8422 patients occurred during 2002-03 and spread to 29 countries globally. 9,10 merscov emerged in middle eastern countries in 2012 but was imported into china. 11, 12 the sequence of 2019ncov is relatively different from the six other coronavirus subtypes but can be classified as betacoronavirus. sarscov and merscov can be transmitted directly to humans from civets and dromedary camels, respectively, and both viruses origi nate in bats, but the origin of 2019ncov needs further investigation. [13] [14] [15] 2019ncov also has enveloped virions that measure approximately 50-200 nm in diameter with a single positivesense rna genome. 16 clubshaped glycoprotein spikes in the envelope give the virus a crownlike or coronal appearance. transmission rates are unknown for 2019ncov; however, there is evidence of humantohuman transmission. none of the 99 patients we examined were medical staff, but 15 medical workers have been reported with 2019ncov infection, 14 of whom are assumed to have been infected by the same patient. 17 the mortality of sarscov has been reported as more than 10% and merscov at more than 35%. 5, 18 at data cutoff for this study, mortality of the 99 included patients infected by 2019ncov was 11%, resembling that in a previous study. 3 however, additional deaths might occur in those still hospitalised. we observed a greater number of men than women in the 99 cases of 2019ncov infection. merscov and sarscov have also been found to infect more males than females. 19, 20 the reduced susceptibility of females to viral infections could be attributed to the protection from x chromosome and sex hormones, which play an important role in innate and adaptive immunity. 21 additionally, about half of patients infected by 2019ncov had chronic underlying diseases, mainly cardiovascular and cerebrovascular diseases and diabetes; this is similar to merscov. 19 our results suggest that 2019ncov is more likely to infect older adult males with chronic comorbidities as a result of the weaker immune func tions of these patients. [19] [20] [21] [22] some patients, especially severely ill ones, had co infections of bacteria and fungi. common bacterial cultures of patients with secondary infections included a baumannii, k pneumoniae, a flavus, c glabrata, and c albicans. 8 the high drug resistance rate of a baumannii can cause difficulties with antiinfective treatment, leading to higher possibility of developing septic shock. 23 for severe mixed infections, in addition to the virulence factors of pathogens, the host's immune status is also one of the important factors. old age, obesity, and presence of comorbidity might be associated with increased mor tality. 24 when populations with low immune function, such as older people, diabetics, people with hiv infection, people with longterm use of immuno suppressive agents, and pregnant women, are infected with 2019ncov, prompt administration of antibiotics to prevent infection and strengthening of immune support treatment might reduce complications and mortality. in terms of laboratory tests, the absolute value of lymphocytes in most patients was reduced. this result suggests that 2019ncov might mainly act on lympho cytes, especially t lymphocytes, as does sarscov. virus particles spread through the respiratory mucosa and infect other cells, induce a cytokine storm in the body, generate a series of immune responses, and cause changes in peripheral white blood cells and immune cells such as lymphocytes. some patients progressed rapidly with ards and septic shock, which was eventually followed by multiple organ failure. therefore, early identification and timely treatment of critical cases is of crucial importance. use of intra venous immunoglobulin is recommended to enhance the ability of antiinfection for severely ill patients and steroids (methylprednisolone 1-2 mg/kg per day) are recommended for patients with ards, for as short a duration of treatment as possible. some studies suggest that a substantial decrease in the total number of lymphocytes indicates that coronavirus consumes many immune cells and inhibits the body's cellular immune function. damage to t lymphocytes might be an important factor leading to exacerbations of patients. 25 the low absolute value of lymphocytes could be used as a reference index in the diagnosis of new coronavirus infections in the clinic. in general, the characteristics of patients who died were in line with the early warning model for predicting mortality in viral pneumonia in our previous study: the mulbsta score. 8 the mulbsta score system contains six indexes, which are multilobular infiltration, lympho penia, bacterial coinfection, smoking history, hyper tension, and age. further investigation is needed to explore the applicability of the mulbsta score in predicting the risk of mortality in 2019ncov infection. this study has several limitations. first, only 99 patients with confirmed 2019ncov were included; suspected but undiagnosed cases were ruled out in the analyses. it would be better to include as many patients as possible in wuhan, in other cities in china, and even in other countries to get a more comprehensive understanding of 2019ncov. second, more detailed patient information, particularly regarding clinical outcomes, was unavailable at the time of analysis; however, the data in this study permit an early assess ment of the epidemiological and clinical characteristics of 2019ncov pneumonia in wuhan, china. in conclusion, the infection of 2019ncov was of clustering onset, is more likely to infect older men with comorbidities, and can result in severe and even fatal respiratory diseases such as ards. contributors nc, xd, fg, yh, yq, jw, yl, yw, jx, ty, and lz collected the epidemiological and clinical data and processed statistical data. nc and mz drafted the manuscript. jq and xz revised the final manuscript. xz is responsible for summarising all data related to the virus. lz is responsible for summarising all epidemiological and clinical data. 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middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation evidence for camelto human transmission of mers coronavirus surveillance of bat coronaviruses in kenya identifies relatives of human coronaviruses nl63 and 229e and their recombination history origin and evolution of pathogenic coronaviruses fatal swine acute diarrhoea syndrome caused by an hku2related coronavirus of bat origin evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for the risk of human transmission wuhan coronavirus has strong ability to infect humans. press release from sars to mers, thrusting coronaviruses into the spotlight prevalence of comorbidities in the middle east respiratory syndrome coronavirus (merscov): a systematic review and metaanalysis sexbased differences in susceptibility to severe acute respiratory syndrome coronavirus infection sexual dimorphism in innate immunity pathophysiology and burden of infection in patients with diabetes mellitus and peripheral vascular disease: focus on skin and softtissue infections clinical findings in 111 cases of influenza a (h7n9) virus infection clinical features of three avian influenza h7n9 virusinfected patients in shanghai tcell immunity of sarscov: implications for vaccine development against merscov this study was funded by the national key r&d program of china (number 2017yfc1309700). we thank all patients involved in the study. key: cord-326721-2v5wkjrq authors: xiao, wenlei; liu, qiang; huan, j; sun, pengpeng; wang, liuquan; zang, chenxin; zhu, sanying; gao, liansheng title: a cybernetics-based dynamic infection model for analyzing sars-cov-2 infection stability and predicting uncontrollable risks date: 2020-03-17 journal: nan doi: 10.1101/2020.03.13.20034082 sha: doc_id: 326721 cord_uid: 2v5wkjrq since december 2019, covid-19 has raged in wuhan and subsequently all over china and the world. we propose a cybernetics-based dynamic infection model (cdim) to the dynamic infection process with a probability distributed incubation delay and feedback principle. reproductive trends and the stability of the sars-cov-2 infection in a city can then be analyzed, and the uncontrollable risks can be forecasted before they really happen. the infection mechanism of a city is depicted using the philosophy of cybernetics and approaches of the control engineering. distinguished with other epidemiological models, such as sir, seir, etc., that compute the theoretical number of infected people in a closed population, cdim considers the immigration and emigration population as system inputs, and administrative and medical resources as dynamic control variables. the epidemic regulation can be simulated in the model to support the decision-making for containing the outbreak. city case studies are demonstrated for verification and validation. the spread speed of sars-cov-2 has been emergently challenging many cities in china, especially those cities in hubei province (wuhan, huanggang, xiaogan, etc.) [1] . during the currently still happening disaster, people and governments have gradually enhanced the strength of responses. three chinese cities (wuhan, huanggang and ezhou) were shut down on jan 23, 2020 to contain the rapidly-spreading virus; in most of chinese cities, the first-level public health emergency response was activated on jan 24, 2020; huoshenshan and leishenshan hospitals were built in less than two weeks to admit and treat patients at the epicenter of the virus; after feb 2, 2020, wuhan start to convert gymnasiums and exhibition centers into temporary shelter(fangcang) hospitals to accept and quarantine patients with mild symptoms. tens of thousands of doctors and nurses from all over china have been sent to wuhan. it seams we have always been pushed into a defensive position, that the responses were always later than the developing epidemic status. as a spontaneously summoned team, we have continuously followed the progress of this epidemic, and believe that we have found a novel forecast model to solve this problem. base on this model, corresponding responses could be activated before the uncontrollable risks really happen. recently, control engineering has been maturely applied in industry. it has successfully proved its ability in analyzing the complex mechanism in a physical system. however, the control engineering has seldom been used in modeling the transmission pattern of the epidemic. comparing its basic mechanism with an instable system, we found the dynamic infection process of covid-19 in a city could be depicted as a cybernetic model with a positive feedback and multiple delays, and the system instability is the most issue that people and the government concern. in contrast to other classic transmission models like sir/-seir (the susceptible, [exposed] , infectious and recovered model), which are mostly described by a set of ordinary differential equations [2] , the feedback system is constituted by a chain of discrete function blocks, such as proportional, time delayed, integral(or accumulative) blocks, and positive/negative feedback or feed-forward loop, etc. dynamic manipulations, such as quarantining activities, medical supplies, etc., are also considered in the model. in those consideration, the model is named as cybernetics-based dynamic infection model (cdim). according to the daily reported numbers of confirmed and suspected covid-19 cases from the national health commission of china [3] , we found that cities may have non-ignorable differences on their r 0 . after the administrative activities carried out in most chinese cities, such as the first-level response, the fangcang hospitals, etc., r 0 also fluctuates in time significantly. normally, those dyfigure 1 : the sir/seir models namic and nonlinear impacts are hard to be considered in classical transmission models (sir, seir, etc.) with ordinary differential equations. in addition, the dynamic considerations can derive polymorphic city-oriented models for analyzing the uncontrollable risks in different cities with higher precision and dexterity. after several days of validation, we found the model can successfully forecast the epidemic trends in most of cities. potential usage of this model could be a warning system for faster activating responses and predicting the shortage of medical supplies. in this section, we are going to discuss the disadvantages of sir/seir models in epidemic forecasting, and explain how the cybernetics-based model can solve those problems. nowadays, sir/seir and their extended or modified versions are the most commonly used models to describe the spread of disease. in a closed population, the models (shown in fig. 1 ) track the number of people in each of the following categories: • susceptible: individual is able to become infected. • exposed: individual has been infected with a pathogen, but due to the pathogens incubation period, is not yet infectious. • infectious: individual is infected with a pathogen and is capable of transmitting the pathogen to others. • recovered: individual is either no longer infectious or removed from the population. wherein, the infection rate β controls the rate of spread, the incubation rate σ is the rate of latent individual becoming infectious, and the recovery rate γ is determined by the average duration of infection. there are several disadvantages in the sir/seir models: 1. immigrated and emigrated populations are not considered in the model. nevertheless, the traffic is far more convenient than ever before in china, so it has a significant impact on the spread. 2. the models are usually written as ordinary differential equations(ode). it is not concise enough to help human comprehensively model the nonlinear dynamics in detail. 3. the models are relatively too simple to introduce the time-variant and probabilistic variables into the models. 4. all the parameters should be identified for estimation. in the early stage, the shortage of data makes the models infeasible to exactly forecast the trend of spread. 5. emergency responses and medical supplies are not considered in the model, so the prediction of status has no direct recommending value to the administrative activities. 6. the parameter identification in the models strongly relies on the fidelity of real data. when the reported data have a severe deviation (like in wuhan), it will easily lead to a forecasting failure. in fact, what we really need to forecast is the severe situations that would happen in the future, especially at the early stage when data are in serious shortage. for example, if the short of hospital beds could be foreseen on feb 26, 2020, the fangcang hospitals could be established much earlier. due to the aforementioned disadvantages, sir/seir cannot answer those questions. in the view of modeling, there exists indeed far more advanced theories and methods in the field of control engineering. its development is mainly benefited from the industry revolution, so that it has become a ubiquitous technology in nearly all automatic machines. in the 1940s, contemporary cybernetics began as an interdisciplinary study connecting wide fields of control systems, electrical network theory, mechanical engineering, logic modeling, evolutionary biology and neuroscience. it certainly could be employed to model the spread of epidemic. fig. 2 gives the comparison between the current modeling methods in use for epidemic and mechanical systems. obviously, it can be seen that the cybernetics-based modeling methods can provide more diversity in describing a system. not only can the system be better depicted, but also can the modeling work be significantly simplified. in 2003, a cybernetics-based model had been firstly proposed by the authors (ji huan and qiang liu), and successfully forecasted the spread of sars in beijing. fig. 3 shows the sars model that was used to estimate the confirmed cases in beijing and the corresponding result. the spread of sars epidemic can be represented in a very concise manner. the positive feedback path emulates the rapid reproductive process of the epidemic, while the negative feedback represents the regulation effect from hospital (all patients are isolated at the moment of symptom onset). the result is give in fig. 3 is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. . https://doi.org/10.1101/2020.03.13.20034082 doi: medrxiv preprint nonetheless, there exists several basic differences in between sars and sars-cov-2: 1. sars-cov-2 is contagious even in the incubation (sars was not). 2. the traffic must be carefully depicted in the model. 3 . the epidemic in multiple cities needs be forecasted. in views of those differences, we improved the sars model to cdim, as shown in fig. 4 . the infection from immigration or the origin source (i.e. the huanan seafood wholesale market in wuhan) is taken as the system input. the infection main loop generates the rapid reproduced infection. the equivalent infection rate c 0 indicates the infected cases per virus carrier per day. the contact tracing rate 1 − c 1 represents the effect of contact tracing of patients. the incubation bypass emulates the process of symptom onset. since the incubation period t 1 follows a poisson distribution, the factor λ should be identified (see eq. 1). the medical regulation functions as a negative channel to control the incremental numbers of infection in the main loop. the basic model in fig. 1 is based on a theoretical assumption, that all the patients are isolated at the moment of symptom onset (after the incubation period). when people start to wear masks and voluntarily stay indoors, r 0 (namely c 0 ) decreases accordingly. in the responsive condition, when a patient is confirmed, certain close contacts that are still in the asymptomatic incubation period would also be isolated. we introduce c 1 , named the contact tracing rate, to reflect this effect. when c 1 ≈ 0, that means no contact tracing is imposed, the system could easily fall into an instable state if r 0 ≥ 1.0. the infection model is discretized with a cyclic period of one day. in summary, t 0 and t 1 are mostly determined by the epidemic, c 0 is determined by both epidemic and the social stress, and c 1 is determined majorly by administrative activities. eq. 2 gives the difference equations of the basic cdim. even with the qualitative analysis, some conclusions could 3 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint : effective infectious increment (can be negative); : total non-isolated cases (asymptomatic carriers); : patient increment (symptom onset); : total isolated cases (confirmed patients after symptom onset); figure 4 : basic principle of the cybernetics-based dynamic infection model be made. for example, as sars-cov-2 is contagious in its incubation, it is spreading much faster than sars and more hard to be controlled. consequently, experiences from sars should not be simply copied to control the current status. this is very important issue at the early stage that should be but was not emphasized in hubei province. in china, there exists two types of city-oriented models. a typical city of the first type is shanghai. it has enough medical supplies to admit all the patients with symptom onset, and original infectious cases were imported from immigration. wuhan is of the second type. it was facing a serious shortage of medical supplies. especially, the number of hospital beds in wuhan is far less than the real needs. moreover, due the limitation of diagnosis, there exist a confirming delay of 23 days. all those phenomenons should be considered in the two types of models. as the models are strongly featured by cities, we name the two types of models as shanghai model and wuhan model. at the beginning, when the novel coronavirus from wuhan causes concern in public, delayed and missed detection may exist in the reported number of cases. it brings troubles in estimating the epidemiological parameters and epidemic predictions [4, 5] . most estimated r 0 ranges from 1.5 to 4.0 [1, 6, 7, 8] . as of jan 29, 2020, the first investigated incubation period from patients was reported, which had a mean of 5.2 days(95% confidence interval [ci], 4.1 to 7.0) and followed a poisson distribution, and the basic reproductive number was estimated to be 2.2 (95% ci, 1.4 to 3.9) [6] . however, the early sampled 425 patients had a median age of 59 years and 56% were male. given those bias on the samples, the estimated epidemiological parameters may have deviations that might lead to great errors in the simulation. in the view of this, we used the data from shanghai, a relatively well controlled city, to identify and calibrate the key parameters of the incubation period and the basic reproductive number. subsequently, those parameters were used to evaluate the status of other cities (except for those cities in hubei province). in shanghai model, there is no worry about the shortage of medical supplies, so a negative summation channel performs a direct control effect on the positive feedback infection loop, which is thus of paramount importance in reducing the number of total infectious cases. two factors in the system can be regulated by the administration, c 0 and c 1 . the confirmation delay does not affect the infecting process, but brings a direct hinder in inspecting the real number of confirmed cases. the input of the shanghai model mainly comes from the inspected cases from wuhan, so the number of daily imported cases should be given by r 1 x 1 , where r 1 is the infection rate of immigration, and x 1 is the daily immigrated population from wuhan. on jan 23, 2020, wuhan went into lockdown to contain the outbreak of the epidemic. since then, the input from immigration was switched off. those sudden events changed the system dynamics dramatically, and is difficult to be estimated or approximated by other transmission models. other similar cities can reuse the shanghai model with some modification on the parameters c 0 and c 1 . nonetheless, the 4 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint poisson distribution of incubation periods should not be changed in other cities, for the patients were derived from the same pathogeny. comparing the reproductive speeds in different cities (as shown in fig. 5 ), we found that different cities may have different reproductive gain c 0 (1 − c 1 ), which may depend on the generation of imported epidemic and local administrative activities. there are major differences between the city wuhan and other cities such as shanghai, beijing, etc. firstly, wuhan was facing a serious shortage of medical supplies against the outbreak of sars-cov-2. consequently, we designed an integral saturation module on the incubation bypass, whose capability is mostly limited by the total hospital beds; secondly, since the original source of the coronavirus locates in wuhan, the system input should be replaced with a spontaneous infection source; thirdly, 5 million population had been exported outside wuhan until jan 23, 2020. the model should be supplemented by this emigration, as it took a large proportion of the total population (5 million left versus 9 million remained). for those sakes, wuhan model is designed as fig. 6 . from the daily reported news, we collected all the numbers of hospital beds with dates, including those in designated, makeshift, huoshenshan and leishenshan hospitals. those numbers of beds with dates were employed in the module, admission capability of hospitals, so that the dynamic consumption of medical resources could be emulated. the system input is replaced with a spontaneous infection source, which can be simplified as a unit impulse signal, while its exact date should be deduced from later confirmed infected cases. until the city went into lockdown, emigration had exported a number of infected patients. the factor r 2 represents the infection rate at kth day of the city population m (k), which were decreasing iteratively and evenly by the daily emigration x 2 (k). the iterative formulas of r 2 (k) and m (k) are given as follow: the exported infected cases are subtracted from the infection main loop. we figured out several ways to determine the parameters in the wuhan model. obviously, the incubation period can be introduced from shanghai, while c 0 and c 1 should be approximated by real data. other data such as the input and emigration were derived from collected news and reports. before simulation, there are basically three parameters need to be identified in the models: the possion distributed incubation (namely λ), the reproductive gain k = c 0 (1 − c 1 ), and the traffic data. the traffic data could be derived from big data systems, while λ and k should be identified from real data. note that, the reproductive gain k is related to the reproductive number r 0 : where,t 1 is the mean incubation. we demonstrate the simulation result of shanghai in fig. 8 . as of jan 24, 2020, according to the international confirmed cases [9] and the international flights of wuhan tianhe airport [10] , we estimated the mean ratio of infection in the emigration from wuhan (r 1 ) was 0.0246%. the is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint intercity traffic from wuhan to shanghai is searched from baidu map big data. after simulation, the fitted curve of shanghai is given in fig. 4 . the poisson distribution factor λ of the incubation period was estimated to be 5.5 (as shown in fig. 7) , and the basic reproductive number r 0 in shanghai was 2.5 (before the first-level response) and 0.55 (after the first-level response, 95% ci, 0.48 to 0.59). provided the latest r 0 is stabilized, the final number of infected cases in shanghai was estimated to be 344 (95% ci, 311 to 378). is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. with the parameters identified from shanghai, beijing was firstly tested to evaluate its risk of stability on feb 30, 2020. as of feb 30 (6 days after the first-level response), it becomes clear to exactly identify the factors λ and k. beijing and shanghai are the two most important megalopolises in the main land of china, thus could share the same set of factors. in view of this, we reuse the parameters from shanghai and deduce the fact that beijing should postpone the end of the holiday (chinese new year) from feb 2, 2020 to feb 9, 2020. after the city resumed work, we supposed r 0 would rebound to 0.8. the simulation was conducted under this assumption, and fig. 9 reveals the difference between these two setups. the results show that the postpone of resuming work could significantly reduce the incremental infected numbers in beijing ( 77.3%). this case study shows the capability of the model to support the decision-making for controlling the epidemic in a city. wenzhou is another featured city that was found particular with a relatively high r 0 , up to 4.5 (as shown in fig. 10 ). deeper investigations were taken, and it was found that the imported infectious cases from wuhan to wenzhou were mostly from huanan seafood wholesale market. so we may consider wenzhou as a sub-sample of wuhan. this phenomenon can be thus explained, and alerts should have been announced to eliminate the instable risk and slow down the spread speed in wenzhou. in contrast, the inter link between wuhan and wenzhou helps to observe the current status of wuhan, whose parameters could be reused in spite of the differences in their model types. after the first-level response on jan 23, 2020, r 0 decreases significantly down to 0.5 (95% ci, 0.435 to 0.556), which means both social and administrative manipulations start to work correspondingly. provided the latest r 0 is stabilized, the final number of infected cases in wenzhou is estimated to be 527 (95% ci, 475 to 582). from the fitted curve, we could have deduced the stability of wenzhou even early at feb 01, 2020. with the study of wenzhou, it was found that the linkage between wenzhou and wuhan could be used to estimate the parameters in wuhan. at that moment (2020.02.01), the status in wuhan was extremely confusing, as a lot of infected patients were not confirmed. the hospital beds might be facing a serious shortage. based on the collected bed data from designated, makeshift, huoshenshan and leishenshan hospitals, the model simulated the real situation. what can be confirmed was that emergent quarantining actions should be more strictly taken to admit the infected patients, and much more hospital beds should be prepared to contain the outbreak in wuhan. fig. 11 shows the simulated results. we estimated the number of infection based on the confirmed cases from the japanese and german evacuation. there were 1.4% confirmed cases in the total evacuated population. fig. 11(a) shows the risk of instability, and fig. 11(b) gives the result when the forced isolation (namely the subsequent fancang hospitals) was activated since feb 02, 2020 to curb the spread of the virus. some days later, the forced isolation in wuhan was implemented by those temporary shelter hospitals or fangcang. due to the lack of data, there might exist significant errors in the simulated results. in spite of that, the epidemic stability in wuhan was successfully estimated, and the model proves that the fancang hospitals played a vitally important role in containing the outbreak at last. the simulation of wuhan implies a fact that, stability oriented analysis is far more important than accuracy oriented analysis. in order to make a quick decision, administrative responses could activated according to the forecasted risk of instability rather than the forecasted infected numbers. this is because the estimation of stability is usually much faster than the estimation of accuracy. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. we present a cybernetics-based dynamic infection model to simulate the epidemiologic characteristics of sars-cov-2. two polymorphic models for different city types are derived with considerations on their medical, immigration/emigration population and administrative conditions. shanghai, beijing, wenzhou and wuhan were studied to validate the infection models. more simulated results based on the successive data from 37 cities in china are listed in the appendix. results demonstrate that the model can successfully simulate the dynamic infecting process of covid-19, and uncontrollable risks in a city can be predicted before they come true. additionally, administrative management can be verified by the model so that decisions can be made in time with more confidence according to the forecasts and warnings. combined with big data of the intercity traffics, the research work is even more help-ful to future epidemic predictions. uncontrollable risks in multiple cities could be monitored in parallel, emergency responses could be activated faster, and medical supplies would be produced precisely and transported to the right place at the right time. currently, the outbreak in china is almost brought under control, while the international spread is developing rapidly. the global transmission is just like the situation in china one month ago. in view of this, many parameters could be reused to forecast the spread in foreign countries (south korea, italy, iran, etc.), experiences should be learned from china to prevent more cities from instability. from the proposed model, we could infer the following conclusions: (1) medical responsibility: medical supplies should be prepared abundantly to admit all the patient with symptom onset; (2) social responsibility: people should reduce contacts as much as possible, so that the factor c 0 can be decreased; (3) administrative responsibility: the contact tracing rate c 1 plays a vitally significant role in stabilizing the spread. all the above mentioned responsibilities should be emphasized, so that the current situation could be stabilized before the end of may. in order to validate the cdim model, 37 cities were simulated on feb 9, 2020, and more data (yellow points) 8 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. . were used to verify the precision of estimation. most of cities fit well with the estimation, though some cities have some deviations. this is mainly caused by the dynamic quarantining level that changes r 0 . it implies that, in order to better estimate the epidemic, a dynamic parameter identification algorithm should be developed in future work. . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 17, 2020. . https://doi.org/10.1101/2020.03.13.20034082 doi: medrxiv preprint nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study a mathematical model for simulating the phase-based transmissibility of a novel coronavirus feb 12 daily briefing on novel coronavirus cases in china complexity of the basic reproduction number (r0) estimating the basic reproductive number during the early stages of an emerging epidemic. emerging infectious disease 2020 estimating the basic reproductive number during the early stages of an emerging epidemic estimating the unreported number of novel coronavirus (2019-ncov) cases in china in the first half of january 2020: a data-driven modelling analysis of the early outbreak early transmission dynamics in wuhan, china, of novel coronavirusinfected pneumonia up to 24:00 on 24 january the latest situation of pneumonia caused by novel coronavirus infection. national health commission of the peoples republic of china destinations of the five million passengers from wuhan? big data tell you key: cord-267574-etnjo4nz authors: zhao, shi; zhuang, zian; ran, jinjun; lin, jiaer; yang, guangpu; yang, lin; he, daihai title: the association between domestic train transportation and novel coronavirus (2019-ncov) outbreak in china from 2019 to 2020: a data-driven correlational report date: 2020-02-29 journal: travel medicine and infectious disease doi: 10.1016/j.tmaid.2020.101568 sha: doc_id: 267574 cord_uid: etnjo4nz nan travel medicine and infectious disease journal homepage: www.elsevier.com/locate/tmaid the association between domestic train transportation and novel coronavirus (2019-ncov) outbreak in china from 2019 to 2020: a data-driven correlational report the atypical pneumonia case, caused by a novel coronavirus (2019-ncov), was first identified and reported in wuhan, china in december, 2019 [1] . as of january 21, 2020 (11:59 a.m., gmt+8), there have been 215 cases of 2019-ncov infections confirmed in mainland china. there were 198 domestic cases in wuhan including 4 deaths, and 17 cases identified outside wuhan including 8 in shenzhen, 5 in beijing, 2 in shanghai and 2 in other places. the 2019-ncov cases were also reported in thailand, japan and republic of korea, and all these cases were exported from wuhan china, see who news release https://www.who.int/csr/don/en/from january 14-20, 2020. the first case outside wuhan was confirmed in shenzhen on january 3, 2020. then, many major chinese cities reported events of 'imported 2019-ncov cases', thereafter, including beijing and shanghai. the outbreak is still on-going. and a recently published preprint by imai et al. estimated that a total of 1723 (95%ci: 427-4471) cases of 2019-ncov infections in wuhan had onset of symptoms by january 12, 2020 [2] . inspired by ref. [3] , which indicated the likelihood of travel related risks of 2019-ncov spreading, we suspected the spread of infections could be associated with the domestic transportations in mainland china. thus, we examine and explore the association between load of domestic passengers from wuhan and the number of 2019-ncov cases confirmed in different cities. the daily numbers of domestic passengers by means of transportation, i.e., car (road), train and flight, were obtained from the location-based services database of tencent company from january 2016 to june 2019, see https://heat.qq.com/document. php (in chinese). we calculated the daily average number of passengers from wuhan to six selected major cities, including beijing, shanghai, guangzhou, shenzhen, chengdu and chongqing, from december 16 to january 15 of the next year. the location of the selected six major cities are shown in fig. 1(a) . since the most recent transportation dataset, i.e., 2019-20, was not yet available, we used the data of the same period in the past three years, i.e., 2016-19, as the proxy in the analysis. the association can be constructed as in eqn (1). here, the function e(•) is the expectation. the 'period' is a dummy variable accounting for the difference in the passenger loads in the different periods of time. thus, the α represents the effect of different period, which accounts for a period-varying interception term. the β is the regression coefficient to quantify the association. the 'passenger' is the daily number of domestic passengers, and it is in logarithm form with base of 10 in the regression model. hence, the β can be interpreted as the number of imported 2019-ncov cases associated with 10-fold increase in the daily number of passengers in average. we estimated and tested the βs for three means of transportation, i.e., car, train and flight. the p-value less than 0.05 is considered as statistical significance. we found strong and significant association between travel by train and the number of 2019-ncov cases, whereas the associations of the other two means of transportation failed to reach statistical significance, see table 1 . we estimated that 10-fold increase in the number of train passengers from wuhan is likely to associated with 8.27, 95%ci: (0.35, 16.18), increase in the number of imported cases, see fig. 1(b) . as for sensitivity analysis, by slightly varying the time period of the transportation data, currently it is from december 16 to january 15 of the next year, this association still holds strongly and significantly. we remark that the estimates of β could be different as the 2019-ncov outbreak situation updating, e.g., more reports on the imported cases in other cities, but the statistical significance of this relationship is unlikely to vary. although this is a data-driven analysis, our findings suggest that disease control and prevention measures are preferred in the travelling procedure by trains. we remark that the analysis was conducted based on the epidemic data at early outbreak, and further investigation can be improved from more detailed datasets. fig. 1 . the map of major cities with imported ncov cases and the its regression fitting results against train transportation. panel (a) shows the locations of the major cities with ncov cases as of january 20, 2020. the red star represents beijing, gold diamond represents wuhan, which is believed to be the source of ncov, and shanghai, guangzhou, shenzhen, chengdu and chongqing are indicated by the green circles. the blue curves are the yellow river (upper) and yangtze river (lower). panel (b) shows the daily number of passengers by train versus the total number of imported ncov cases in each city. the observed data are in blue, the fitted regression model is the red line, and the 95%ci is shown as the red dashed line. (for interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) table 1 the summary table of the estimated association between transportation and number of imported ncov cases. the interpretation of the regression coefficient ('coeff.') is the number of imported ncov cases associated with 10-fold increase in daily number of passengers in average. this work was not funded. the funding agencies had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; or decision to submit the manuscript for publication. emergencies preparedness, response, disease outbreak news estimating the potential total number of novel coronavirus (2019-ncov) cases in wuhan city, china. preprint published by the imperial college london pneumonia of unknown etiology in wuhan, china: potential for international spread via commercial air travel the authors would like to acknowledge anonymous colleagues for helpful comments. all authors conceived the study, carried out the analysis, discussed the results, drafted the first manuscript, critically read and revised the manuscript, and gave final approval for publication. the authors declared no competing interests. key: cord-344423-jhdfscyw authors: lian, xinbo; huang, jianping; huang, rujin; liu, chuwei; wang, lina; zhang, tinghan title: impact of city lockdown on the air quality of covid-19-hit of wuhan city date: 2020-06-30 journal: sci total environ doi: 10.1016/j.scitotenv.2020.140556 sha: doc_id: 344423 cord_uid: jhdfscyw abstract a series of strict lockdown measures were implemented in the areas of china worst affected by coronavirus disease 19, including wuhan, to prevent the disease spreading. the lockdown had a substantial environmental impact, because traffic pollution and industrial emissions are important factors affecting air quality and public health in the region. after the lockdown, the average monthly air quality index (aqi) in wuhan was 59.7, which is 33.9% lower than that before the lockdown (january 23, 2020) and 47.5% lower than that during the corresponding period (113.6) from 2015 to 2019. compared with the conditions before the lockdown, fine particulate matter (pm2.5) decreased by 36.9% and remained the main pollutant. nitrogen dioxide (no2) showed the largest decrease of approximately 53.3%, and ozone (o3) increased by 116.6%. the proportions of fixed-source emissions and transported external-source emissions in this area increased. after the lockdown, o3 pollution was highly negatively correlated with the no2 concentration, and the radiation increase caused by the pm2.5 reduction was not the main reason for the increase in o3. this indicates that the generation of secondary pollutants is influenced by multiple factors and is not only governed by emission reduction. j o u r n a l p r e -p r o o f recently, a new type of coronavirus has caused mass viral pneumonia , thus posing a major threat to international health . at present, the epidemic constitutes a public health emergency of international concern (who, 2020). since the middle of december 2019, a number of family clustering outbreaks and transmission from patients to health-care workers have occurred, which shows that human-to-human transmission has happened through close contact . most countries have imposed city lockdown and quarantine measures to reduce transmission to control the epidemic. the chinese health authorities have made considerable efforts, including the positive detection of cases and retrospective investigation of patient clusters. public risk communication activities have been performed to improve public awareness of self-protection (hui, 2020) . the chinese government has gradually implemented a strict lockdown on wuhan and surrounding cities as of january 23. some processing and light industries have been shut down, and the catering and entertainment industries have temporarily closed, and flights, trains and public transport have been suspended . in addition to reducing the spread of the disease, the lockdown measures may also have additional health benefits. after the lockdown of city traffic, personnel flow control became the most important aspect. traffic pollution produces nitrogen monoxide (no), carbon monoxide (co), carbon dioxide (co 2 ), diesel-exhaust particles, and ozone (o 3 ), nitrogen dioxide (no 2 ), secondary aerosols formed through physical and chemical processes, and pollutants that arise from brake wear, tire wear and re-suspended particles (e.g., trace metals) j o u r n a l p r e -p r o o f 4 (beckerman, 2008 , guo, 2020 . there was a notable association between traffic-related air pollution and premature mortality, and the risk of respiratory and cardiovascular diseases increased in residents living close to high-traffic pollution areas (brugge, 2007 , im, 2019 . reducing the emissions from motor vehicles, especially trucks and buses, could produce considerable health benefits (kheirbek, 2016) . a survey of hospital visits in busan city before and after the asian games shows that the traffic flow control over 14 consecutive days is associated with a significant decline in the hospitalization rate of children with asthma (lee, 2007) . in addition, the reduction in industrial activities after the lockdown also imposes certain environmental and health effects. for example, oil shale mining and power generation processes discharge excessive sulphur dioxide (so 2 ), particulate matter (pm 10 ) and nitrogen oxides (no x ), as well as various other industrial pollutants, such as benzene and phenol, and trace elements (saurabh, 2016) .the spatial lag model with fixed effects demonstrates that industrial air pollution causes an increase in medical expenses (zeng, 2019) . compared to nonindustrial areas, the residents of industrial areas more frequently reported wheezing, chest tightness, shortness of breath, hypertension, heart diseases, etc (orru, 2018) . wuhan is the transportation and trade center of central china, a megacity and national central city of china, with a well-developed transportation system and a large number of motor vehicles. due to the lack of central heating and chemical industry, in addition to the emissions from coal-fired enterprises such as power plants and the pollution transported from surrounding rural biomass burning activities, vehicle emissions are responsible for the most important pollution source affecting the air quality and public health in wuhan (daoru liu, j o u r n a l p r e -p r o o f 5 2020). wang et al. found that regional traffic has a significant impact on the formation of haze in wuhan, and the main potential pollution sources are located in the north and south of wuhan (si wang, 2017) . liao et al. found that the increase in secondary organics (nh 4 ) 2 so 4 and nh 4 no 3 caused by vehicle exhaust and coal burning as well as the increased environmental moisture absorption were the main causes of pollution in wuhan (liao weijie, 2020). in this report, we studied the change in air quality one month before and after the lockdown in wuhan and compared it to that during corresponding periods. we analyzed the real-time concentrations of the six air pollutants monitored by the state control station, including fine particulate matter (pm 2.5 ), pm 10 , so 2 , no 2 , co, and o 3 , and compared the effects of the lockdown on the concentrations of the different pollutants. we studied the changes in pm 2.5 , no 2 , and o 3 in hubei province one month before and after the closure of major cities severely affected by the epidemic and to further analyze the impact of human activities and the lockdown on atmospheric pollutant concentrations. the daily aqi data of wuhan, from 1 january 2016 to 31 february 2020, were provided by the wuhan ecology and environment bureau (http://hbj.wh.gov.cn/). the ground observation daily data of hubei province were provided by the china national environmental monitoring centre (http://www.cnemc.cn/). considering the retention of air pollutants, the data from 24 january 2020, to 23 february 2020, are selected as the representative data after j o u r n a l p r e -p r o o f 6 the lockdown, and the data from 24 december 2019, to 23 january 2020, are selected as the representative data before the lockdown. the historical data for the sake of comparison during the same period is from 24 january to 23 february, 2015-2020, which includes the yearly chinese spring festival holiday. all monitoring instruments of the wuhan air quality automatic monitoring system operate automatically 24 h a day. the monitoring items are pm 2.5 , pm 10 , so 2 , no 2 , co and o 3 . the automatic monitoring of pm 2.5 and pm 10 adopts the micro-oscillating balance method and the β-absorption method, respectively (ambient air quality standards, gb 3095-2012), and their measuring instruments are a tapered element oscillating microbalance (teom) (rupprecht & patashnick co, usa) and a bam 1020 (met one instrument, usa), respectively. so 2 , no 2 , co and o 3 were measured by instruments of tei-43i, tei-42i, tei-48i and tei-49i (thermo fisher scientific, usa), respectively. the experimental methods are as follows the ultraviolet fluorescence method (so 2 ), the chemiluminescence method (no 2 ), the nondispersion infrared absorption method and gas filter correlation infrared absorption method (co), and the uv-spectrophotometry (o 3 ). the average air quality index (aqi) is a dimensionless index, which is calculated according to the chinese ambient air quality standard (g b3095-2012) and includes six pollutants in the calculation, i.e., so 2 , no 2 , pm 10 , pm 2.5 , o 3 and co. the subindex of each pollutant is first calculated according to the fractional concentration and is labeled iaqi p . in equation (1), iaqip is the air quality subindex of pollutant p; c p is the mass concentration of pollutant p; bp hi is the upper limit value of the pollutant concentration close (1) j o u r n a l p r e -p r o o f 7 to c p in table 1 ; bp lo is the lower limit value of the pollutant concentration close to c p in table 1 ; iaqi hi is the air quality subindex corresponding to bp hi in table 1 ; and iaqi lo is the air quality subindex corresponding to bp lo in table 1 . when the aqi is higher than 50, the pollutants with the highest air quality subindex are the primary pollutants. if there are two or more pollutants with the highest air quality subindex, they are listed as the primary pollutants. in addition, the pollutants with an iaqi higher than 100 are overstandard pollutants. a high aqi indicates that serious and concentrated air pollution will not only affect the outdoor activities of humans but also damage their health. the main administrative regions of wuhan are relatively concentrated and the population difference is notable, the population density decreases from the central regions to the peripheral regions ( fig. 1a) . after the lockdown, the aqi in the different administrative regions in wuhan decreased, of which the air quality at wujiashan station and qiaokou gutian station exhibited the most notable improvement (decreasing 37.4% and 37.3%, respectively), while xinzhou district station attained the smallest decrease of 15.5%. the results show that the aqi improvement rate increased with the increase in population density ( fig. 1b) . the average aqi improvement rate in districts with a population density of less than 5,000 was 25.7%, whereas that in areas with a population density of more than 20,000 was 34.9%. this difference was due to the frequent traffic congestion in populated areas j o u r n a l p r e -p r o o f 8 before the blockade, leading to additional emissions of exhaust gas. the wear and tear of roads, tires, and brakes caused by congestion are also sources of particulate matter (han, 2019) . furthermore, the high density of buildings reduces the wind speed and the diffusion of air pollution . after lockdown, of the nine state-controlled monitoring sites (excluding the background station), hanyang yuehu station had the lowest aqi (54.1) because the site is far from the city's main roads and industrial areas. qingshan ganghua station had the highest aqi (73.2) because it is close to wuhan iron and steel corporation. studies have shown that the contribution rate of pm 2.5 from steel industry pollution sources in wuhan in winter is second only to traffic sources, up to 30.8% (huang, 2019) . therefore, the high aqi of the site during the implementation of government intervention measures may be mainly influenced by heavy industry sources. 3.2. a comparison of the aqi from 2020 with that in 2015-2019 for the same period and before the control. we selected the period december 24, 2019 to january 23, 2020 as the period before the lockdown, and compared this period with the historical corresponding periods of january 24 to february 23 from 2015 to 2019. after the lockdown, the average aqi in wuhan was 59.7, a decrease of 47.5% compared to that during the corresponding period from 2015-2019 (fig. 2a ). compared with before the lockdown, the average aqi decreased by 33.9%, and the differences among monitoring sites also decreased significantly (fig. 2b) . the rate of days j o u r n a l p r e -p r o o f 9 with an aqi <100 was 96.8%, of which 41.9% had an aqi < 50, without moderately and severely polluted days. compared with the corresponding periods, the rate of good days (aqi < 100) increased by 37.4%, which means that during the lockdown, the air quality in wuhan had no significant effect on human health, and only some pollutants may have had a weak impact on the health of a small number of unusually sensitive people. among the 18 pollution days, pm 2.5 was the primary pollutant on 16 days (88.9%), pm 10 and o 3 were the primary pollutants on 1 day (5.6%). on the lightly polluted day (february 5), pm 2.5 and pm 10 both increased considerably. therefore, after the lockdown, the most important influencing factor of the aqi is pm 2.5 in wuhan. the proportion of days with an iaqi pm2.5 < 100 increased substantially, with three stations reaching 100%. this is due to reductions in vehicle emissions and the closure of some industrial plants during government controls, which caused black carbon, organic components, sulphate particulate matter and important precursors such as so 2 , no x and hydrocarbons (ch x ) to be reduced to some extent (richmond-bryant, 2009 ), (daellenbach, 2016) . after the lockdown, the rise of o 3 led to the first polluted day in winter in wuhan with o 3 as the major pollutant since 2015. there were no days with no 2 as the main pollutant during the control, which was a significant improvement compared with the historical period from 2015 -2019 and before the control period. 3.3. the evolution of the pollutant concentration during the lockdown. compared with the average concentration during the historical 2019 period and before the lockdown, the pm 10 , pm 2.5 , so 2 , no 2 , and co concentrations all decreased to some extent, whereas the o 3 concentration increased greatly during the lockdown (fig. 3) . the spatial differences in the pollutant concentrations were small. due to the reduction in fugitive dust caused by the reduction in vehicles and the stoppage of construction after the lockdown, pm 10 decreased by 40.2% compared to before the lockdown. the monthly average pm 2.5 /pm 10 ratio was 0.9, so pm 2.5 was the main particle pollutant that decreased by 36.86% (aldabe, 2011) . no 2 exhibited the most notable improvement, with an average concentration reduction of approximately 53.3%, due to no 2 is highly correlated with traffic pollution. according to the transportation index data, the decrease in national traffic volume was estimated to be 70% during the lockdown (xin .o 3 is an important secondary pollutant in warm months but is generally less important in winter. compared with the conditions before the control measures, the o 3 concentration increased by approximately 116.6%. this may be related to the change in the primary pollutant concentration and meteorological conditions. in addition, o 3 lasts longer in cold weather, which may contribute to its accumulation . the smaller decrease in so 2 of only 3.9% may be related to the increase in domestic heating and cooking during the lockdown period. compared with the summer of 2019, the so 2 concentration only increased by approximately 0.6 μg/m 3 . this shows that the so 2 emissions in wuhan mainly come from power plant emissions and industrial and domestic coal combustion, and the correlations with traffic and heating were low. co is a product of domestic combustion and power generation. the average co j o u r n a l p r e -p r o o f 11 concentration was 0.9 mg/m 3 (down 22.7%), and the decrease in co varied greatly among different sites, from 3.2% to 34.5%. 3.4. the diurnal variation in the pm 2.5 , no 2 and o 3 concentrations. the average daily variation data for 1 month before and after the blockade were selected to analyze pm 2.5 , no 2 , and o 3 . because pm 2.5 comes from complex sources and the generation of secondary aerosols is affected by a variety of factors, the average daily variation range of pm 2.5 is small and highly discrete. the daily variation trend in pm 2.5 after the lockdown was similar to that before, although the range of variation increased and a significant decrease occurred at 18:00, which was attributed to the vertical expansion of the boundary layer and the vertical diffusion of pollutants during the day. (shi, 2020) (fig. 4a) . the concentration of no 2 prior to the lockdown showed a peak in the morning and during evening traffic hours (8-11 a.m. and 6-9 p.m., respectively). however, during the lockdown, no 2 did not exhibit peaks associated with morning rush hours, further indicating that traffic was not a major source of no 2 during this period (fig. 4b) . before the lockdown, the diurnal peaks in o 3 occurred at 7:00 and from 15:00. after the lockdown, the range of the daily variation increased considerably. only the peak from 15:00 was retained and some deviation occurred. in contrast to the control before the lockdown, o 3 showed a downward trend from 00:00 to 10:00, which may be related to the decrease in no 2 in the peak morning period. when o 3 reached its maximum value, no 2 and pm 2.5 decreased to the minimum values. this was probably due to the photolysis consumption of no 2 and the attenuation of solar radiation j o u r n a l p r e -p r o o f 12 caused by the reduction of pm 2.5 accelerating the formation of o 3 . (ma, 2019) (fig. 4c) . in the actual atmosphere, the o 3 concentration is also affected by meteorological elements and important precursors such as volatile organic compounds (vocs) and co. when the voc concentration and no x ratio are unbalanced, this will also affect the steady-state cycle (chung, 1996) . in the atmosphere, [no 2 ]/[so 2 ] is often adopted to indicate the change in the contribution rates of mobile and fixed emission sources. studies have reported that the so 2 emissions from motor vehicles in northern china is far lower than the nox emissions, and the emission ratio of [no 2 ]/[so 2 ] from motor vehicles ranged from 24 to 119 (fiedler et al., 2009 ). both no x and so 2 are discharged from stationary sources, with relatively more so 2 . the ratio of [no 2 ]/[so 2 ] from stationary sources ranged from 0.2 to 0.8 (fiedler et al., 2009) . after the lockdown, [no 2 ]/[so 2 ] decreased significantly (p < 0.01), and the contribution rate of fixed sources increased (factories, power plants, chimneys and boilers, etc.), while the contribution rate of mobile sources decreased, which was consistent with the reduction in vehicle emissions (fig. 5a) can be adopted to roughly evaluate the impact and contribution of local pollutant discharge and external pollutant transportation on the pollution process, with higher ratios indicating higher local contributions (tang, 2015) . after the lockdown, [co]/[so 2 ] decreased significantly (p < 0.01) in wuhan, which indicated that the contribution rate of local emissions decreased, and the air pollution in local areas was affected by surrounding or remote sources (fig. 5b) . the transport pathways in wuhan were identified to be the northwest, east and south pathways (with relative contribution rates of 40%, 17% and 43%, respectively), and the major potential source regions were western henan, northern shanxi and southwestern shanxi (huang, 2019) . 3.6. the air quality improvement in hubei province during the lockdown period. as shown in fig. 6 , 12 cities in hubei province were selected for analysis. after the lockdown, the average monthly pm 2.5 concentration in each city ranged from 31.2 μg/m 3 (xianning) to 64.6 μg/m 3 (xiangyang). according to the chinese ambient air quality standards (caaqs) (gb3095-2012), the average monthly iaqi pm2.5 in xianning city was 44, thus reaching good level, and the average monthly iaqi pm2.5 values in the other 11 cities were moderate. the reason for the high pm 2.5 concentration in xiangyang may be that the area has a large population, and the area of cultivated land ranks first in hubei province, which generates more agricultural pollution (ammonia-nitrogen fertilizers) (wu, 2016) . the improvement rate of no 2 is substantially higher than other pollutants, with an average concentration range of 8.1 μg/m 3 (xianning) -21.4 μg/m 3 (wuhan) after the lockdown. the j o u r n a l p r e -p r o o f 14 average concentration range of o 3 was 73.0 μg/m 3 (xianning) -88.2 μg/m 3 (jingmen), which was much higher than that before the lockdown, and it did not exceed the air quality standards in terms of potentially harming human health. the improvement rates of the aqi and pm 2.5 are lowest, 23.7% and 28.6%, respectively, when the population density ranged from 400-800 person/km 2 . the population density of wuhan reached 1,304.6 person/km 2 , and the improvement rate was significantly higher than that in the other cities except yichang and xianning. the transportation industry in yichang and xianning is relatively well developed, and the passenger traffic volume was larger than 50 million in 2018 in xianning (statistics., 2020). the restrictions on vehicles during the control period may be the main reasons for the high improvement rate of pm 2.5 in the two regions. (khalil, 1988) . after the lockdown, the decline in co was far lower than 50%, and there was no clear trend of daily co change, which shows that after the lockdown, the co emissions from industrial boiler fuel and domestic coal combustion in the wuhan area j o u r n a l p r e -p r o o f 15 account for a large proportion. the main source of gaseous so 2 is the combustion of sulfur-containing fuels (oil, coal and diesel) . after the control period, the so 2 improvement was not distinct. on the one hand, many coal-fired industries were not shut down, mainly due to the effectiveness of pollution control in recent years. compared to 2015, the so 2 concentration decreased 20.5 μg/m 3 , which is due to the upgrading of key industrial industries (power and steel), especially the role of the ultralow emissions of electric power generation, elimination of small and medium-sized coal-fired boilers, conversion of rural heating from coal to gas and electricity and other policies in recent years. the drop in pm 2.5 and pm 10 after the lockdown was not as major as expected, which may be related to a number of factors. first, after the lockdown, the most intensive control concerned traffic, and traffic pollution is not the most important source of pm 2.5 in wuhan (zong, 2020) . second, since the implementation of the national policy on smog governance, the fine particulate emissions in china have been effectively controlled, especially in areas where central heating is generally not provided, such as central and southern china . since 2013, the national average annual concentration of pm 2.5 has dropped substantially, and the number of heavily polluted days has decreased drastically, especially in autumn and winter (ministry, 2020b). third, due to the epidemic control period and the return of migrant workers, the proportion of bulk coal heating users has increased, which may also have mitigated some of the reductions in pm 2.5 , no x and so 2 due to the decreased vehicle emissions (ministry, 2020a) . recently studies have shown that the formation of secondary particles significantly enhanced during the lockdown (xin huang, 2020). in the j o u r n a l p r e -p r o o f 16 early stage, wuhan coal combustion was the main source of no x (41.0% ± 13.7%), and motor vehicle emissions were the second main source (21.8%) from 2013 to 2014 (zong, 2020) . after the implementation of emission standards of coal-fired power plants, multiple technical improvements such as scr, sncr, etc, greatly decreased the no 2 emissions from coal-fired sources, which further led to the most notable improvement in no 2 after the traffic control due to the increasing of the proportion of no 2 traffic source emissions. at present, o 3 pollution has occurred in most parts of china in summer and tends to be a complex type of air pollution (pm 2.5 pollution in winter and o 3 pollution in summer). this study shows that the o 3 concentration may also become a major pollutant in winter, requiring further analysis of the reasons for its rise to avoid more serious o 3 pollution in winter. after the lockdown, the no x control effect is very distinct; however, the effectiveness of the voc control measures needs to be further studied. a change in no x to voc ratio may also lead to an increase in o 3 generation (owoade, 2015) . the transformation and connection between pollutants in terms of the quality and quantity are very complicated. although no x is one of the precursors of o 3 , no x reduction has a negative effect on the o 3 concentration. therefore, the generation of secondary pollutants is affected by multiple factors, and its governance is not only related to emission reductions. meteorological elements play significant roles in air pollution formation, transport, deposition and transformation. the relatively low relative humidity and wind speed in winter are conducive to the generation and resuspension of dust, and the height of the boundary layer is low, while precipitation is low, which is conducive to the accumulation of secondary j o u r n a l p r e -p r o o f sulfate and nitrate (miao, 2018) . in wuhan, the formation of o 3 at the urban site is controlled by voc s , while the formation of o 3 at the urban site is controlled by voc s and no . voc s is greatly affected by pollution sources, photochemical reaction processes and regional transportation . a recent study by wang et al suggested that meteorological conditions in most chinese cities caused an increase in pollutants that outweighed the positive impact of emission reductions during covid-19 outbreak, but for wuhan, unfavorable meteorology had less effect compared with emission changes . however, the reason for the increase in o 3 needs to be combined with meteorological conditions of photochemical production for further research. our results show that the air quality in hubei province and wuhan improved significantly during the covid-19 lockdown, with concentrations of all six standard pollutants, except o 3 , dropping to some extent with the largest decrease in no 2 . the significant increase in the o 3 concentration may be related to the changes in no 2 , voc s , and pm 2.5 , and the reaction mechanism should be studied further in combination with meteorological elements and the photochemical mechanism. air pollution is a complex problem linked to multiple factors. the reduction in pollutant discharge will improve air quality, but it may also bring new problems. the generation mechanism of secondary pollutants should be investigated to provide a more comprehensive scientific basis for formulating pollution prevention and control policies. dr. jianping huang(hjp@lzu.edu.cn)and dr. rujin huang are co-corresponding author. chemical characterisation and source apportionment of pm 2.5 and pm 10 at rural, urban and traffic sites in navarra (north of spain) correlation of nitrogen dioxide with other traffic pollutants near a major expressway near-highway pollutants in motor vehicle exhaust: a review of epidemiologic evidence of cardiac and pulmonary health risks development of ozone-precursor relationships using voc receptor modeling characterization and source apportionment of organic aerosol using offline aerosol mass spectrometry variation trends and principal component analysis of nitrogen oxide emissions from motor vehicles in wuhan city from east asian so 2 pollution plume over europe &ndash; part 1: airborne trace gas measurements and source identification by particle dispersion model simulations remarkable nucleation and growth of ultrafine particles from vehicular exhaust impact of population density on pm 2.5 concentrations: a case study in shanghai clinical features of patients infected with 2019 novel coronavirus in wuhan shuiping chemical characteristics and source apportionment of pm2.5 in wuhan use of a mm5-camx-psat modeling system to study so2source apportionment in the beijing metropolitan region alimuddin petersen, eskild. the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan contributions of nordic anthropogenic emissions on air pollution and premature mortality over the nordic region and the arctic analysis of heavy pollution episodes in selected cities of northern china carbon monoxide in an urban environment: application of a receptor model for source apportionment the contribution of motor vehicle emissions to ambient fine particulate matter public health impacts in new york city: a health burden assessment benefits of mitigated ambient air quality due to transportation control on childhood asthma hospitalization during the 2002 summer asian games in busan characterization of aerosol chemical composition and the reconstruction of light extinction coefficients during winter in wuhan, china the effect of natural and anthropogenic factors on haze pollution in chinese cities: a spatial econometrics approach air pollution characteristics and their relationship with emissions and meteorology in the yangtze river delta region during 2014-2016 impacts of meteorological conditions on wintertime pm2.5 pollution in taiyuan civil coal treatment is still the key direction of the beijing-tianjin-hebei region and its surrounding areas. 2020a. ministry of ecology and environment of the people's republic of china. regional air quality has improved significantly, but air pollution control still has a long way to go aavo tomasova, jelena. residents' self-reported health effects and annoyance in relation to air pollution exposure in an industrial area in eastern-estonia chemical compositions and source identification of particulate matter (pm 2.5 and pm 2.5-10 ) from a scrap iron and steel smelting industry along the ife-ibadan highway associations of pm2.5 and black carbon concentrations with traffic, idling, background pollution, and meteorology during school dismissals identifying the sources of primary air pollutants and their impact on environmental health: a review the response in air quality to the reduction of chinese economic activities during the covid-19 outbreak weiping liu， xianjue zheng. characteristics and origins of air pollutants in wuhan, china, based on observations and hybrid receptor models impact of emission controls on air quality in beijing during apec 2014: lidar ceilometer observations severe air pollution events not avoided by reduced anthropogenic activities during covid-19 outbreak severe air pollution events not avoided by reduced anthropogenic activities during covid-19 outbreak statement on the second meeting of the international health regulations (2005) emergency committee regarding the outbreak of novel coronavirus nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study pm 2.5 pollution is substantially affected by ammonia emissions in china qiang zhang, kebin he. enhanced secondary pollution offset reduction of primary emissions during covid-19 lockdown in china does industrial air pollution drive health care expenditures? spatial evidence from china potential sources of nitrous acid (hono) and their impacts on ozone: a wrf-chem study in a polluted subtropical region a pneumonia outbreak associated with a new coronavirus of probable bat origin o3 photochemistry on o3 episode days and non-o3 episode days in wuhan, central china dual-modelling-based source apportionment of nox in five chinese megacities: providing the isotopic footprint from this work was jointly supported by the national science foundation of china (41305009 and 41405010) and the china university research talents recruitment program (111 project, no. b13045). the authors acknowledge the wuhan bureau of ecology and environment for providing the datasets. http://hbj.wuhan.gov.cn/.author contributions x. l . and j. h. are first co-author. j. h. and r. h. designed the study and contributed to the ideas, interpretation and manuscript writing. x. l. l.w.and t.z. contributed to the data analysis, interpretation and manuscript writing. all of the authors contributed to the data analysis, key: cord-352030-hnm54k4r authors: liu, jie; ouyang, liu; guo, pi; wu, hai sheng; fu, peng; chen, yu liang; yang, dan; han, xiao yu; cao, yu kun; alwalid, osamah; tao, juan; peng, shu yi; shi, he shui; yang, fan; zheng, chuan sheng title: epidemiological, clinical characteristics and outcome of medical staff infected with covid-19 in wuhan, china: a retrospective case series analysis date: 2020-03-13 journal: nan doi: 10.1101/2020.03.09.20033118 sha: doc_id: 352030 cord_uid: hnm54k4r backgrounds since december 2019, a novel coronavirus epidemic has emerged in wuhan city, china and then rapidly spread to other areas. as of 20 feb 2020, a total of 2,055 medical staff confirmed with coronavirus disease 2019 (covid-19) caused by sars-cov-2 in china had been reported. we sought to explore the epidemiological, clinical characteristics and prognosis of novel coronavirus-infected medical staff. methods in this retrospective study, 64 confirmed cases of novel coronavirus-infected medical staff admitted to union hospital, wuhan between 16 jan, 2020 to 15 feb, 2020 were included. two groups concerned were extracted from the subjects based on duration of symptoms: group 1 (<= 10 days) and group 2 (>10 days). epidemiological and clinical data were analyzed and compared across groups. the kaplan-meier plot was used to inspect the change in hospital discharge rate. the cox regression model was utilized to identify factors associated with hospital discharge. findings the median age of medical staff included was 35 years old. 64% were female and 67% were nurses. none had an exposure to huanan seafood wholesale market or wildlife. a small proportion of the cohort had contact with specimens (5%) as well as patients in fever clinics (8%) and isolation wards (5%). fever (67%) was the most common symptom, followed by cough (47%) and fatigue (34%). the median time interval between symptoms onset and admission was 8.5 days. on admission, 80% of medical staff showed abnormal il-6 levels and 34% had lymphocytopenia. chest ct mainly manifested as bilateral (61%), subpleural (80%) and ground-glass (52%) opacities. during the study period, no patients was transferred to intensive care unit or died, and 34 (53%) had been discharged. higher body mass index (bmi) (hr 0.14; 95% ci 0.03-0.73), fever (hr 0.24; 95% ci 0.09-0.60) and higher levels of il-6 on admission (hr 0.31; 95% ci 0.11-0.87) were unfavorable factors for discharge. interpretation in this study, medical staff infected with covid-19 have relatively milder symptoms and favorable clinical course, which may be partly due to their medical expertise, younger age and less underlying diseases. smaller bmi, absence of fever symptoms and normal il-6 levels on admission are favorable for discharge for medical staff. further studies should be devoted to identifying the exact patterns of sars-cov-2 infection among medical staff. in december, 2019, a group of novel atypical pneumonia patients with uncertain etiology but mostly linked to the huanan seafood wholesale market emerged in wuhan, china [1] . a later confirmed pathogen of this previously unknown pneumonia was described as a novel coronavirus, currently named as severe acute respiratory syndrome coronavirus 2 (sars-cov-2; previously known as 2019ncov), was ascertained by unbiased sequencing analysis of lower respiratory tract samples from early cases on 7 jan 2020, following which the protocol of real-time reverse-transcriptase polymerase chain reaction (rt-pcr) assay for this novel coronavirus had also been developed [2] [3] [4] [5] [6] [7] . in fact, the epidemics of the two other novel coronaviruses, namely severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov), have posed a huge threat to public health in the past two decades [8, 9] . sars-cov-2 in this outbreak, like the previous two viruses, is also categorized within the same genus of the subfamily orthocoronavirinae within the family coronaviridae, but shows a strong affinity for human respiratory receptors [10, 11] . by 11 feb 2020, coronavirus disease 2019 (covid19) due to the sars-cov-2 has caused more than 40,000 laboratory confirmed cases and 1,023 deaths among them in china [12] . sufficient evidence indicated that the covid-19 clustered within close-contact human groups, such as family and hospital settings [13] [14] [15] [16] [17] . the sars-cov-2 epidemic has transmitted throughout china and to other countries due to massive population movements before the lunar new year [14] , and consequently escalated as a public health emergency of international concern declared by world health organization (who) [18] . as of 4 mar 2020, more than 90,000 confirmed cases infected with sars-cov-2 have been identified globally [19] . information pointing to the epidemiology and clinical features of general confirmed cases has been accumulating. the previous studies enrolling 41, 99 and 138 confirmed cases admitted to wuhan, respectively, provided an insight into epidemiological characteristics, clinical manifestations, treatment measures and clinical outcomes of these patients [1, 20, 21] . in particular, a recent study in zhejiang province, china indicated that the symptoms of patients outside of wuhan perhaps are relatively mild versus symptoms of initial cases in wuhan [10] . meanwhile, a new finding from a national wide descriptive report drew a huge amount of attention, which declared that the total number of confirmed novel coronavirus-infected medical staff was as high 1,716 as of 11 february 2020, with a peak incidence occurring on 28 january 2020 [12] . hospital-related transmission are one of the causes for infection of health-care workers [21] , especially in the early stages of covid-19 epidemic when there was a lack of knowledge about transmission approaches of sars-cov-2, as well as in the period when facing a shortage of protective materials. nonetheless, the predominant cause of the infection and the failure of protection among health workers remains to be investigated [12] . despite the increased attention towards protecting medical staff from infection, information regarding the epidemiology and clinical features of medical staff confirmed with covid-19 is scarce. this single-centered, retrospective study aimed to describe epidemiological, clinical, laboratory and radiographic features, treatment, and prognosis of a group of medical staff confirmed with covid-19 who were admitted to union hospital, wuhan. we hope the findings in the present study will provide an insight into the prevention and treatment of this novel coronavirus for the global community. we performed a single-centered, retrospective study on a group of novel coronavirus-infected medical staff at wuhan union hospital, one of the hospitals treating patients confirmed with covid-19 at the earliest time. diagnosis of . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint cases with sars-cov-2 infection conforms to the who interim guidance [7] . details regarding laboratory confirmation protocol for sars-cov-2 were described by previous studies [1, 21] . throat-swab specimens were screened for sars-cov-2 and other respiratory viruses (influenza, respiratory syncytial virus, etc.) by real-time rt-pcr assays. a total 64 medical staff, who were confirmed by sars-cov-2 real-time rt-pcr test on respiratory secretions collected by throat swab and undergone serial chest ct scans following their admission to isolation wards of union hospital between 16 jan and 15 feb, 2020, were enrolled. this retrospective study was approved by the ethics of committees of union hospital, tongji medical college, huazhong university of science and technology. written informed consent was waived due to the rapid emergence of this infectious disease. the epidemiological data, medical and nursing records, laboratory examinations, chest computed tomography (ct) of all patients were reviewed and abstracted with concerted efforts of experienced clinicians. data were collected at the time of symptoms onset, presentation for medical advice and in-patient admission. the clinicians who had experience of treating patients with confirmed sars-cov-2 infection reviewed and collected the medical records of patients, and preliminarily collated the data. the clinical data were extracted through a standardized form for case report as previously described [23] . epidemiological data, including exposure histories before symptoms onset (whether there is a history of exposure to the huanan seafood wholesale market, or wildlife), and close contact with laboratory-confirmed or suspected cases of covid-19 in a work environment (fever clinics, or isolation wards), specimens (pharyngeal swab, blood, sputum specimens, etc.) or family members with covid-19 were collected. in addition, information about preventive medication among medical staff was also collected. we have also collected the data on demographics, clinical manifestations, laboratory . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted march 13, 2020. . examinations and radiological studies. these included age, sex, occupation (doctor, or nurse), body mass index (bmi ≥ 24, or <24 kg/m 2 ), current smoking status (yes, or no), disease severity (non-severe, or severe), date of symptom onset, symptoms before hospital admission (fever, cough, fatigue, sore throat, myalgia, sputum production, difficulty breathing or chest tightness, chill, loss of appetite, diarrhea, and chest pain), coexisting conditions (e.g. hypertension, diabetes, etc.), laboratory testing indicators on admission (leucocyte count, lymphocyte count, platelet count, d-dimer, creatinine, creatine kinase, lactose dehydrogenase, alanine aminotransferase, aspartate aminotransferase, hemoglobin, ferritin, c-reactive protein, amyloid a, total bilirubin, procalcitonin, erythrocyte sedimentation rate, interleukin-6 (il-6) and lymphocyte subsets, etc.), radiologic assessments of chest ct (lung involvement, lung lobe involvement, predominant ct changes, predominant distribution of opacities, etc.), treatment measures (antibiotics agents, antiviral agents, traditional chinese medicine, immune globulin, thymosin, corticosteroids and oxygen therapy), and complications (e.g. pneumonia, acute respiratory distress syndrome, acute cardiac injury, acute kidney injury, shock, etc.). all ct images were analyzed by two radiologists (j.l. and f.y., who had 5 and 21 years of experience in thoracic radiology, respectively) utilizing the institutional digital database system without access to clinical and laboratory findings. images were reviewed independently, and final decisions were reached by discussion and consensus. we estimated the time interval from symptom onset to admission with maximum information available -that is, all the exact date of initial symptoms provided by the patients. then the aggregated data was sent to data analysis group. prior to statistical analysis, the aggregated data were cross -checked by group members to guarantee the correctness and completeness of data. the clinical outcomes and prognosis were continuously observed up to 24 feb 2020. we defined the primary outcomes as discharge. the discharge criteria of inpatients included all the following three conditions [24] : (1) body temperature return to normal for more than 3 days and respiratory symptoms improvement; (2) resolution of lung . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint involvement demonstrated by chest ct; (3) two consecutive rt-rcr tests, with sampling interval of more than 1 day, showing a negative result. secondary outcomes consisted of hospital discharge rate and length of hospital stay. given that treatment and monitoring of some patients in our study were still ongoing, a fixed time-interval of observation was not applied to these clinical outcomes. this study devoted to report the epidemiological, clinical characteristics and prognosis of medical staff confirmed with covid-19. continuous variables were checked for distribution normality by means of the kolmogorov-smirnov test, following which they were summarized as either means with standard deviations (sd) or medians with interquartile ranges (iqr) as appropriate. counts and percentages were utilized to describe categorical variables. given the cut-off point at 10th day of symptoms onset proposed by previous studies [1, 21] , we assigned the patients into either one of two groups based on duration of symptoms: group 1 (≤10 days) and group 2 (>10 days). we applied a kaplan-meier plot to inspect the change of hospital discharge rate. the proportional hazard cox regression model was utilized to ascertain factors associated with hospital discharge. univariate models with a single variable once at a time were first fitted. the statistically significant risk factors as well as age and sex were, then, included into a final multivariate cox regression model. the hazards ratios (hrs) along with the 95% confidence intervals (95% cis) were calculated. statistical tests were two-sided with significance set at α less than 0.05. we performed all data analyses by r software version 3.6.2 (r foundation for statistical computing). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . during the study period, epidemiological and clinical data were collected on 64 medical staff with laboratory-confirmed sars-cov-2 infection from wuhan union hospital, of whom 62 (97%) provided an exact date of symptom onset and only 1 case (2%) was severe. the patients aged between 23 and 63 years old, and median age was 35 years (iqr 29-43 years). the median age in group 1 was 37 years (iqr 32-44 years), and in group 2 it was 30 years (iqr 27-36 years). more than half of the cohort were female (64%) and nurse (67%). there were 7 (11%) overweight cases (bmi ≥ 24 kg/m 2 ) and only 1 was current smoker. among the 64 medical staff recruited, no one had an exposure to huanan seafood wholesale market or wildlife, while 4 (6%) medical staff had family members confirmed with sars-cov-2 infection. during patient care, 5 (8%) and 3 (5%) cases had contact with patients in fever clinics and isolation wards, respectively, and 3 (5%) had direct contact with specimens collected from confirmed patients. 10 (16%) of 64 medical staff have used preventive medications (table 1) . the median duration between symptoms onset and admission was 8. days in group 2. there were 8 (13%) cases, most of whom were assigned to group 1, with one or more co-morbidities: 3 (5%) had hypertension, 2 (3%) had uterine fibroids, and one (2%) each had diabetes, depressive disorder, thyroid nodules or abdominal lymphatic tuberculosis. the three most common symptoms were fever (67%), cough (47%) and fatigue (34%). the relatively less common symptoms were sore throat, myalgia, difficulty breathing or chest tightness, sputum production, headache, chill, loss of appetite, diarrhea, and chest pain (table 1) . table 2 shows the laboratory and radiographic findings of 64 medical staff with confirmed covid-19. on admission, the blood counts of 11 (17%) cases showed leukocytopenia and only one (2%) showed leukocytosis. 22 (34%) presented with . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint lymphocytopenia and 7 (11%) presented thrombocytopenia. most cases demonstrated normal levels of d-dimer, creatinine, and creatine kinase, but elevated c-reactive protein and amyloid a levels were presented in 45% and 59% of cases, respectively. elevated levels of alanine aminotransferase (13%) and aspartate aminotransferase (9%) were less common. a small proportion (3%) of cases had abnormal procalcitonin serum level (>0.5 ug/l). notably, 47 (80%) of cases had high levels of il-6 (>2.9 pg/ml). medical staff of group 1 had more prominent laboratory abnormalities (i.e., leukocytes, lymphocytes, platelet, alanine aminotransferase, amyloid a and il-6) as compared with those in group 2. as evidenced by table 2 of the study participants, no person was transferred to an intensive care unit for mechanical ventilation due to acute respiratory distress syndrome. 9 (14%) patients needed an electrocardiograph monitoring, among whom 8 were in group 1. empirical intravenous antibiotic treatment was administered in 55 (86%) patients. all the patients were given empirical antiviral therapy. meanwhile, 13 (20%) were offered traditional chinese medicine, 23 (36%) patients were given immune globulin, 33 (52%) were given thymosin, and 7 (11%) received corticosteroids. as for oxygen therapy, 32 (50%) used nasal cannula and only 2 (3%) used face mask, while no one . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . needed invasive mechanical or ventilation extracorporeal membrane oxygenation. as a whole, despite the negligible difference of antiviral treatment between two groups, most of the cases who received electrocardiogram monitoring, antibiotics, immune globulin, thymosin and oxygen therapy belonged to group 1, whereas the proportion given traditional chinese medicine was higher in group 2 (table 3) . by 24 feb, 2020, 34 (53%) of the cases have been discharged and none had died, the remaining cases were still in hospital to receive supportive therapy. the median length of hospital stay was 12.5 (iqr 9.0-19.8) days in total, 18.0 (iqr 13.0-20.5) days in group 1 and 9.0 (iqr 6.0-11.0) days in group 2 ( table 3 ). the overall median discharge time (i.e. equal to the time that half of the patients left the hospital) was 20 days (figure 2a ). it should be noted that the endpoint of cox model was discharge, and patients who continued to be hospitalized as of 24 feb 2020 would be regarded as censored data. the hr metric derived from multivariate cox regression model was utilized to ascertain factors significantly associated with the endpoint of patients infected with sars-cov-2. results of the final multivariate cox regression model showed that larger bmi (≥ 24 kg/m 2 ) (hr 0.14; 95% ci 0.03-0.73), fever symptoms (hr 0.24; 95% ci 0.09-0.60) and increased il-6 levels (> 2.9 pg/ml) on admission (hr 0.31; 95% ci 0.11-0.87) were unfavorable factors for hospital discharge (all hrs <1 and all p-values <0.05) according to cox regression mode ( figure 2b ). by 20 feb, 2020, 476 hospitals across china had reported, in total, 2,055 laboratory-confirmed cases of medical staff with sars-cov-2 infection, of which the majority (88%) were from hubei province [25] . according to china-who joint investigation report, most of the infections among medical staff occurred in the early stages of the covid-19 outbreak in wuhan, when there was a lack of knowledge . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint about transmission approaches and experience to fight with the sars-cov-2 [25] . despite the outbreak of covid-19 occurring in few scattered hospitals (e.g. 15 medical staff were infected at one hospital in wuhan), hospital-related transmission is not the main transmission feature of covid-19 in china [25] . our findings advocate this viewpoint. according to our data, a small proportion of 64 novel coronavirus-infected medical staff had a direct contact with specimens of patients (5%) as well as patients in fever clinics (8%) and isolation wards (5%) during patient care. in addition, none of the 64 medical staff had an exposure to huanan seafood market or wildlife, and 4 (6%) had family members with confirmed covid-19. the exact mode of medical staff infection remains unclear. the findings are consistent with previous reports [12, 25] . the demographic characteristics and clinical manifestations of medical staff with confirmed covid-19 in wuhan were not exactly the same as general confirmed patients included in recent studies [10, 12, 26] . in our study, most of the novel coronavirus-infected medical staff analyzed were females and nurses, and had a smaller median and range of age. the medical staff infected with sars-cov-2 have similar signs and symptoms with general confirmed infection patients [12, 26] . the infected medical staff tended to manifest on chest ct with bilateral, subpleural ground-glass opacities, which is consistent with the recent radiological reports on covid-19 pneumonia [27] [28] [29] [30] . furthermore, abnormal d-dimer levels as well as abnormal functions of kidney, heart and liver was relatively rare among medical staff with sars-cov-2 infection. in our study, only one of 64 medical staff with sars-cov-2 infection was severe case, none developed acute respiratory distress syndrome or transferred to intensive care unit. more than half of the cases were discharged by 24 feb, 2020. previous studies suggested that 13.8% of the general confirmed patients were severe cases, among whom older age, male sex, chronic diseases are more common [25, 31, 32, 33] . contrarily, our study revealed that medical staff have relatively milder symptoms, . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint which may be partly due to their medical expertise, younger age and less underlying diseases. medical staff with symptoms onset for less than 10 days by the time of admission were compared with those with symptoms of more than 10 days. we found that medical staff with symptoms for less than 10 days had more prominent laboratory abnormalities on admission, and they also experienced relatively worse clinical course and longer hospital stay. furthermore, the median time between symptoms onset and admission of infected medical staff in this study was 8.5 days, longer than general population as described in recent publications [10, 21] . we believe that mild cases of infected medical staff without an early hospitalization was mainly because they made admirable concessions to provide the limited-number of isolation wards for infected patients with worse conditions during the peak time of covid-19 epidemic in wuhan. predictors of hospital discharge among infected medical staff were identified by cox model. smaller bmi, absence of fever and normal levels of il-6 on initial stage were favorable factors for recovery and discharge. a recent study revealed that fever was identified in only half of the patients on presentation but increased to nearly 90% after hospitalization [26] . elevated il-6 levels were observed in 80% of infected medical staff on admission, which is associated with inflammatory response [34, 35] . to explore how absence of fever and il-6 levels on initial stage affect the length of hospital stay and discharge of medical staff with sars-cov-2 infection, further studies are needed. given that epidemiology and clinical features of medical staff infected with sars-cov-2 is unclear, our study provides an insight to prevention and treatment of medical staff at risk of covid-19 infection. so far, more than 40,000 medical personnel outside hubei province gathered in wuhan for the battle against the epidemic, and china has attached great importance to infection prevention among . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint medical staff [25] . although some safeguards have been introduced in the aspects including salary, injury suffered on the job, rest, and psychological adjustment for medical staff, the next step will continue to strengthen the promotion of these measures. meanwhile, some potential problems remain to be solved, such as unclear patterns of infection, mental health care for medical staff [36] , and the possibility of airborne transmission from aerosol production by medical practices in health care facilities [25] . a recent study from singapore found that surface environmental and personal protective equipment contamination caused by respiratory droplets and fecal shedding from patients infected with sars-cov-2, suggesting that the environment is a potential viral vector [37] . further investigations should be devoted to identifying the exact patterns of sars-cov-2 infection among medical staff. we acknowledge some limitations of this study. first, only 64 for medical staff with confirmed covid-19 from a single hospital in wuhan were included. however, the population from which they were sampled was large and we did not include all of the cases during the study period. in fact, there are 2,055 laboratory-confirmed cases of covid-19 in medical staff as of 20 feb 2020 [25] . this limitation in our study may result in deviations in epidemiological and clinical observation characteristics. we hope that the findings presented here will encourage a more comprehensive assessment of sars-cov-2 infection in for medical staff. second, more detailed information, particularly regarding specific causes of sars-cov-2 infection among for medical staff, was unavailable at the time of analysis; however, this is a retrospective, observational study and the data used in this study only provide a preliminary insight into epidemiological features and clinical outcomes of a group of for medical staff confirmed with covid-19. further research on this regard is needed. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . the study medical staff have relatively milder symptoms and favorable clinical course, which may be partly due to their medical expertise, younger age and less underlying diseases. smaller bmi, absence of fever symptoms and normal il-6 levels on admission are favorable for recovery and hospital discharge for medical staff infected all authors declare no competing interests. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted march 13, 2020. there were 62 of 64 novel coronavirus-infected medical staff provided an exact date of onset, of which 37 were assigned to group 1 and 25 to group 2. the remaining 2 patients without an exact date of onset were not grouped. data are presented as medians (interquartile ranges, iqr) and n (%). for each item, the effective sample size of total population, group 1 and group 2 is 64, 37 and 25 unless stated otherwise. * the group of patents with symptoms onset for 10 or less days by the time of admission. † the group of patents with symptoms onset for more than 10 days by the time of admission. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted march 13, 2020. there were 62 of 64 novel coronavirus-infected medical staff provided an exact date of onset, of which 37 were assigned to group 1 and 25 to group 2. the remaining 2 patients without an exact date of onset were not grouped. data are presented as medians (interquartile ranges, iqr) and n (%). * the group of patents with symptoms onset for 10 or less days by the time of first admission. † the group of patents with symptoms onset for more than 10 days by the time of first admission. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033118 doi: medrxiv preprint clinical features of patients infected with 2019 novel coronavirus in wuhan, china genomic characterization and epidemiology of 2019 novel coronavirus: implications of virus origins and receptor binding a novel coronavirus outbreak of global health concern a novel coronavirus from patients with pneumonia in china genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan who. coronavirus disease (covid-19) technical guidance: laboratory testing for 2019-ncov in humans identifcation of a novel coronavirus in patients with severe acute respiratory syndrome middle east respiratory syndrome coronavirus (mers-cov): announcement of the coronavirus study group clinical findings in a group of patients infected with the 2019 novel 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clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china the international severe acute respiratory and emerging infection consortium (isaric) national health commission of the people's republic of china. new coronavirus pneumonia diagnosis and treatment program (trial version 5, revised version) central people's government of the people's republic of china. china-who joint investigation report for novel coronavirus pneumonia (covid-19) clinical characteristics of coronavirus disease 2019 in china radiological findings from 81 patients with covid-19 pneumonia in wuhan, china: a descriptive study imaging profile of the covid-19 infection: radiologic findings and literature review chest imaging appearance of covid-19 infection clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study cancer patients in sars-cov-2 infection: a nationwide analysis in china characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the chinese center for disease control and prevention into the eye of the cytokine storm. microbiol il-6 induces an anti-inflammatory response in the absence of socs3 in macrophages mental health care for medical staff in china during the covid-19 outbreak surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) from a symptomatic patient creatine kinase alanine aminotransferase we would like to thank all colleagues for helping us during the current study. the authors would like to express their appreciation for all of the emergency services, nurses, doctors, and other hospital staff for their efforts to combat the covid-19 outbreak. key: cord-351567-ifoe8x28 authors: rabi, firas a.; al zoubi, mazhar s.; kasasbeh, ghena a.; salameh, dunia m.; al-nasser, amjad d. title: sars-cov-2 and coronavirus disease 2019: what we know so far date: 2020-03-20 journal: pathogens doi: 10.3390/pathogens9030231 sha: doc_id: 351567 cord_uid: ifoe8x28 in december 2019, a cluster of fatal pneumonia cases presented in wuhan, china. they were caused by a previously unknown coronavirus. all patients had been associated with the wuhan wholefood market, where seafood and live animals are sold. the virus spread rapidly and public health authorities in china initiated a containment effort. however, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers), and causing widespread media attention and panic. based on clinical criteria and available serological and molecular information, the new disease was called coronavirus disease of 2019 (covid-19), and the novel coronavirus was called sars coronavirus-2 (sars-cov-2), emphasizing its close relationship to the 2002 sars virus (sars-cov). the scientific community raced to uncover the origin of the virus, understand the pathogenesis of the disease, develop treatment options, define the risk factors, and work on vaccine development. here we present a summary of current knowledge regarding the novel coronavirus and the disease it causes. coronaviruses, named for the crown-like spikes on their surface (latin: corona = crown), are positive-sense rna viruses that belong to the coronvirinae subfamily, in the coronaviridae family of the nidovirales order [1] . they have four main subgroups-alpha, beta, gamma, and delta-based on their genomic structure. alpha-and betacoronaviruses infect only mammals, usually causing respiratory symptoms in humans and gastroenteritis in other animals [2, 3] . until december of 2019, only six different coronaviruses were known to infect humans. four of these (hcov-nl63, hcov-229e, hcov-oc43 and hku1) usually caused mild common cold-type symptoms in immunocompetent people and the other two have caused pandemics in the past two decades. in 2002-2003, the severe acute respiratory syndrome coronavirus (sars-cov) caused a sars epidemic that resulted in a 10% mortality. similarly, the middle east respiratory syndrome coronavirus (mers-cov) caused a devastating pandemic in 2012 with a 37% mortality rate. in late 2019, a cluster of pneumonia cases in wuhan city, hubei province, china were identified as with a novel betacoronavirus, first called the 2019 novel coronavirus (2019-ncov) and often referred to as the wuhan coronavirus. when the genomics of the 2019-ncov was sequenced, it shared 79.5% of the genetic sequence of the sars-cov that caused the 2002-2003 pandemic [4] and the international committee on taxonomy of viruses renamed the 2019-ncov as sars-cov-2 [5] . patients began to present in november and december with various degrees of respiratory distress of unknown etiology and treated at the time as possible influenza infections. as it became apparent that most cases had a shared history of exposure to the huanan seafood wholesale market (the so-called "wet market"), the wuhan local health authority issued an epidemiologic alert on 30 december 2019 and the wet market was closed. about a week later, on 9 january 2020, chinese researchers shared the full genetic sequence of the novel coronavirus, now called sars-cov-2 [6] . since the novel coronavirus was recognized, the disease it caused was termed coronavirus disease 2019 (covid19) , and several reports on the clinical presentation, epidemiology, and treatment strategies have been published [7] [8] [9] [10] . in addition, several websites have been setup to track the epidemic and the case detection rate, which are being updated as often as hourly [11] [12] [13] [14] . on 30 january 2020, the world health organization (who) declared the covid-19 outbreak to be a global public health emergency, sixth after h1n1 (2009), polio (2014), ebola in west africa (2014), zika (2016) and ebola in the democratic republic of congo (2019), and on 11 march 2020, the who characterized covid-19 as a pandemic [15] . the timeline of events is summarized in figure 1 . all coronaviruses that have caused diseases to humans have had animal origins-generally either in bats or rodents [16] . previous outbreaks of betacoronaviruses in humans involved direct exposure to animals other than bats. in the case of sars-cov and mers-cov, they were transmitted directly to humans from civet cats and dromedary camels respectively ( figure 2 ). animal origins of human coronaviruses. severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) and were transmitted to humans from bats by civet cats and dromedary camels, respectively. the 2019 sars-cov-2 was likely transmitted to humans through pangolins that are illegally sold in chinese markets [16, 17] . the sars-related coronaviruses are covered by spike proteins that contain a variable receptor-binding domain (rbd). this rbd binds to angiotensin-converting enzyme-2 (ace-2) receptor found in the heart, lungs, kidneys, and gastrointestinal tract [18] thus facilitating viral entry into target cells. based on genomic sequencing, the rbd of sars-cov-2 appears to be a mutated version of its most closely related virus, ratg13, sampled from bats (rhinolophus affinis) [19] . it is, therefore, believed that the sars-cov-2 also originated from bats and, after mutating, was able to infect other animals. the mutation increased the rbd affinity to ace-2 in humans, but also other animals such as ferrets and malayan pangolins (manis javanica; a long-snouted, ant-eating mammal sold illegally for use in traditional chinese medicine), but also decreased the rbd affinity to ace-2 found in rodents and civets. the pangolin is believed to be the intermediate host of sars-cov-2 [17] . there was some early speculation that sars-cov-2 emerged from a manmade manipulation of an existing coronavirus, but there is no evidence to support such a theory. in fact, anderson et al. suggest that the particular mutation that was found in the rbd of sars-cov-2 is different to what would have been predicted based on previously used genetic systems. the authors, however, stated that "it is currently impossible to prove or disprove the other theories of [the sars-cov-2] origin [19] ". since sars-cov and sars-cov-2 are so similar, the biochemical interactions and the pathogenesis are likely similar. binding of the sars-cov to the angiotensin-converting enzyme 2 (ace-2) receptors in the type ii pneumocytes in the lungs triggers a cascade of inflammation in the lower respiratory tract [20] . it has been demonstrated that when the sars spike protein binds to the ace-2 receptor ( figure 3a ), the complex is proteolytically processed by type 2 transmembrane protease tmprss2 leading to cleavage of ace-2 and activation of the spike protein ( figure 3b ) [21, 22] , similar to the mechanism employed by influenza and human metapneumovirus, thus facilitating viral entry into the target cell ( figure 3c ). it has been suggested that cells in which ace-2 and tmprss2 are simultaneously present are most susceptible to entry by sars-cov [23] . early indications are that sars-cov-2 virus also requires ace-2 and tmprss2 to enter cells [24] . in the first published review of the clinical presentation of 41 patients admitted to hospital with covid-19 [9] , 98% of patients had a fever, 76% had a cough, and 55% had shortness of breath on admission. however, those admitted may have had less severe symptoms for 2 to 14 days prior to presentation, during which they were likely contagious. by the time patients developed shortness of breath, they had been sick for an average of eight days. once admitted to the hospital, all patients developed clinical pneumonia supported by chest ct findings, and 13 of the 41 patients (32%) developed hypoxic respiratory failure necessitating icu admission. four patients (10%) required mechanical ventilation, two of which received extracorporeal membrane oxygenation due to refractory hypoxia. in total, six patients died, giving a case fatality rate (cfr) of 15% and triggering panic that quickly spread worldwide. while early media reports suggested that deaths were more likely in patients with comorbid conditions, of the 41 patients described in the chinese review, only 38% had comorbid conditions and the average age was 49. as of march 16, 0700 gmt, there were 169,930 confirmed cases, about half of which (80,860 cases, 47.6%) were within mainland china. about 18% of ill people had severe disease, and 82.0% had mild disease and a total of 889 tested-positive cases were asymptomatic [13, 25] . while initially confined to china among those who visited the wuhan wet market, over the course of about 3 months the sars-cov-2 has to date been confirmed in 157 countries and one cruise ship [13] . the chinese cdc published the epidemiologic characteristics of the covid-19 outbreak as of 11 february 2020 (table 1 ) [26] . initial data suggests that the majority of patients (73%) were over age 40 years, and that the risk of death increases with age. no deaths were reported in patients younger than 10 years old, and only 2.6% of the total fatalities were in patients younger than 40 years of age. [26] . [11, 13] . due to aggressive containment strategies in china, including a mass quarantine of the entire 11 million population of wuhan, the acceleration of new cases in china has slowed whereas that outside of china has increased. as of march 2nd, the number of daily new cases outside of china was nine times higher than those within china. many countries have instituted travel bans and/or quarantine procedures for incoming travelers. closures of public schools and social gatherings have been instituted in many countries in an effort to contain the spread of covid-19 and decrease the public health burden [27, 28] and the cdc has released recommendations on school closure criteria [29] . in comparison, the 2002 sars pandemic, which also originated in china, resulted in 8096 people infected and 774 deaths (9.6%). on the other hand, the 2012 mers pandemic infected 2494 people causing 858 deaths (34.4%). therefore, although mers and sars had higher mortality, the much larger number of people infected with sars-cov-2, and the rate at which the number is increasing, raises red epidemiologic flags. to assess the magnitude of the risk posed by the sars-cov-2, we review four parameters that we believe important: the transmission rate, the incubation period, the case fatality rate (cfr), and the determination of whether asymptomatic transmission can occur. the reproduction number, or "r naught" (r0), is a mathematical term that defines contagiousness [30] . specifically, it is the number of people that one sick host can infect. if the r0 is less than one the disease will disappear. if the r0 ≥ 1 then the disease will spread between people. estimates of the r0 of sars-cov-2 have ranged from 2.24 to as high as 3.58 [31] although the world health organization estimates it is between 1.4 and 2.5 [32] . for the purposes of comparison, the mean r0 for seasonal influenza is between 1.1 and 2.3 (variable by region and immunization rates), whereas for sars was between 1 and 2.75. the slightly higher r0 for sars-cov-2 may be because it has a longer prodromal period, increasing the period during which the infected host is contagious. coronaviruses are generally thought to be spread most often by respiratory droplets, not to be confused with airborne transmission [33] . droplets are larger and tend to fall to the ground close to the infected host and only infect others if the droplet is intercepted by a susceptible host prior to landing. droplet transmission is typically limited to short distances, generally less than 2 m. however, the airborne route involves much smaller droplets that can float and move longer distances with air currents. under certain humidity and temperature environments, airborne droplets can remain in flight for hours. generally, pathogens that are transmissible via the airborne route have higher r0, because infected particles can remain in the air long after the infected individual has left the premises. this airborne route occurs, for example, in measles (r0 between 12 and 18 [34] ) and chicken pox (r0s between 3.7 and 5.0 [35] ). once infected droplets have landed on surfaces, their survivability on those surfaces determines if contact transmission is possible. based on our current understanding from other betacoronaviruses, including sars and mers, coronaviruses can survive, and remain infectious, from 2 h up to 9 days on inanimate surfaces such as metal, glass, or plastic, with increased survival in colder and dryer environments [36] [37] [38] . for this reason, the chinese government has been reported to be disinfecting and even destroying cash in an effort to contain the virus [39] . reassuringly, cleansing of surfaces with common biocidals such as ethanol and sodium hypochlorite is very effective at inactivation of the coronaviruses within 1 min of exposure [36] . the timing of maximum infectivity is currently being assessed. a small study of 17 patients showed that nasal viral load peaks within days of symptom onset, suggesting that transmission of disease is more likely to occur early in the course of infection [40] . understanding incubation periods is very important as it allows health authorities to introduce more effective quarantine systems for suspected cases. the best current estimates of the sars-cov-2 infection range from 2 to 14 days. analysis of the first 425 cases of covid-19 in wuhan a mean incubation period of 5.2 days [41] . a later report, based on 1324 cases, reported a mean incubation period of 3.0 days [42] . yet another report, on 88 cases who traveled to wuhan between 20 and 28 january, had incubation period ranges from 2.1 to 11.1 days, with a mean of 6.4 days [43] . to calculate the case fatality rate (cfr) of an infection, one must divide the mortality number (m) by all those who were infected. the total number of those infected includes those who were infected and recovered without presentation (i r ), infected and presented to a health care facility (i p ), and infected and died (i d ). the cfr would be m/(i r + i p + i d ). clearly, one must have an accurate estimation of each of these parameters to accurately determine the cfr of covid-19. while the (m) is generally easier to count, and a focus of media, the denominator can take much longer to calculate. during the early phases of a deadly epidemic, the number of those who were infected and recovered (i r ) is not yet known, since only those who were infected and became seriously ill are recognized and tested. in addition, because this is a novel virus, there were no existing detection methods, so early deaths due to clinical entities such as influenza, for example, may have been mis-attributed to covid-19. the viral genome was published about 2 weeks after the start of the outbreak, and pcr analysis was quickly used to diagnose suspected cases [6] . public health officials can now test suspected cases, especially close contacts of known cases, and others with mild symptoms, but the testing capabilities can become saturated, potentially limiting the ability to get an accurate estimation of i p . for example, the initial ability of the wuhan health authority was limited to 200 tests per day, but that number has grown to 4196 tests per day [44] . the combination of these factors leads to a gross underestimation of the denominator of the cfr calculation, and thus an exaggeration of the mortality. until we are able to accurately represent i r and i p , it is currently impossible to precisely estimate the cfr of sars-cov-2. however, during the course of a potentially fatal pandemic, an accurate estimation of cfr is important. while it is tempting to estimate the cfr by dividing the number of known deaths by the total number of confirmed cases, the resulting number may be off by orders of magnitude, especially since infected individuals at one point in time may die x days later. using the lag period approach and dividing the current number of deaths to the number of cases x days ago may be a more acute estimator of cfr. nucleuswealth.com applied this method by using the number of deaths at any particular day and dividing by number of cases 4, 8, or 12 days prior. as seen in figure 4 , as time progresses, whether whichever number of days is used for x, the cfr seems to converge at just under 5% for cases within hubei, and about 0.8% for cases outside of hubei [14] . the higher mortality in wuhan may be overestimated because early in the course of this epidemic, viral testing was limited to only the severe cases. however, the china national health commission admits that wuhan has a relative lack of medical resources, which may have contributed to the higher mortality rate. pathogens 2020, 9, x for peer review 8 of 15 and dividing the current number of deaths to the number of cases x days ago may be a more acute estimator of cfr. nucleuswealth.com applied this method by using the number of deaths at any particular day and dividing by number of cases 4, 8, or 12 days prior. as seen in figure 4 , as time progresses, whether whichever number of days is used for x, the cfr seems to converge at just under 5% for cases within hubei, and about 0.8% for cases outside of hubei [14] . the higher mortality in wuhan may be overestimated because early in the course of this epidemic, viral testing was limited to only the severe cases. however, the china national health commission admits that wuhan has a relative lack of medical resources, which may have contributed to the higher mortality rate. infection transmission by asymptomatic individuals can make control of disease spread challenging. since late january, sars-cov-2 transmission from infected but still asymptomatic individuals has been increasingly reported [45, 46] . assessment of the viral loads in symptomatic individuals not only showed that the viral loads peak within the first few days of symptoms, but also that asymptomatic patients can have a similarly high viral load without showing symptoms [40] . it was suggested that viral testing should no longer be limited to symptomatic individuals, but also include those who have traveled to affected areas [47] . at such an early phase of the covid-19 pandemic, it is difficult to accurately describe the populations most at risk, especially when teasing out risk factors for infection from risk factors for death from disease. early on, it became clear that those who have visited the wuhan wet market were most at risk of infection, but the population visiting the market is not an accurate reflection of the general population. the chinese cdc published the epidemiologic characteristics of the covid-19 outbreak along with associated risk factors for death [26] . the largest risk factor for death is age. other risk factors include male sex and the presence of comorbid conditions (table 2 ). however, in addition to real age-specific mortality, the age-based risk could reflect underlying comorbidities among the elderly and the distribution of the underlying population in wuhan, where the outbreak initiated. infection transmission by asymptomatic individuals can make control of disease spread challenging. since late january, sars-cov-2 transmission from infected but still asymptomatic individuals has been increasingly reported [45, 46] . assessment of the viral loads in symptomatic individuals not only showed that the viral loads peak within the first few days of symptoms, but also that asymptomatic patients can have a similarly high viral load without showing symptoms [40] . it was suggested that viral testing should no longer be limited to symptomatic individuals, but also include those who have traveled to affected areas [47] . at such an early phase of the covid-19 pandemic, it is difficult to accurately describe the populations most at risk, especially when teasing out risk factors for infection from risk factors for death from disease. early on, it became clear that those who have visited the wuhan wet market were most at risk of infection, but the population visiting the market is not an accurate reflection of the general population. the chinese cdc published the epidemiologic characteristics of the covid-19 outbreak along with associated risk factors for death [26] . the largest risk factor for death is age. other risk factors include male sex and the presence of comorbid conditions (table 2) . however, in addition to real age-specific mortality, the age-based risk could reflect underlying comorbidities among the elderly and the distribution of the underlying population in wuhan, where the outbreak initiated. table 2 . fatality rate by age, sex, and pre-existing medical conditions. the death rate represents the probability (%) of the corresponding group of dying from sars-cov-2 [26] . with what we know about the pathogenesis of the sars-cov virus, it seems reasonable to assume that those with higher levels of ace-2 receptors may be at greatest risk. there was some speculation that the expression of ace-2 receptors may be linked to race, specifically after an early report suggested that asian males had higher ace-2-expressing cell ratios than white and african americans [48] . however, the sample size contained only eight different individuals (five african americans, two whites, and one asian) and extrapolating those findings to a whole race is impractical. yet, in another study assessing ace-2 receptor expression in tissues of 224 patients with lung cancer, there were no significant disparities in ace-2 gene expression between racial groups (asian vs. caucasian), age groups (older or younger than 60 years old), or gender groups (male vs. females) [49] . ace-2 gene expression was, however, significantly elevated in smokers suggesting that smoking history should be considered in identifying susceptible populations. since smoking in china is predominantly a male attribute (54% of men, 2.6% of women) [50] , this may help to explain the gender difference seen in the hospitals in china. early in the covid-19 epidemic, it appeared that children were a protected group, but this may have been because they were less likely to have frequented the wuhan wet market, or because they were more likely to have asymptomatic or mild disease and thus less likely to have been tested. covid-19 has affected infants as young as 1 month of age [51] , most with mild or asymptomatic disease. there have been no reported cases of adverse infant outcomes for mothers who developed covid-19 during pregnancy. second to the hubei population, the other population at increasing risk is healthcare workers. as of february 17, 2020, total of 1716 healthcare workers in china have been infected, five of whom fatally [25] . the current best strategy of treatment of patients with covid-19 is purely supportive. clinicians and intensive care specialists are applying much of what they have learned during the sars epidemic to guide current therapy of covid-19. recommendations for admission to critical care units, guidelines for infection control, and procedures to minimize nosocomial transmission are being established [52] . however, there are several fronts that are being studied to develop targeted treatments. the most efficient approach to the treatment of covid-19 is to test whether existing antiviral drugs are effective. in previous betacoronavirus epidemics, several antiviral drugs, such as ribavirin, interferon, lopinavir-ritonavir, and darunavir/cobicistat (prezcobix) were tested, with some showing promising in vitro results [53] . remdesivir, an adenosine analog used against rna viruses (including sars and mers-cov), was a candidate ebola treatment with promising in vitro results but disappointing in vivo effects against ebola [54, 55] . there is currently in vitro evidence that remdesivir may be effective in controlling sars-cov-2 infection [56] . in fact, compassionate use of remdesivir was employed in the treatment of the first covid-19 case in the united states, during a period of rapid clinical deterioration, and within one day there was dramatic improvement of the clinical condition [57] . randomized double-blinded, placebo-controlled clinical trials are currently underway in china and usa to evaluate the efficacy of remdesivir and initial results are expected by the end of april 2020 [58, 59] . other existing drug candidates include chloroquine and camostat mesylate. chloroquine is a widely used anti-malarial drug that is known to block virus-cell fusion and has been shown to interfere with the glycosylation of sars-cov and ace-2 cellular receptors, rendering the ace-2-sars-cov interaction less efficient [60] . there is also in vitro evidence that chloroquine may be effective in preventing sars-cov-2 cellular entry [56] . camostat mesylate, also known as foy 305 [61] , was initially developed and currently approved for the treatment of chronic pancreatitis in japan [62, 63] . camostat mesylate targets the tmprss2 protease, theoretically preventing viral entry. researchers in germany showed that camostat mesylate reduced the amount of sars-cov-2 viral replication [64] . a simple but very effective treatment modality is the use of convalescent plasma, or serum from patients who have recovered from the virus, to treat patients. patients with resolved viral infection will have developed a specific antibody response which may be helpful in neutralizing viruses in newly infected individuals. this modality was successfully employed during the 2014-2015 ebola outbreak [65, 66] . however, the use of convalescent sera is of limited benefit in an outbreak situation since the exponential growth of infected patients exceeds the ability of previous patients to provide donor plasma. the recent finding that sars-cov-2 binds to the same ace-2 receptors targeted by the 2002 sars-cov [24] opens up the possibility of using the previous research on the 2002 sars epidemic and applying it to covid-19. the first strategy would be to employ either a small receptor-binding domain (rbd) or a neutralizing antibody targeting the ace-2 receptor, thus blocking the binding of s protein and preventing virus entry into cells. initial in vitro results have shown promising results [67, 68] and specific monoclonal antibodies are being contemplated as candidates for treatment [69, 70] . the main limitation of using rbds or antibodies is that the treatment must be given within a specific time window, before the initiation of viral replication [20] . in addition, the side effects of ace-2 blockade, especially since ace-2 is also present in non-pulmonary tissue, must be understood and minimized before implementation. in addition, finally, the turnover of ace-2 receptors would influence how often the therapeutic rbd or antibody would have to be administered. a second strategy is to create an ace-2-like molecule that would bind to the s protein of the coronavirus itself. again, research in to the 2002 sars virus demonstrated that soluble ace-2 proteins blocked the sars virus from infecting cells in vitro [68, 71] . the additional benefit to using this strategy lies in the possible prevention of s protein-mediated ace-2 shedding that has been shown to induce the pulmonary edema characteristic of sars [72, 73] . a phase ii clinical trial of recombinant ace-2 in ards reported significant modulation of inflammatory proteins, but no significant differences in respiratory parameters [74] . further research is necessary to assess if the animal studies will translate to clinical benefit. there are currently more than 80 clinical trials to test a variety of potential sars-cov-2 treatments [75] . the long-term goal of sars-cov-2 research is developing an effective vaccine to yield neutralizing antibodies. the national institutes of health in the us, and baylor university in waco, texas, are working on a vaccine based on what they know about the coronavirus in general, using information from the sars outbreak. in 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and immunogenicity study of 2019-ncov vaccine (mrna-1273) to treat novel coronavirus-full text view-clinicaltrials.gov this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license funding: this research received no external funding. the authors declare no conflict of interest. pathogens 2020, 9, 231 key: cord-332387-rmmmhrjy authors: ma, chang-jin; kang, gong-unn title: air quality variation in wuhan, daegu, and tokyo during the explosive outbreak of covid-19 and its health effects date: 2020-06-09 journal: int j environ res public health doi: 10.3390/ijerph17114119 sha: doc_id: 332387 cord_uid: rmmmhrjy this study was designed to assess the variation of the air quality actually measured from the air pollution monitoring stations (aqms) in three cities (wuhan, daegu, and tokyo), in asian countries experiencing the explosive outbreak of covid-19, in a short period of time. in addition, we made a new attempt to calculate the reduced dose(pm)(2.5) (μg) at the bronchiolar (br.) and alveolar-interstitial (ai) regions of the 10-year-old children after the city lockdown/self-reflection of each city. a comparison of the average pm(2.5) of a month before and after the lockdown (wuhan) and self-reflection (daegu and tokyo) clearly shows that the pm(2.5) concentration was decreased by 29.9, 20.9, and 3.6% in wuhan, daegu and tokyo, respectively. wuhan, daegu and tokyo also recorded 53.2, 19.0, and 10.4% falls of no(2) concentration, respectively. wuhan, which had the largest decrease of pm(2.5) concentration due to covid-19, also marked the largest reduced dose(pm)(2.5 10-year-old children) (μg) (3660 μg at br. and 6222 μg at ai), followed by daegu (445 μg at br. and 1287 μg at ai), and tokyo (18 μg at br. and 52 μg at ai), over two months after the city lockdown/self-reflection. our results suggest that the city lockdown/self-reflection had the effect of lowering the concentration of pm(2.5), resulting in an extension of the period it took to the acute allergic airway inflammation (aai) for the 10-year-old children. since the initial report of cases in wuhan (see figure 1 ), china, on 31 december 2019, the coronavirus disease 2019 (covid-19) spread worldwide in a short period of time and is still in progress [1] . during the pandemic, 4,445,920 confirmed cases were reported in 213 countries and 298,440 people have died so far from the covid-19 outbreak, as of 14 may 2020 [2] . in response to the rapid increase in the covid-19 case, the chinese administrative authorities have sealed off the entire city of wuhan. as a concrete city blockade, they blocked traffic and banned people from moving out of town. to prevent the spread of covid-19, they also closed various educational institutions and established numerous quarantines [3] . as shown in figure 2 , in the case of daegu metropolitan city, south korea, the number of cases sharply increased at the time when the number of confirmed cases of wuhan was on the decline. in daegu, just 17 days after the first case was reported on 18 february, an explosive outbreak of covid-19 occurred. the authorities of daegu also implemented various administrative regulations to prevent the outbreak of covid-19, and the number of newly confirmed cases decreased to 5 cases per day on 5 april (see figure 3 ). the authorities of daegu also implemented various administrative regulations to prevent the outbreak of covid-19, and the number of newly confirmed cases decreased to 5 cases per day on 5 april (see figure 3 ). the authorities of daegu also implemented various administrative regulations to prevent the outbreak of covid-19, and the number of newly confirmed cases decreased to 5 cases per day on 5 april (see figure 3 ). meanwhile, the number of confirmed cases increased in tokyo following the sharp drop in daegu, reaching 197 daily confirmed cases on 11 april (see figure 2 drawn from the data of toyo keizai online [4] ). as covid-19 spread rapidly, tokyo also issued executive orders, such as temporary closure request for public schools (3 march) , request for self-reflection at home (25 march) , and declaration of the state of emergency (7 april) (see figure 3 ). as mentioned above, on 23 january 2020, the central government of china imposed a lockdown in wuhan (see figure 3 ) and other cities in hubei, when the cumulative confirmed cases reached 1410. daegu and tokyo have requested self-reflection on 23 february and 25 march, when the cumulative confirmed cases were 319 and 212, respectively. until the official city lockdown was lifted by 8 april, all vehicles and people in wuhan were not allowed to move. there was no compulsion like wuhan, but the number of vehicles and floating population dropped sharply after the request for self-reflection in daegu and tokyo, too. meanwhile, while people were facing covid-19 worldwide, the unexpected positive effects of environmental pollution decreasing have been reported. among them, the satellite imagery of nasa [5] has shown how no 2 has improved drastically in big cities across china during the covid-19 pandemic. according to a report from the world health organization (who) [6] , the exposure to toxic air, both indoors and outdoors, kills some 600,000 children under the age of 15 each year. brauer [7] also suggested that air pollution kills seven million people, especially for infants and the elderly, worldwide every year, and more than 90% of people around the world breathe polluted air. even in european countries, 193,000 people died in 2012 because of airborne particulate matter [8] . meanwhile, the number of confirmed cases increased in tokyo following the sharp drop in daegu, reaching 197 daily confirmed cases on 11 april (see figure 2 drawn from the data of toyo keizai online [4] ). as covid-19 spread rapidly, tokyo also issued executive orders, such as temporary closure request for public schools (3 march), request for self-reflection at home (25 march) , and declaration of the state of emergency (7 april) (see figure 3 ). as mentioned above, on 23 january 2020, the central government of china imposed a lockdown in wuhan (see figure 3 ) and other cities in hubei, when the cumulative confirmed cases reached 1,410. daegu and tokyo have requested self-reflection on 23 february and 25 march, when the cumulative confirmed cases were 319 and 212, respectively. until the official city lockdown was lifted by 8 april, all vehicles and people in wuhan were not allowed to move. there was no compulsion like wuhan, but the number of vehicles and floating population dropped sharply after the request for self-reflection in daegu and tokyo, too. meanwhile, while people were facing covid-19 worldwide, the unexpected positive effects of environmental pollution decreasing have been reported. among them, the satellite imagery of nasa [5] has shown how no2 has improved drastically in big cities across china during the covid-19 pandemic. according to a report from the world health organization (who) [6] , the exposure to toxic air, both indoors and outdoors, kills some 600,000 children under the age of 15 each year. brauer [7] also suggested that air pollution kills seven million people, especially for infants and the elderly, worldwide every year, and more than 90% of people around the world breathe polluted air. even in european countries, 193,000 people died in 2012 because of airborne particulate matter [8] . it is well known that the exposure to particulate matter with a diameter of less than 2.5 µm (pm 2.5 ) has been related to both acute and chronic respiratory diseases. many epidemiologic studies have suggested that children are more vulnerable to pm 2.5 [9, 10] . according to the results of several previous studies, it can be said that air pollution causes far more human deaths than covid-19 from a long-term perspective. it is quite meaningful to assess the improvement of air quality during the covid-19 pandemic through actual measurement data and to evaluate the health effects of the improved amount, especially on children. in this study, the air quality variation with the trend of covid-19 at wuhan in china, daegu in south korea, and tokyo in japan experienced explosive outbreaks in a short period of time, which was estimated based on the actual measured data from air pollution monitoring stations (aqms). the health effect of the reduced pm 2.5 dose due to covid-19 on 10-year-old children in each city was also quantitatively assessed. wuhan is the capital city of hubei province in china, with a population of over 11.08 million. it covers an area of around 8,494 km 2 and has a humid subtropical climate, with abundant rainfall in summer and four distinctive seasons [11] . by the end of 2018, the total number of registered motor vehicles in wuhan was 2.97 million, accompanied by increasing urban traffic pressure [12] . daegu metropolitan city, south korea is the fourth-largest after seoul, busan, and incheon. its major industries are the textile industry, metals and machinery, the automobile component industry, mobile development, and medical care. as of may 2019, the population and area of this city are 2.49 million and 883.54 km 2 , respectively. the total number of cars registered was 1,190,154, of which gasoline, diesel, lpg, cng and hybrid were 561,643, 470,569, 114,533, 2617, and 26,026, respectively [13] . tokyo, the capital of japan, is located at the head of tokyo bay on the pacific coast of the central honshu. this metropolitan area is the largest industrial, commercial, and financial center in japan. the area and population of tokyo are approximately 2188 km 2 and 13.95 million, as of 1 january 2020 [14] . in 2019, a total of 3.95 million motor vehicles were registered in tokyo. total motor vehicles include cars, trucks and buses, as well as special purpose vehicles [15] . in this study, the data of pm 2.5 and no 2 measured continuously at one-hour intervals at the air quality monitoring stations (aqmss) of three cities were studied. the data monitored at the aqmss of three cities from 9 january to 29 april 2020 became the subjects of this study. the data of wuhan were monitored at the hankoujiangtan urban aqms (30.59 n, 114 .30 e) and published on the website of the ministry of environmental protection (mep) in china [16] . the average monthly temperature in wuhan ranged between 5.1 and 17.3 • c from january to april, 2020. those of relative humidity and wind speed during the same period are 58.8-78.4% and 2.38-2.97 m/s, respectively. the atmospheric environment standards of pm 2.5 and no 2 in china are below 35 µg/m 3 and 40 ppb, respectively, on annual average concentration. the data of daegu were monitored at the suchang-dong aqms (35.52 n, 128.36 e), installed in an urban area. the average monthly temperature ( • c), relative humidity (%), wind speed (m/s) in daegu during the measurement period ranged from 3.8-13.5 • c, 52-61%, and 2.1-2.4 m/s, respectively. the environmental quality standards in south korea for the 24-h average and annual average of pm 2.5 are <35 and <15 µg/m 3 , respectively. in the case of no 2 , the daily average for hourly values shall be within the 40-60 ppb or below this zone. the selected aqms in tokyo was shinjuku (35.69 n, 139.70 e), a major commercial and administrative center for the government of tokyo. wind speed (m/s), temperature ( • c), and relative humidity (%) at the monitoring sites of shinjuku ranged from 0-2.9 m/s, 0.9-22.1 • c, and 21.8-97.7%, respectively. the environmental quality standards are the same as those of korea. to better represent the time series trend of pm 2.5 concentration over the whole measurement period, all data were treated with the 5-day simple moving average (sma) c d sma by the following equations: where c d is the daily average of measured data every hour, and n is the number of days in an interval of daily average data (5-day in this study). the c d sma can help us distinguish between typical measurement noise and actual trends. typical measurement noise and actual trends. figure 4 shows the time series variation of the concentration of pm2.5 in wuhan, daegu, and tokyo, with their cumulative confirmed cases of covid-19. unlike tokyo, where the concentration was not high before the self-restraint regulation, there was a clear reduction in the pm2.5 concentration in wuhan and daegu. although it was not a continuous reduction, the concentration of pm2.5 in wuhan showed a significant decrease. it is necessary to assess whether this is a simple seasonal variation or a change due to the city lockdown. the results of our study are compared with those of gong et al. [17] , which investigated the monthly concentration of pm2.5 in wuhan in 2015. in their study, the monthly average of pm2.5 from january to april was 146, 82, 87, and 72 μg/m 3 . meanwhile, in this study, the concentrations of pm2.5 in each month during the same period were 80.8, 51.7, 52.0, and 48.8 μg/m 3 . although our results are like the seasonal trends in 2015, the pm2.5 concentrations for each month from january to april were greatly reduced by 44.7, 37.0, 40.3, and 32.3%, compared to those of 2015. in february, when the number of the confirmed covid-19 cases was at its peak, pm2.5 concentration was 57.3% lower than that in february 2017 (121.2 μg/m 3 ) [18] . therefore, it can be said clearly that the city lockdown has resulted in a great reduction in pm2. 5 . in daegu, the concentration of pm2.5 shows a temporary increase or decrease, but the trend of decline was evident in the overall period. the overall decline of the pm2.5 in tokyo is not seen, but it is clearly decreasing after request for self-reflection on 25 march. apart from the overall pattern of decline, several short reduction intervals due to rainfall were also clearly found in all three cities. figure 5 shows the result of comparing the average pm2.5 of a month before and after the lockdown (wuhan) and self-reflection (daegu and tokyo) in each city. the decreasing rate of pm2.5 concentration in each city was 29.9, 20.9 and 3.6% in wuhan, daegu and tokyo, respectively. unlike tokyo, where the concentration was not high before the self-restraint regulation, there was a clear reduction in the pm 2.5 concentration in wuhan and daegu. although it was not a continuous reduction, the concentration of pm 2.5 in wuhan showed a significant decrease. it is necessary to assess whether this is a simple seasonal variation or a change due to the city lockdown. the results of our study are compared with those of gong et al. [17] , which investigated the monthly concentration of pm 2.5 in wuhan in 2015. in their study, the monthly average of pm 2.5 from january to april was 146, 82, 87, and 72 µg/m 3 . meanwhile, in this study, the concentrations of pm 2.5 in each month during the same period were 80.8, 51.7, 52.0, and 48.8 µg/m 3 . although our results are like the seasonal trends in 2015, the pm 2.5 concentrations for each month from january to april were greatly reduced by 44.7, 37.0, 40.3, and 32.3%, compared to those of 2015. in february, when the number of the confirmed covid-19 cases was at its peak, pm 2.5 concentration was 57.3% lower than that in february 2017 (121.2 µg/m 3 ) [18] . therefore, it can be said clearly that the city lockdown has resulted in a great reduction in pm 2.5 . in daegu, the concentration of pm 2.5 shows a temporary increase or decrease, but the trend of decline was evident in the overall period. the overall decline of the pm 2.5 in tokyo is not seen, but it is clearly decreasing after request for self-reflection on 25 march. apart from the overall pattern of decline, several short reduction intervals due to rainfall were also clearly found in all three cities. figure 5 shows the result of comparing the average pm 2.5 of a month before and after the lockdown (wuhan) and self-reflection (daegu and tokyo) in each city. the decreasing rate of pm 2.5 concentration in each city was 29.9, 20.9 and 3.6% in wuhan, daegu and tokyo, respectively. xu et al. [19] reported that, during the defined 3-week lockdown period, wuhan's pm2.5 level went down 44% from 2019. in the case of tokyo, the decreasing rate was significantly lower compared to the two cities, probably because of usual low pm2.5 concentration. figure 6 shows the daily variations of the concentration of no2 in wuhan, daegu, and tokyo, with the cumulative confirmed cases of covid-19. the concentration of no2 in wuhan significantly decreased while the city was in lockdown from 23 january to 8 april. no2 is generally emitted from traffic and factories and is therefore a good indicator of human activity outside the home. a large peak appeared around 8 april, when the wuhan lockdown officially ended, may be because of the comeback of a floating population and traffic amount. although smaller than this, the peak also appeared in the distribution of pm2.5 (see figure 4 ). in the cases of daegu and tokyo, the continuous reduction in no2 concentration was more evident than that of pm2.5. although there were occasional temporary reductions in no2 because of the wash-out, the overall decline might also be due to people's efforts, such as the reduction of traffic volume and the partial shutdown of industrial facilities under autonomous self-reflection. xu et al. [19] reported that, during the defined 3-week lockdown period, wuhan's pm 2.5 level went down 44% from 2019. in the case of tokyo, the decreasing rate was significantly lower compared to the two cities, probably because of usual low pm 2.5 concentration. figure 6 shows the daily variations of the concentration of no 2 in wuhan, daegu, and tokyo, with the cumulative confirmed cases of covid-19. xu et al. [19] reported that, during the defined 3-week lockdown period, wuhan's pm2.5 level went down 44% from 2019. in the case of tokyo, the decreasing rate was significantly lower compared to the two cities, probably because of usual low pm2.5 concentration. figure 6 shows the daily variations of the concentration of no2 in wuhan, daegu, and tokyo, with the cumulative confirmed cases of covid-19. the concentration of no2 in wuhan significantly decreased while the city was in lockdown from 23 january to 8 april. no2 is generally emitted from traffic and factories and is therefore a good indicator of human activity outside the home. a large peak appeared around 8 april, when the wuhan lockdown officially ended, may be because of the comeback of a floating population and traffic amount. although smaller than this, the peak also appeared in the distribution of pm2.5 (see figure 4 ). in the cases of daegu and tokyo, the continuous reduction in no2 concentration was more evident than that of pm2.5. although there were occasional temporary reductions in no2 because of the wash-out, the overall decline might also be due to people's efforts, such as the reduction of traffic volume and the partial shutdown of industrial facilities under autonomous self-reflection. the concentration of no 2 in wuhan significantly decreased while the city was in lockdown from 23 january to 8 april. no 2 is generally emitted from traffic and factories and is therefore a good indicator of human activity outside the home. a large peak appeared around 8 april, when the wuhan lockdown officially ended, may be because of the comeback of a floating population and traffic amount. although smaller than this, the peak also appeared in the distribution of pm 2.5 (see figure 4 ). in the cases of daegu and tokyo, the continuous reduction in no 2 concentration was more evident than that of pm 2.5 . although there were occasional temporary reductions in no 2 because of the wash-out, the overall decline might also be due to people's efforts, such as the reduction of traffic volume and the partial shutdown of industrial facilities under autonomous self-reflection. figure 7 shows the result of comparing the average no 2 of a month before and after the city lockdown (wuhan) and self-reflection (daegu and tokyo) in each city. wuhan, daegu, and tokyo recorded 53.2, 19.0, and 10.4% fall of no 2 , respectively. although it is a short-term decline, it can be said that this result is very meaningful for the citizens' health of three cities, especially wuhan citizens. the model calculation by dutheil et al. [20] suggested that the reduction of no 2 in china due to covid-19 epidemic during a time period of two months saved around 100,000 lives in china. wuhan, daegu, and tokyo recorded 53.2, 19.0, and 10.4% fall of no2, respectively. although it is a short-term decline, it can be said that this result is very meaningful for the citizens' health of three cities, especially wuhan citizens. the model calculation by dutheil et al. [20] suggested that the reduction of no2 in china due to covid-19 epidemic during a time period of two months saved around 100,000 lives in china. exposure to pm2.5 can cause lung function abnormalities including increased airflow obstruction and airway hyper responsiveness [21] . according to research done by gauderman et al. [22] , the short-term exposure of pm2.5 on chronic obstructive pulmonary disease demonstrated the impact of pm2.5 on years of life lost. li et al. [23] suggested that the deficits in the growth of the expiratory volume in one second for the ages between 10 and 18 years old were associated with exposure to pm2.5. airborne allergens usually develop by 10 years of age, and this reaches its peak in the teens or early twenties [24] . as mentioned above, the difference in the average concentration of pm2.5 in the month before and after self-reflection were 18.0, 5.3, and 0.36 μg/m 3 in wuhan, daegu, and tokyo, respectively. to find out what the reduced pm2.5 concentration in each city means for health, we calculated the exposure dose of pm2.5 (dosepm2.5) amount, namely, how much pm2.5 penetrates our respiratory system. first, we tried to calculate the reduced dosepm2.5 (μg) for the 10-year-old children (dosepm2.5 10-yearold children) per day and over two months after the city lockdown/self-reflection of each city. the calculation of the reduced dosepm2.5 10-year-old children was made by modifying the formula proposed by löndahl et al. [25] reduced dosepm2.5 10-year-old children (μg) = reduced cpm2. where the reduced cpm2.5 are 18.0, 5.3, and 0.36 μg/m 3 in wuhan, daegu, and tokyo, respectively, i/o ratio is the average indoor/outdoor (i/o) ratio of pm2.5 concentration at three different cities [26] [27] [28] . fdep. is the maximum deposition fraction at bronchiolar (br.) additionally, alveolar-interstitial (ai) regions suggested by yamada et al. [29] , texp. is the exposure time (1-day or 60-day), and rbre. is breathing rate (m 3 /h). the fdep. and rbre. are decided by the activity patterns of 10-year-old children. in this study, their daily activity patterns were classified into sleep, sitting or rest, light activities (exercise or movement), and heavy activities. the time allocated for each activity of the day is 9, 4, 10, and 1-h, respectively (see table 1 ). four kinds of their daily activity patterns were set up, assuming that they would have spent most of their time at home due to requests for self-reflection. the variables and the calculated reduced dosepm2.5 (μg) for the 10-year-old children per day and over two months after the self-reflection of each city are summarized in table 1 . exposure to pm 2.5 can cause lung function abnormalities including increased airflow obstruction and airway hyper responsiveness [21] . according to research done by gauderman et al. [22] , the short-term exposure of pm 2.5 on chronic obstructive pulmonary disease demonstrated the impact of pm 2.5 on years of life lost. li et al. [23] suggested that the deficits in the growth of the expiratory volume in one second for the ages between 10 and 18 years old were associated with exposure to pm 2.5 . airborne allergens usually develop by 10 years of age, and this reaches its peak in the teens or early twenties [24] . as mentioned above, the difference in the average concentration of pm 2.5 in the month before and after self-reflection were 18.0, 5.3, and 0.36 µg/m 3 in wuhan, daegu, and tokyo, respectively. to find out what the reduced pm 2.5 concentration in each city means for health, we calculated the exposure dose of pm 2.5 (dose pm2.5 ) amount, namely, how much pm 2.5 penetrates our respiratory system. first, we tried to calculate the reduced dose pm2.5 (µg) for the 10-year-old children (dose pm2. 5 10-year-old children ) per day and over two months after the city lockdown/self-reflection of each city. the calculation of the reduced dose pm2. 5 10-year-old children was made by modifying the formula proposed by löndahl et al. [25] reduced dose pm2. 5 10-year-old children (µg) = reduced c pm2.5 × i/o ratio × f dep. × t exp. × r bre. (2) where the reduced c pm2.5 are 18.0, 5.3, and 0.36 µg/m 3 in wuhan, daegu, and tokyo, respectively, i/o ratio is the average indoor/outdoor (i/o) ratio of pm 2.5 concentration at three different cities [26] [27] [28] . f dep. is the maximum deposition fraction at bronchiolar (br.) additionally, alveolar-interstitial (ai) regions suggested by yamada et al. [29] , t exp. is the exposure time (1-day or 60-day), and r bre. is breathing rate (m 3 /h). the f dep. and r bre. are decided by the activity patterns of 10-year-old children. in this study, their daily activity patterns were classified into sleep, sitting or rest, light activities (exercise or movement), and heavy activities. the time allocated for each activity of the day is 9, 4, 10, and 1-h, respectively (see table 1 ). four kinds of their daily activity patterns were set up, assuming that they would have spent most of their time at home due to requests for self-reflection. the variables and the calculated reduced dose pm2.5 (µg) for the 10-year-old children per day and over two months after the self-reflection of each city are summarized in table 1 . in table 1 figure 8 shows the reduced dose pm2. 5 10-year-old children (µg) at br. and ai regions over two months after the city lockdown/self-reflection of each city. (2014), respectively. figure 8 shows the reduced dosepm2.5 10-year-old children (μg) at br. and ai regions over two months after the city lockdown/self-reflection of each city. wuhan, which had the largest decrease of pm2.5 concentration (18 μg/m 3 ), also showed the largest reduced dosepm2.5 10-year-old children (3,660 μg at br. and 6,222 μg at ai), followed by daegu (445 μg at br. and 1,287 μg at ai) and tokyo (18 μg at br. and 52 μg at ai) additionally, the reduced dosepm2.5 10-year-old children (μg) varied greatly depending on the children's behavior patterns. in all three cities, the reduced dosepm2.5 10-year-old children (μg) was high, in order of light activity > heavy activity > sleep > sitting/rest. the reason why the light activity was assessed to be a higher dose than heavy activity is because the activity time was set to be ten times higher. it is also clear that much more pm2.5 deposits at ai, a deeper part of the lungs, than in the bronchiolar. through the thymic stromal lymphopoietin activation in mice, liu et al. [30] suggested that the exposure to concentrations of pm2.5 equivalent to moderate pollution (31.6 μg of pm2.5) and severe pollution (100 μg of pm2.5) has been linked to the allergic airway inflammation (aai) in mice. it is very meaningful to calculate the amount of the exposure dose that can cause inflammation in humans (dosehuman (mg/kg)) indirectly through the experimental results with mice. therefore, we tried to calculate the dose for 10-year-old children (dosepm2.5 10-year-old children (mg/kg)) through the following equation, for the dose conversion from mouse to human introduced by balakrishnan and jacob [31] . dosepm2.5 10-year-old children (mg/kg) = dosemouse(mg/kg) × km ratio where km ratio = . each km i.e., km mouse and km 10-year-old children can be calculated with the following equation: the km 10-year-old children for the chinese, korean, and japanese were calculated by the average weight and body surface area (bsa) of boys and girls in each country. their bsa were also wuhan, which had the largest decrease of pm 2.5 concentration (18 µg/m 3 ), also showed the largest reduced dose pm2. 5 10-year-old children (3,660 µg at br. and 6,222 µg at ai), followed by daegu (445 µg at br. and 1,287 µg at ai) and tokyo (18 µg at br. and 52 µg at ai) additionally, the reduced dose pm2. 5 10-year-old children (µg) varied greatly depending on the children's behavior patterns. in all three cities, the reduced dose pm2. 5 10-year-old children (µg) was high, in order of light activity > heavy activity > sleep > sitting/rest. the reason why the light activity was assessed to be a higher dose than heavy activity is because the activity time was set to be ten times higher. it is also clear that much more pm 2.5 deposits at ai, a deeper part of the lungs, than in the bronchiolar. through the thymic stromal lymphopoietin activation in mice, liu et al. [30] suggested that the exposure to concentrations of pm 2.5 equivalent to moderate pollution (31.6 µg of pm 2.5 ) and severe pollution (100 µg of pm 2.5 ) has been linked to the allergic airway inflammation (aai) in mice. it is very meaningful to calculate the amount of the exposure dose that can cause inflammation in humans (dose human (mg/kg)) indirectly through the experimental results with mice. therefore, we tried to calculate the dose for 10-year-old children (dose pm2. 5 10-year-old children (mg/kg)) through the following equation, for the dose conversion from mouse to human introduced by balakrishnan and jacob [31] . dose pm2. 5 10-year-old children (mg/kg) = dose mouse (mg/kg) × k m ratio (3) where k m ratio = k m mouse k m 10−year−old children the k m 10-year-old children for the chinese, korean, and japanese were calculated by the average weight and body surface area (bsa) of boys and girls in each country. their bsa were also calculated from following [32] [33] [34] : then, the dose pm2.5 for the aai of 10-year-old children, i.e., the aai dose pm2. 5 10-year-old children (mg), can be calculated by following: aai dose pm2. 5 10-year-old children (mg) = dose pm2. 5 10-year-old children (mg/kg) × weight 10-year-old children (kg) (6) in this study, the aai dose pm2. 5 10-year-old children (mg) was calculated by the dose mouse (mg/kg), with 1.58 mg/kg (31.6 µg per mouse), on the assumption of medium air quality [30] . additionally, the time (day) to reaching the aai dose pm2. 5 10-year-old children can be calculated by the following: day to reaching aai dose pm2. 5 where the daily dose pm2. 5 10-year-old children is the reduced dose pm2.5 (µg) at the bronchiolar of the 10-year-old children per day during the city lockdown/self-reflection and is specified in table 2 . figure 9 , the number of days it takes to cause allergic airway inflammation (aai) by pm2.5 exposure, before and after the city lockdown/self-reflection at each city. in the case of wuhan, it took 25 days before the city lockdown, but 35 days after the city lockdown. meanwhile, it was calculated that it took 130 to 164 days in daegu and 570 to 587 days in tokyo. while it is easy to predict that inhaling clean air is good for children's health, this study was able to quantitatively evaluate that the temporarily reduced pm 2.5 concentration due to covid-19 was effective for the delaying the aai in three cities of asia. meanwhile, there is still a possibility that much more harmful household air pollutants may have been exposed by staying indoors during the city lockdown/self-reflection periods. figure 9 . the number of days it takes to cause allergic airway inflammation (aai) by pm2.5 exposure, before and after the city lockdown/self-reflection at each city. figure 9 . the number of days it takes to cause aai by pm2.5 exposure, before and after the city lockdown/self-reflection at each city. in the case of wuhan, it took 25 days before the city lockdown, but 35 days after the city lockdown. meanwhile, it was calculated that it took 130 to 164 days in daegu and 570 to 587 days in tokyo. while it is easy to predict that inhaling clean air is good for children's health, this study was able to quantitatively evaluate that the temporarily reduced pm2.5 concentration due to covid-19 was effective for the delaying the aai in three cities of asia. meanwhile, there is still a possibility that much more harmful household air pollutants may have been exposed by staying indoors during the city lockdown/self-reflection periods. in this study, the air quality variation was estimated in three cities in asian countries experiencing the explosive outbreak of covid-19, in a short period of time. the data assessment based on the actual measurements from the air pollution monitoring stations of each city clearly showed a quantitative reduction of pm2.5 and no2. the health effect of the pm2.5 dose (reduced due to covid-19) on 10-year-old children in each city was also quantitatively assessed. especially, this study was able to quantitatively evaluate that the temporarily reduced pm2.5 concentration due to covid-19 was effective for the delaying the aai in three cities of asia. there are many unmeasured factors other than pm2.5 level responsible for making the delay on aai. therefore, the delay effect of aai estimated in the present study may be limited only by the effects of the reduced pm2.5. according to the study of cohen et al. [10] , 4.6 million people are dying annually because of the diseases and illnesses directly related to poor air quality. therefore, the delay effect of aai estimated in this study is limited only by the effects of the reduced pm2.5. according to the study of cohen et al. [10] , 4.6 million people are dying annually because of the diseases and illnesses directly related to poor air quality. therefore, in terms of long-term human health hazards, the threat of air pollution can be much greater than that of covid-19. therefore, we should not only try to overcome the current situation of the covid-19 pandemic, but at the same time seriously consider the new eco-lifestyle that we have to pursue after the end of covid-19 pandemic. in this study, the air quality variation was estimated in three cities in asian countries experiencing the explosive outbreak of covid-19, in a short period of time. the data assessment based on the actual measurements from the air pollution monitoring stations of each city clearly showed a quantitative reduction of pm 2.5 and no 2 . the health effect of the pm 2.5 dose (reduced due to covid-19) on 10-year-old children in each city was also quantitatively assessed. especially, this study was able to quantitatively evaluate that the temporarily reduced pm 2.5 concentration due to covid-19 was effective for the delaying the aai in three cities of asia. there are many unmeasured factors other than pm 2.5 level responsible for making the delay on aai. therefore, the delay effect of aai estimated in the present study may be limited only by the effects of the reduced pm 2.5 . according to the study of cohen et al. [10] , 4.6 million people are dying annually because of the diseases and illnesses directly related to poor air quality. therefore, the delay effect of aai estimated in this study is limited only by the effects of the reduced pm 2.5 . according to the study of cohen et al. [10] , 4.6 million people are dying annually because of the diseases and illnesses directly related to poor air quality. therefore, in terms of long-term human health hazards, the threat of air pollution can be much greater than that of covid-19. therefore, we should not only try to overcome the current situation of the covid-19 pandemic, but at the same time seriously consider the new eco-lifestyle that we have to pursue after the end of covid-19 pandemic. clinical features of patients infected with 2019 novel coronavirus in covid-19 coronavirus/death toll: national health commission (nhc) of the people's republic of china isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-ncov) outbreak coronavirus disease (covid-19) situation report in japan nasa: airborne nitrogen dioxide plummets over china air pollution kills 600,000 children each year according to who how long, what, and where: air 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neural network in wuhan impact of the covid-19 event on air quality in central china covid-19 as a factor influencing air pollution? environ. pollut. 2020, 263, 114466 divergent effects of urban particulate air pollution on allergic airway responses in experimental asthma: a comparison of field exposure studies the effect of air pollution on lung development from 10 to 18 years of age the short term burden of ambient fine particulate matter on chronic obstructive pulmonary disease in ningbo all about allergies, kidshealth size-resolved respiratory-tract deposition of fine and ultrafine hydrophobic and hygroscopic aerosol particles during rest and exercise indoor/outdoor relationships of airborne particles under controlled pressure difference across the building envelope in field investigation of pm 2.5 in schoolchildren's houses and classrooms in changsha situations and countermeasure for indoor pm2 influences of biometrical parameters on aerosol deposition in the icrp 66 human respiratory tract model: japanese and caucasians fine particulate matter aggravates allergic airway inflammation through thymic stromal lymphopoietin activation in mice a simple practice guide for dose conversion between animals and human standardization of the body surface area (bsa) formula to calculate the dose of anticancer agents in japan determination of hand surface area by sex and body shape using alginate human body surface area database and estimation formula this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license the data of aqmss were published online by the environmental authorities of each city. these data were the basis of this paper and provided a great reference of data discussion. the authors observe the rules of the use of open data, and also express their deep appreciation for the provision of data. the authors declare no conflict of interest. key: cord-252804-u7tz6xzz authors: ciotti, marco; angeletti, silvia; minieri, marilena; giovannetti, marta; benvenuto, domenico; pascarella, stefano; sagnelli, caterina; bianchi, martina; bernardini, sergio; ciccozzi, massimo title: covid-19 outbreak: an overview date: 2020-04-07 journal: chemotherapy doi: 10.1159/000507423 sha: doc_id: 252804 cord_uid: u7tz6xzz background: in late december 2019, chinese health authorities reported an outbreak of pneumonia of unknown origin in wuhan, hubei province. summary: a few days later, the genome of a novel coronavirus was released (http://virological.org/t/novel-2019-coronavirus-genome/319; wuhan-hu-1, genbank accession no. mn908947) and made publicly available to the scientific community. this novel coronavirus was provisionally named 2019-ncov, now sars-cov-2 according to the coronavirus study group of the international committee on taxonomy of viruses. sars-cov-2 belongs to the coronaviridae family, betacoronavirus genus, subgenus sarbecovirus. since its discovery, the virus has spread globally, causing thousands of deaths and having an enormous impact on our health systems and economies. in this review, we summarize the current knowledge about the epidemiology, phylogenesis, homology modeling, and molecular diagnostics of sars-cov-2. key messages: phylogenetic analysis is essential to understand viral evolution, whereas homology modeling is important for vaccine strategies and therapies. highly sensitive and specific diagnostic assays are key to case identification, contact tracing, identification of the animal source, and implementation of control measures. in december 2019, an outbreak of pneumonia of unknown origin was reported in wuhan, hubei province, china. most of these cases were epidemiologically linked to the huanan seafood wholesale market. inoculation of bronchoalveolar lavage fluid obtained from patients with pneumonia of unknown origin into human airway epithelial cells and vero e6 and huh7 cell lines led to the isolation of a novel coronavirus, sars-cov-2, previously named 2019-ncov [1] . coronaviruses belong to the family coronaviridae and are positive single-stranded rna viruses surrounded by an envelope. they are divided into four genera: alpha-, beta-, gamma-, and deltacoronavirus. to date, seven human coronaviruses (hcovs) have been identified, which fall within the alpha-and betacoronavirus genera. the alphacoronavirus genus includes hcov-nl63 and hcov-229e, while the betacoronavirus genus comprises hcov-oc43, hcov-hku1, sars-cov (severe acute respiratory syndrome coronavirus), mers-cov (middle east respiratory syndrome-related coronavirus), and the novel sars-cov-2 (severe acute respiratory syndrome coronavirus 2) [2] [3] [4] [5] [6] [7] . the alphacoronaviruses hcov-nl63 and hcov-229e and the betacoronaviruses hcov-oc43 and hcov-hku1 usually cause common colds, but also severe lower respiratory tract infections, especially in the elderly and children [8] . hcov-nl63 infection has also been significantly associated with croup (laryngotracheitis) [9, 10] , and hcov-oc43 infection with severe lower respiratory tract infection in children [11] . sars-cov and mers-cov are zoonotic in origin; they cause severe respiratory syndrome and are often fatal [12] . since the beginning of the epidemic in late december 2019, sars-cov-2 has now spread to all continents, and as of march 18, 2020 , the who communicated 179,111 confirmed cases and 7,426 deaths globally (situation report-57). in this review, we try to summarize the most recent knowledge about some epidemiological parameters including clinical symptoms, transmissibility of the virus, and the incubation period. furthermore, the molecular diagnostics, protein modeling of the spike glycoprotein, and phylogenesis of the virus will be discussed. patients infected with sars-cov-2 can present a wide range of symptoms ranging from mild to severe. fever, cough, and shortness of breath are the most common symptoms reported in 83, 82, and 31% of patients [13] . in those patients who develop pneumonia, multiple mottling and ground-glass opacity are described on chest xray [1, 13] . patients that develop acute respiratory distress syndrome may worsen rapidly and die of multiple organ failure [13] . it has also been reported that about 2-10% of the patients with covid-19 had gastrointestinal symptoms such as vomiting, diarrhea, and abdominal pain [13, 14] . diarrhea and nausea preceded the development of fever and respiratory symptoms in 10% of patients [13] . at present, the exact mechanism of transmission of sars-cov-2 is still not completely understood. humanto-human transmission via droplets is the main route of transmission within a susceptible population. chinese health authorities reported an r 0 of 1.4-2.5 on january 23, 2020, to the who international health regulations (2005) emergency committee. transmission by asymptomatic carriers cannot be ruled out. actually, it was reported that an asymptomatic family member who traveled from the epidemic center of wuhan was most likely responsible for a familial cluster of covid-19 pneumonia once back home. her reverse transcription polymerase chain reaction (rt-pcr) result was positive for sars-cov-2, but her chest ct images did not show significant alterations [15] . another route of possible viral transmission is the oral-fecal route. the scientific literature showed that sars-cov and mers-cov are viable in environmental conditions that facilitate oral-fecal transmission. sars-cov has been detected in sewage water of two chinese hospitals in which patients with sars were treated, and mers-cov was found to be viable on different surfaces at low temperature and low humidity [16, 17] . sars-cov-2 was detected in stool of patients with covid-19 pneumonia, as well as in respiratory samples [18] . thus, it is plausible that also sars-cov-2 can be transmitted via the oral-fecal route as well as via fomites. to know the incubation period of sars-cov-2 infection is key for implementing control measures and surveillance. it has been estimated that the median incubation period is 5.1 days (95% ci, 4.5-5.8), and 97.5% of the infected subjects will develop symptoms within 11.5 days (95% ci, 8.2-15.6) of infection. based on these estimates, it can be assumed that 101 out of 10,000 cases will develop symptoms after 14 days of observation or quarantine [19] . these estimates are consistent with those of other studies that reported a mean incubation period of 6.4 days (95% credible interval: 5.6-7.7), ranging from 2.1 to 11.1 days (2.5th to 97.5th percentile) [20] or 5.2 days (95% ci, 4.1-7.0), with the 95th percentile of the distribution at 12.5 days [21] . thus, 14-day monitoring is advised following contact with a probable or confirmed sars-cov-2 case [22] . confirmation of cases with suspected sars-cov-2 infection is performed by detection of unique viral sequences with nucleic acid amplification tests such as reverse real-time pcr (rrt-pcr). as soon as on january 7, 2020, the chinese health authorities had declared that a novel coronavirus was responsible for this outbreak of pneumonia in wuhan, a european network of academic and public laboratories designed an rrt-pcr protocol based on the comparison and alignment of previously available sars-cov and bat-related coronavirus genome sequences as well as five sequences derived from the novel coronavirus sars-cov-2 made available by the chinese authorities [23] . three assays were developed. the first-line assay targets the e gene encoding for the envelope protein, which is common to the sarbecovirus subgenus, while the second specific assay targets the rdrp gene encoding for rna-dependent rna polymerase. this assay contains two probes: one probe, which reacts with the sars-cov and sars-cov-2 rdrp gene, and a second probe (rdrp_sarsr-p2) which is specific to sars-cov-2. finally, the third additional confirmatory assay targets the nucleocapsid (n) gene. this last assay was not further validated because it is slightly less sensitive [23] . this protocol was adopted in more than 30 european laboratories [24] . recently, a novel rrt-pcr assay targeting a different region of the rdrp/hel gene of sars-cov-2 has been developed that showed a higher sensitivity and specificity than the rdrp-p2 assay [25] . currently, several amplification protocols are available on the market and validated for in vitro diagnostic use (ce marked): genefinder tm covid-19 plus real-amp kit (osang healthcare co., ltd, south korea); genesig ® real-time pcr coronavirus (covid-19) (genesig, uk); allplex tm 2019-ncov assay (seegene, south korea), etc. highly sensitive and specific diagnostic assays are key to the identification of cases, contact tracing, identification of the animal source, and implementation of control measures [26] [27] [28] . when performing nucleic acid amplification test assays, it is useful to remind ourselves that several factors can be responsible for a negative result in an infected individual, such as the poor quality of a specimen, the time of specimen collection (specimen collected too early or too late during infection), inappropriate handling or shipment of the specimen, and technical reasons. coronavirus entry into the host cell is mediated by the transmembrane spike (s) glycoprotein that forms homotrimers that protrude from the viral surface [29] . the s protein is composed of the two subunits s1 and s2 responsible for binding to the host cell receptor and fusion of the viral and cellular membranes, respectively. different coronaviruses use different domains within the s1 subunit to enter the cell. these domains are named s a and s b . sars-cov and sars-related coronaviruses interact with the angiotensin-converting enzyme 2 (ace2) via domain s b to enter target cells [30] [31] [32] [33] [34] . it has recently been shown that sars-cov-2 binds the ace2 receptor via the s b domain similarly to sars-cov, and that murine polyclonal antibodies inhibited sars-cov-2 entry into the cell mediated by s. these data suggest that crossneutralizing antibodies targeting conserved s epitopes elicited by vaccination could be used against sars-cov-2, sars-cov, and sars-related coronaviruses [35] . previous studies have shown the presence of positive selective pressure on the nucleocapsid, spike glycoprotein, and orf1ab regions, while until now no evidence of a positive selective pressure has been found on the envelope, membrane, and other orf proteins. in the nucleocapsid region, significant (p < 0.05) pervasive episodic selection was found in 2 sites. in amino acid position 380 of the wuhan coronavirus sequence there is a gln residue instead of an asn, while in amino acid position 410 there is a thr residue instead of an ala. significant (p < 0.05) pervasive negative selection in 6 sites (14%) has been evidenced and confirmed by fubar (fast unconstrained bayesian approximation) analysis [36] . in the spike glycoprotein region, significant (p < 0.05) pervasive episodic selection was found in 2 different sites (536th and 644th nucleotide position using the reference sequence). in the 536th amino acid position of the wuhan coronavirus sequence there is an asn residue instead of an asp acid residue, while in amino acid position 644 there is a thr residue instead of an ala residue. significant (p < 0.05) pervasive negative selection in 1,065 sites (87%) has been evidenced and confirmed by fubar analysis, suggesting that the s region could be highly conserved [36] . regarding the sites under positive selective pressure found on the spike glycoprotein, the results have shown that amino acid position 536 in covid-19 has an asn residue, while the bat sars-like coronavirus has a gln 4 doi: 10.1159/000507423 residue; the sars virus, instead, has an asp residue. in amino acid position 644 of the covid-19 sequence there is a thr residue, while the bat sars-like virus has a ser residue; instead, the sars virus has an ala residue. another study highlighted that several key residues responsible for binding of the sars-cov receptor-binding domain to the ace2 receptor were variable in the cov-id-19 receptor-binding domain (including asn439, asn501, gln493, gly485, and phe486; covid-19 numbering), and a number of deletion events in amino acid positions 455-457, 463-464, and 485-497 occurred in the bat-derived strains [37] . also in the orf1ab region, potential sites under positive selective pressure have been found (p < 0.05). particularly, in the amino acid position 501, covid-19 has a gln residue, the bat sars-like coronavirus has a thr residue, and the sars virus has an ala residue. in position 723 of the covid-19 sequence there is a ser residue, while the bat sars-like virus and the sars virus have a gly residue. in amino acid position 1,010, covid-19 has a pro residue, the bat sars-like coronavirus has a his residue, and the sars virus has an ile residue. as for the residue in position 723 (543 in the nsp3 protein), the covid-19 sequence displays a ser, replacing for gly in the bat sars-like and sars coronaviruses. in this case, it may be argued that this substitution could increase local stiffness of the polypeptide chain both for a steric effect (in contrast to ser, gly has no side chain) and for the ability of the ser side chain to form h-bonds. moreover, ser can act as a nucleophile in determined structural environments, such as those of enzymes' active sites, and can be a phosphorylation site. however, within the i-tasser model, this position is predicted to have low solvent accessibility. regarding the amino acid position 1,010 (corresponding to position 192 of the nsp3 protein), the homologous region of the bat sars-like coronavirus and sars virus has a polar and an apolar amino acid, respectively, while covid-19 has a pro residue. in this case, it may be speculated that due to the steric bulge and stiffness of pro, the molecular structure of covid-19 may undergo a local conformational perturbation compared to the proteins of the other two viruses. in nsp3, the mutation falls near the polyprotein domain similar to a phosphatase present also in the sars coronavirus (pdb code 2acf) playing a key role in the replication process of the virus in infected cells [38] . according to the i-tasser model, the position is partially accessible to the solvent. the sites under positive selective pressure in this protein may suggest a possible interpretation of some clinical features of this virus compared to sars and bat sars-like coronavirus. this analysis should find which are probably the most common sites undergoing an amino acid change, providing insight into some important proteins of covid-19 that are involved in the mechanism of viral entry and viral replication. these data should contribute to improving our understanding of how this virus acts in its pathogenicity. furthermore, to identify a potential molecular target is fundamental to follow the molecular evolution of the virus, which can suggest some interesting sites for a potential therapy or vaccine. the structural similarity of the region in which the positive selective pressure occurs, and the stabilizing mutation falling in the endosome-associated protein-like domain of the nsp2 protein, should be probable reasons why this virus is more contagious than sars. instead, the destabilizing mutation located near the phosphatase domain of the nsp3 protein may explain why viral replication is slower than in sars with a longer incubation period. anyway, further studies are needed on this aspect [39] . the availability of protein structural information is an essential prerequisite for the interpretation of biological phenomena. in this case, knowledge of the virus's protein structure would greatly enhance the possibility of understanding the biological meaning of the observed muta-tions. now, only the x-ray structure of covid-19 nsp5 protease (pbd code 6lu7) is available, although it is expected that many other structures will become available soon. in the meantime, homology modeling could provide preliminary structural clues. homology modeling needs structural templates sharing sufficient sequence similarity to the targets. in figure 1 and table 1 , a list of potential templates for homology modeling of the proteins coded by the covid-19 genome is displayed. the structures with the largest coverage and the greatest sequence identity have been incorporated into figure 1 and table 1 . according to this list, it is evident that most of the viral proteins are at modeling distance from pdb structures. this information should be exploited as soon as possible. phylogenetic analysis of the sars-cov-2 genomes showed that the novel coronavirus responsible for the pneumonia outbreak in wuhan, china, belongs to the betacoronavirus genus, subgenus sarbecovirus [37] . within the betacoronavirus genus, 2019-ncov (sars-cov-2) is distant from sars-cov (about 79% identity) and mers-cov (about 50% identity) responsible for the 2002-2003 [4] and 2012 [7] epidemics, respectively, but closely related (88% identity) to the two bat-derived (sars)-like coronaviruses bat-sl-covzc45 and bat-sl-covzxc21 [37] . the origin of the virus is still unclear; however, genomic analysis suggests that sars-cov-2 is most closely related to viruses previously identified in bats (fig. 2) . it is plausible that there were other intermediate animal transmissions before its introduction into humans. how-ever, there is no evidence of snakes as an intermediary [36] . using 74 publicly shared novel coronavirus (ncov) genomes, we examined genetic diversity to infer the date of the common ancestor and the rate of spread. the high similarity of the genomes suggests they share a recent common ancestor. otherwise, we would expect a greater number of differences between the samples. the jump from bats to humans most likely occurred in late november or early december 2019 (november 25, 2019; 95% hpd: september 28, 2019; december 21, 2019) [40] . previous research on related coronaviruses suggests that these viruses accumulate between 1 and 3 changes in their genome per month (rates of 3 × 10 -4 to 1 × 10 -3 per site per year). molecular clock calibration estimated the evolutionary rate of the sars-cov-2 whole genome sequences at 6.58 × 10 -3 substitutions per site per year (95% hpd: 5.2 × 10 -3 to 8.1 × 10 -3 ). the outbreak first started in wuhan, china, but cases have been identified in many east and south-east asian countries, the usa, australia, the middle east, and europe. vietnam, japan, and germany have reported transmission within the country, albeit always with a known link to wuhan, china (fig. 3) . this study is a picture of the current research on molecular evolution, epidemiology, and diagnostics in response to the outbreak of covid-19. many studies have been published within different scientific disciplines with the intent to control and prevent this pandemic. phylogenetic analysis and homology modeling add new knowledge together with epidemiological and diagnostic methods. studies exploring the genome and the structure of the viral proteins are essential in order to define preven-tion and control measures to minimize the impact of the outbreak. all this knowledge will pave the way for the development of a vaccine and antiviral therapy. a novel coronavirus from patients with pneumonia in china the morphology of three previously uncharacterized human respiratory viruses that grow in organ culture isolation from man of "avian infectious bronchitis viruslike" viruses (coronaviruses) similar to 229e virus, with some epidemiological observations severe acute respiratory syndrome identification of a new human coronavirus characterization and complete genome sequence of a novel coronavirus, coronavirus hku1, from patients with pneumonia isolation of a novel coronavirus from a man with pneumonia in saudi arabia recently discovered human 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middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease structural insights into coronavirus entry isolation and characterization of a bat sars-like coronavirus that uses the ace2 receptor stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis cryo-em structure of the sars coronavirus spike glycoprotein in complex with its host cell receptor ace2 angiotensin-converting enzyme 2 is a functional receptor for the sars coronavirus structure of sars coronavirus spike receptor-binding domain complexed with receptor structure, function, and antigenicity of the sars-cov-2 spike glycoprotein the 2019-new coronavirus epidemic: evidence for virus evolution genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding structural basis of severe acute respiratory syndrome coronavirus adp-ribose-1′′-phosphate dephosphorylation by a conserved domain of nsp3 cov-id-2019: the role of the nsp2 and nsp3 in its pathogenesis the global spread of 2019-ncov: a molecular evolutionary analysis. pathog glob health the authors have no conflicts of interest to declare. there was no funding for this review. key: cord-030934-t7akdu6x authors: bahrami, afsane; ferns, gordon a title: genetic and pathogenic characterization of sars-cov-2: a review date: 2020-08-26 journal: nan doi: 10.2217/fvl-2020-0129 sha: doc_id: 30934 cord_uid: t7akdu6x the first case of coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was reported in december 2019. this virus belongs to the beta-coronavirus group that contains a single stranded rna with a nucleoprotein within a capsid. sars-cov-2 shares 80% nucleotide identity to sars-cov. the virus is disseminated by its binding to the ace2 receptors on bronchial epithelial cells. the diagnosis of covid-19 is based on a laboratory-based reverse transcription polymerase chain reaction (rt-pcr) test together with chest computed tomography imaging. to date, no antiviral therapy has been approved, and many aspects of the covid-19 are unknown. in this review, we will focus on the recent information on genetics and pathogenesis of covid-19 as well as its clinical presentation and potential treatments. mers-cov s protein s1 s1 sars-cov s protein 55´3 a orf1a mers-cov ( constitute the viral envelope [36] . accessory proteins appear to promote the adaptation of covs to human host cells [37] . genomic analysis of ten genome of sars-cov-2 isolated from nine patients demonstrated 99.98% nucleotide identity [38] . another report found that 99.8-99.9% sequence similarity in sample of five infected patients [39] . phylogenetic analysis demonstrates that sars-cov-2 shares 50 and 80.0% nucleotide identity to mers-cov and sars-cov, respectively [8, 13, 38] . the sars-cov-2 constitutes a clade among the sub-genus sarbecovirus [40] . bioinformatics analysis of the viral genome from one covid-19 patient shared 89 and 82% sequence similarity with bat sars-like-covzxc21 and human sars-cov, respectively [41] . however, the external subunit of spike rbd of sars-cov-2 has only 40% amino acid (aa) identity with other sars-associated covs [41] . the s-protein of sars-cov-2 is longer (1282 aa) than for other viruses such as sars-cov (1255 aa) and bat sars-like covs (1246 aa). the s-glycoprotein of sars-cov-2 has been found to have three short insertions at the n-terminal end, with four variations in the receptor binding site within the rbd compared with sars-cov [42] . notably, sars-cov-2 orf3b codifies a new short protein. moreover, its novel orf8 sequence possibly encode a secreted protein with an α-helical structure with a β-sheet(s) consisting of six strands [41] . the high levels of genetic identity (96.3%) between the sars-cov-2 and bat-cov ratg13 does not indicate the precise variant that may have led to the outbreak in humans, although it has been suggested that the likelihood that the novel cov has derived from bats is very probable [43] . sars-cov-2 and ratg13 differ with respect to the number of major genomic properties, in which sars-cov-2 harbors a polybasic (furin) cleavage site insertion at the connection of the two subunits of the s-protein, s1 and s2 [44] . the n-protein is hidden within phospholipid bilayers and coated via two distinctive forms of s-proteins including the spike glycoprotein trimmer which is present in all covs, as well as the hemagglutinin-esterase (he) solely found in certain covs. for instance, sars-cov-2 does not appear to have the he gene. the m and e proteins are found inside the s-glycoproteins within the viral envelope [45] . the s, e, m, n and orf3a genes of sars-cov-2 are predicted to be 3822, 228, 669, 1260 and 828 nucleotides in length, respectively. moreover, sars-cov-2 has been predicted to contain an orf8 gene, of 366 nucleotide size, situated between the m and n corresponding orf genes [45] . the sars-cov sequence reveals serine substituting for glycine in the residue at position 543 of the nsp3 protein in bat sars-like and sars-cov. this aa substitution could promote local stiffness of the polypeptide chain for steric impact and potency of the serine side-chain to constitute h-bonds. beside, serine is a nucleophile that can establish structural environments, like those at active sites of enzyme. mutations in the nsp3 protein were reported to affect the replication of sars-cov-2 in infected cells [46, 47] . it has been reported that the single n501t variant in sars-cov-2's s-protein may enhance binding affinity for the ace2 cellular receptor [28] . furthermore, a single n439r mutation in sars-cov-2 rbd promotes its ace2-receptor binding and, thus potentially enhances human-to-human transmission [48, 49] . by studying the crystal structure of sars-cov-2 rbd binding to the human ace2 receptor has shown that the ace2 receptor-binding ridge in sars-cov-2 rbd results in a more compact conformation, leading structural alterations at the rbd/ace2 interface versus the sars-cov [48] . overall, sars-cov-2 binding affinity for ace2 is 10-20-times greater than for other sars-associated covs [50] . a missense mutation at the 614 position of s protein (aspartate to glycine, d614g mutation), in the spike protein of sars-cov-2, which has emerged as a predominant clade in europe (66% sequences) and is spreading worldwide (44% sequences). the d614g mutation promotes viral infectivity and transduction of multiple human cell types and mitigates neutralization sensitivity to individual convalescent sera [51] [52] [53] [54] . lipids play important roles at different stages in the covs life cycle. covs recruit intracellular membranes of the host cells to produce new compartments, or double membrane vesicles, which are used for the replication of the virion particle genome [55] . recently, an important lipid processing enzyme, known as cpla2 α has been reported to be related to the formation of double membrane vesicle and cov's amplification [56] . it has been demonstrated that the enzyme, phospholipase a2 group iid, is involved in anti-inflammation or proresolving lipid mediator regulation which may lead to worse outcomes in a sars-cov infection animal model by modulating the immune response [57] . it has been shown that there is a distinct insert that includes basic aas in the s1/s2 priming loop of sars-cov-2, which is not found in sars-cov or any sars-associated covs. it may substantially alter the entry pathway of sars-cov-2 compared with other viruses of the β-covs lineage b [58] . in a recent report it was shown that sars-cov-2's s-protein entry into 293/human ace2 receptor cells is primarily mediated via endocytosis, and that pikfyve, a tpc2 and cathepsin l are crucial for virus entry. pikfyve is the key enzyme in the early endosome involved in the synthesis of pi(3,5)p2 and its main downstream effector, tpc2. the s protein of sars-cov-2 could also stimulate syncytia in 293/human ace2 cells independently of exogenous protease [59] . in a study of 452 sars-cov-2 infected patients, it was found that severely affected cases had lower numbers of blood lymphocytes, percentages of monocytes, basophils and eosinophils as well as increased leukocytes numbers and neutrophil-lymphocyte-ratio. in most patients with unfavorable progression of covid-19, elevated concentrations of infection-associated markers and inflammatory cytokines was observed. the frequency of t cells was significantly lower, and less effective in severely affected subjects. both t helper (th) cells and suppressor t cell numbers in patients with covid-19 were below the reference range. the percentage of naive helper t cells was increased, and memory helper t cells and regulatory t cells reduced in severe conditions [60] . furthermore, simultaneous to the infection with sars-cov-2, cd4 + t lymphocytes are quickly over-activated to switch to the pathogenic th1 cells producing gm-csf. the cytokines environment activates inflammatory cd14 + cd16 + monocytes, leading to over-expression of il-6 and enhances the inflammatory response. regarding the increased infiltrations of inflammatory cells that have been found in lungs of severe sars-cov-2 infected patients [61, 62] , these population of abnormal and noneffective pathogenic th1 cells and inflammatory granulocytes may go to the pulmonary circulation and by immune stimulation, lead to functional impairment of the lungs and eventually death [63] . inflammasomes are very large intracellular poly-protein signaling complexes which are constitute in the cytosol as an inflammatory immune reaction to endogenous danger stimuli [64] . nlrp3 responds to wide spectra of pathogens and endogenous signals, and is involved in the molecular pathway of various auto-inflammatory disorders [65] . it has been reported that the sars-cov can induce the nlrp3 inflammasome in macrophages through orf8b. whereas sars-cov infects macrophages or monocytes, sufficient orf8b may be present to impact on the autophagy-lysosome pathway, and nlrp3 inflammasomes. sars-cov replicates efficiently in lung epithelial cells. these cells also amplify nlrp3 and support assembly of nlrp3 inflammasomes. in sars-cov patients, the full effect of the orf-8b on these inflammatory cascades was observed in the lung epithelium. interestingly, orf8b may be involved in the 'cytokine storm' or 'cytokine cascade' and inflammasome induction which happens within intensive sars-cov infection [66] . sars-cov-2 infection stimulates the immune response in two stages. in the early stages, a particular adaptive immune response is necessary to eradicate the virus and to impede progress to a more severe condition. the protective immune response at this phase requires that the host should have excellent general health and a suitable genetic context which provides antiviral immunity [67] . although, when the immune response protection is disabling, virus will disseminate and great damage to the affected tissues occurs, particularly in organs with a high levels of ace2 receptor expression. the injured cells activate innate inflammation within the lungs which is mainly mediated through pro-inflammatory macrophages/monocytes. lung inflammation is the major reason for the fatal respiratory disease at the severe stage of covid-19 [68] . in viral infections, host antiviral micrornas participate in the regulation of immune response to virus and are capable of targeting viral genes and interfere with replication, mrna expression and protein translation of virion particle gene. sardar et al. predicted the antiviral host-micrornas specifically for covid-19. they reported a list of six micrornas related to covid-19 including hsa-let-7a, hsa-mir101, hsa-mir126, hsa-mir23b, hsa-mir378 and hsa-mir98 which has been previously reported to be related to other viral infections, such as hiv [69] . virion particles spread from the respiratory mucosa, by binding to the ace2 receptors on ciliated bronchial epithelial cells, and after that may engage with other cells [70] . in one report from wuhan, the average incubation period of 425 sars-cov-2 infected patients was 5.2 days, but it this differed between individuals [71, 72] . until now, most patients with covid-19 have initially presented with mild manifestations in other words dry cough, sore throat and fever which spontaneously resolve. although, some patients have developed other more severe disease such as organ failure, septic shock, pulmonary edema, dyspnea, myalgia, fatigue and acute respiratory distress syndrome [73] . in contrast to sars-cov, patients infected with sars-cov-2, development of upper respiratory tract signs and manifestations are less common, suggesting that sars-cov-2 may target cells in the lower airway [74] . among cases with severe dyspnea, more than 50% have required intensive care. some covid-19 cases do not present with fever or radiologic abnormalities on admission, which makes initial diagnosis difficult [75] . the main characteristics of covid-19 on preliminary ct examination including bilateral multi-lobar groundglass opacities with a peripheral/posterior distribution and patchy consolidation, primarily in the lower lobes and fewer inside the right middle lobe [76] . the main reported laboratory test abnormalities in cases with severe covid-19 infection include: increased levels of liver enzymes (ldh, alt and ast), total bilirubin, creatinine, cardiac troponin, d-dimer, prothrombin time, procalcitonin and crp [77] . the histology of liver specimens of sars-cov infected patients have revealed a remarkable liver injury with an increase in mitotic cells, along with eosinophilic bodies as well as balloon-like hepatocytes [78] . cardiac involvement is another prominent manifestation of covid-19 and is closely related to a poor outcome [79] . in a recent systematic review, the incidence rate of diarrhea varied from 2 to 50% in covid-19 patients. it may develop earlier, or following the respiratory symptoms. findings of several studies showed that viral rna shedding is detect for a longer time period compared with nasopharyngeal swabs [50] . in an investigation on 1099 covid-19 patients, of whom 23.7% had severe disease with comorbidities of hypertension, 16.2% diabetes mellitus, 5.8% coronary heart diseases and 2.3% cerebrovascular disease [80] . another study, of 140 patients with covid-19, found that 30% and 12% had history of hypertension and diabetes, respectively [81] . analysis of 487 covid-19 cases, showed that older age (odds ratio [or] = 1.06; 95% ci: 1.03-1.1), male gender (or 3.7; 95% ci: 1.7-7.7) and hypertension as a comorbidity (or 2.7; 95% ci: 1.3-5.6) are related with more severe disease on admission [82] . moreover, patients with cancer were more vulnerable to severe events from covid-19 such as admission to the intensive care unit needing invasive ventilation, or death [83] . it has been reported that the highest viral load in throat swabs occurs at the time of development of symptoms. however, viral shedding was reported to occur before the onset of symptoms, and a major proportion of transmissibility happened before first symptoms in the index case [84] . furthermore, severe covid-19 cases tend to have an increased viral load and a long virus-shedding time [85] . at present, the diagnosis of covid-19 is largely based on guideline agreement that includes laboratory tests and chest ct imaging technique [75, 86] . pcr testing of asymptomatic or mild symptomatic contacts can be used in the evaluation of peoples who have been in contact with a covid-19 case [87] , and the who has not accepted the results of a chest ct without rt-pcr conformation in the diagnosis of covid-19 [88] . chest ct is a routine imaging tool for the diagnosis of pneumonia, which is relatively easy and rapid to perform. chest ct shows typical radiographic characteristics in almost all covid-19 cases, such as peripheral/posterior distribution and patchy consolidation, and/or interstitial alterations with a peripheral distribution, so may provide benefit for diagnosis of covid-19 [89] . respiratory tract samples were collected for the diagnosis and screening of patients with sars-cov-2 pneumonia; in the 5-6 days of the initiation of symptoms, patients with covid-19 have increased viral loads in their upper and lower respiratory tracts [90, 91] . for suspected cases, real-time fluorescence (rt-pcr) was performed to detect the positive nucleic acid of sars-cov-2 in sputum, throat swabs and secretions of the lower respiratory tract specimens [92] . a nasopharyngeal and/or an oropharyngeal swab are frequently recommended for screening or diagnosis of early infection [10, 93] . a single nasopharyngeal swab has become the preferable swab as it is welltolerated by the patient and safer for the operator. serological testing detects presence of igg, igm or both. a positive elucidation has been defined as a positive lgm, or convalescent sera with a higher lgg titer >four-times in comparison with the acute phase. sars-cov-2 igg and igm are detected in whole blood, plasma, serum or specimens. antibodies increase late in the course of illness; the mean duration of sars-cov-2 igm antibody detection was reported to be 5 days, whereas igg detection about 2 week following the appearance of symptoms [94] . in contrast to respiratory samples which may disturb from false-negative results because of the sampling factors, the presence of antibodies in blood uniformly is detectable. specimens are easier to gather versus respiratory samples, such as fewer risks to the operator. the serological assay is very easy, rapid, availability of elisa platforms, requires no instrumentation and can provide results in just 15 min [95] . based on the recommendation of who, covid-19 management protocols have mostly highlighted infection prevention, patient early detection and monitoring, and best supportive care [96, 97] . no specific antiviral treatment is currently recommended for covid-19 due to lack of evidence. many treatment regimens have been assessed for covid-19, some showing promising preliminary results. a total of 2531 trials on covid-19 have been registered to date in the clinicaltrial.gov (updated 10 july 2020). several pharmacotherapeutic agents have been used including lopinavir/ritonavir, hydroxychloroquine and ifn-β-1a (table 1) . results from several in vitro and clinical studies demonstrated that chloroquine phosphate, an old agent for the treatment of malaria, had significant efficacy and acceptable safety for treatment of covid-19 [98, 99] . findings of an open-label nonrandomized clinical trial among 22 infected patients indicated that hydroxychloroquine treatment significantly reduced viral load in covid-19 cases and its effectiveness is promoted by azithromycin [99] . in a systematic review including six published articles highlighting the potency of chloroquine in attenuation the replication of sars-cov-2-associated virus [100] . but several other studies demonstrated no evidence of a strong antiviral function, or clinical benefit of the hydroxychloroquine for the treatment of patients with severe covid-19 [101, 102] . the combination of lopinavir/ritonavir (lpv-r) is extensively used for treating hiv-infected patients. lpv-r has been suggested for treatment of covid-19. a total of 199 covid-19 patients were randomly assigned to receive lpv-r (n = 99) or standard-care (n = 100). treatment with lpv-r was not different from standard care regarding the time to clinical improvement, mortality rate at 28 days, as well as detection of viral rna at different time points [103] . arbidol as a wide-spectrum antiviral compound that can inhibit viral fusion of influenza. in one study, 50 patients with laboratory-confirmed sars-cov2 were randomly divided into two arms: 34 cases received lpv-r (400 mg/100 mg, two per day) and 16 patients were administrated arbidol (0.2 g a; three per day). no difference was observed concerning fever duration between the two arms. 2 weeks after the intervention, no viral load was found in cases received arbidol, while the viral load was detectable in 44.1% of lpv-r group patients. moreover, no adverse side effects were reported in either arm [104] . nelfinavir (nfv) is a potent hiv-1 protease inhibitor that received us fda approval in 1997 for treatment of hiv infection. the antiviral activity of nfv against sars-cov-2 was reported in vero e6 cells [105] . by using an integrative computational drug-discovery method, nfv was introduced as a potential inhibitor of sars-cov-2 main protease [106] . the main protease of covs (mpro) is an important protein necessary for the proteolytic maturation of the virion particle [107] . therefore, targeting mpro is considered to havepotential as a treatment for covid-19 through suppression of the polypeptide cleavage virus [108] [109] [110] . concerning the results of molecular docking, natural polyphenols such as hesperidin, rutin, diosmin, apiin and diacetyl-curcumin have been reported to have acceptable efficacy to target sars-cov-2 mpro than nfv [111] . cytokine-directed antagonists, in other words adalimumab (tnf-α) and cmab806 (il-6) against sars-cov-2 have been evaluated in clinical trials. the variety of cytokines such as type-i ifn-i contribute to the 'cytokine storm' and pathology of sars-cov-2. therefore, targeting the upstream origin of cytokine generation could be a promising therapeutic approach [112] . utilizing an in silico model, it has been shown that antipolymerase agents including sofosbuvir, idx-184, ribavirin (rbv) and remidisvir (gs-5734; rdv) can target rna-dependent rna polymerase of sars-cov-2 [113] . the first severe-infected patient with sars-cov-2 in the usa was cured by reception of intravenous rdv [114] . due to adverse side effects, the appropriate dose of rbv in clinical setting should be given with caution. in previous experience, for example in pandemic influenza a (h1n1), and avian influenza a (h5n1), passive immunization has been successful for treating of infectious complications [115] . a remarkable reduction in viral load and mortality was observed by using convalescent plasma therapy against severe acute viral respiratory infections, such as those created by covs [116] . patients who have recovered from sars-covs infection often have high titers of neutralizing antibody and may be a precious source of convalescent plasma. the fda has also approved the administration of plasma from recovered individuals for treatment of severe covid-19 patients [117] . monoclonal antibodies sars-cov-specific human monoclonal antibody (mab) can bind potently with sars-cov-2 region. but, some of the most powerful sars-cov-particular neutralizing antibodies (i.e., m396) that target the ace2 binding site of sars-cov did not bind to sars-cov-2 s-protein, indicating that the disparity in the rbd of sars-cov and sars-cov-2 has an important effect impact on the cross-reactivity of these mabs, and so novel mabs that specifically target sars-cov-2 rbd need to be designed [112] . effective sars-cov-2 vaccines are urgently needed in order to reduce infection severity, viral shedding as well as human-human transmission, so assisting the control of the cov outbreaks. because s-protein and associated fragments, in other words rbd of sars-and mers-covs are the main targets for designing vaccines, it is speculated that homologous regions of sars-cov-2 can also be applied as prime targets for designing vaccines against this novel covs [118] . in addition, other conserved regions of sars-cov-2 including two subunits of the s-protein, m-protein as well as n-protein, can be applied as another potential target for design and development of effective vaccines. antiviral vaccines can be categorized into two broad groups: dna-and rna-based vaccines, in which individuals are injected with genetically engineered plasmid containing the dna molecule encoding the antigen against which an immune response is eligible, thus the cells machinery creates the antigen, leading to immunological response; and peptide-or protein-based vaccines that include whole-inactivated virus, individual viral proteins or subdomains, and purified or recombinant proteinaceous antigens proteins from the virus, all of which are manufactured in vitro. the candidate vaccines that have recently entered clinical development include: mrna-1273, ad5-ncov, ino-4800 and lv-smenp-dc and pathogen-specific aapc ( table 2) . several platforms have progressed to development with potential for rapid development, including dna-and rna-based platforms, followed by those for developing recombinant-subunit vaccines. rna and dna vaccines can be made quickly because they do not require culture or fermentation, instead using synthetic processes [119, 120] . even with such promising platforms, sars-cov-2 vaccine development faces serious challenges. although the virus's s glycoprotein is a promising immunogen for protection, optimization of antigen design is crucial to obtaining an optimum host immune system response. another concern is the possible exacerbation of lung disease, either directly or because of antibody-dependent enhancement due to the type 2 helper t-cell response. furthermore, as with naturally acquired infection, the optimal duration of immunity is unknown; similarly, whether single-dose vaccines will confer lengthy immunity is doubtful. in the early phases of the epidemic, early detection assists management of the disease and preventive approaches such as masks, hand hygiene compliances, prevention of public contact, voluntary home quarantine, early diagnosis, contact tracing, intelligence social distance and travel restrictions have been recommended to decrease transmission. other approaches include limiting events that may facilitate superspreader potential including religious services (marriages and funerals) [121] . many dimensions of the sars-cov-2 and corresponding disease are unknown. for instance, the role of ace2 receptors in sars-cov-2 pathogenesis remains uncertain. future studies should be concentrate on profound understating of replication, pathogenesis and biological properties applying the relevant biological methods in other words reverse genetics and molecular techniques. genome wide association studies may provide an opportunity for the identification of potential genetic factors contributed in the development of covid-19. although host genetic studies are expensive and complex, more studies are required to determine the role of host genetics (such as variation in hla genes) in the immune response to covs, and the clinical outcome of covs-mediated disease. understanding of the sar-cov-2 viral genetics during the time and geography specially review regarding to the number and repetition of viral mutations and recombination rates and their association with viral infectivity, transmissibility, severity of disease and clinical manifestation, viral load and disease outcome are important knowledge gaps that navigate our research timetable. until now, no unique antiviral therapy has been approved; so treatment is mainly based on symptomatic therapy and best supportive care. the zoonotic link of sars-cov-2 infection has not been definitively proven; although, phylogenetic analysis shows that sars-cov-2 is very similar to sars-like bat covs. lessons from other human outbreaks from pathogenic viruses such as sars-cov, mers-cov and influenza viruses are very informative and valuable. different wide-spectra antivirals agents previously used for treatment of influenza, sars-and mers-covs are under assessment for repurposing either monotherapy or in combinations to treat covid-19 cases. sars-cov-2 is a novel human pathogen, and may interact with host antiviral defense via a specific pathway. altogether, the infection and development of sars-cov-2 relies on the interplay between the virus and the patient's immune response. investigations of the area of sars-cov-2-host interplay provide response to many crucial questions in virus pathogenesis, disease control and prevention. at present, covid-19 is leading to substantial global concerns. development of valid, accurate and appropriate serological tests is urgently needed. it will be essential to quickly design and develop effective therapeutic regimen and vaccines to prevent or stop infection of this novel covs. the covid-19 has caused more infections and deaths compared with either sars or mers. according to r0 values, it is deemed that sars-cov-2 is more infectious than sars or mers. as imposition of globalization, covs will cause spreads and outbreaks with various mutant strains similarly in the coming years. with promotion of scientific collaboration, which is as a consequence of globalization, we may have more powerful means of combating covs, in which we characterize the genome structure and pathogenesis of sars-cov-2 infection very well in the near future. a present treatment is mainly supportive, but trials of vaccines and antivirals are in progress. differences in the length of the spike as it is longer in sars-cov-2 are likely to play a major role in the pathogenesis and treatment of this virus. robust coordination and collaboration between researchers, vaccine developers, international regulators, policymakers, financiers, national public health institutes and governments will be required to ensure that potential late-stage vaccine candidates can be produced in adequate amount with high safety and efficacy as well as equitably provided to all affected areas, specially low-resource regions. ) and multiple lineage-specific accessory proteins at the 3 -end. • phylogenetic analysis demonstrates that severe acute respiratory syndrome coronavirus 2 (sars-cov-2) shares 50 and 80.0% nucleotide identity to middle east respiratory syndrome cov and sars-cov, respectively. • the s-protein of sars-cov-2 is longer than for other viruses such as sars-cov and bat sars-like covs. • virion particles spread from the respiratory mucosa, by binding to the ace2 receptors on ciliated bronchial epithelial cells, and after that may engage with other cells. • the s-glycoprotein mediates binding of the virus to the sensitive human cell surface receptors, followed by fusion of the virus and host cell membranes to assist viral entrance. • sars-cov-2 infection stimulates the immune response via two stages. at the incubation and nonalarming stages, a particular adaptive immune response is needed to eradicate the virus and to impede progress to severe condition. • the injured cells activate innate inflammation within the lungs, which is mainly mediated through pro-inflammatory macrophages/monocytes. lung inflammation is the major reason for the fatal respiratory disease at the severe stage of coronavirus disease 2019 (covid-19) infection. • the main characteristics of covid-19 on preliminary computed tomography (ct) examination including bilateral multi-lobar ground-glass opacities with a peripheral/posterior distribution and patchy consolidation. • at present, the diagnosis of covid-19 is largely based on laboratory tests pcr and chest ct imaging technique. although, no specific antiviral treatment for covid-19 is currently advised due to lack of evidence. • several pharmacotherapeutic agents have been used for treatment of covid-19 patients consisting lopinavir/ritonavir, hydroxychloroquine and ifn β-1a. • effective sars-cov-2 vaccines are urgently needed in order to decrease infection severity, viral shedding as well as human-human transmission. the most advanced candidates have recently moved into clinical development, including mrna-1273, ad5-ncov, ino-4800 and lv-smenp-dc, and pathogen-specific. all authors contributed to data collection, drafting or revising the article, gave final approval of the version to be published, and agree to be accountable for all aspects of the work. this study was supported by birjand university of medical sciences. the authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. no writing assistance was utilized in the production of this manuscript. sars and mers: recent insights into emerging coronaviruses jumping species -a mechanism for coronavirus persistence and survival a tug-of-war between severe acute respiratory syndrome coronavirus 2 and host antiviral defence: lessons from other pathogenic viruses evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission covid-19 in singapore -current experience: critical global issues that require attention and 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doc_id: 31001 cord_uid: x4iiqq5e objective: to identify the effectiveness of a personnel protection strategy in protection of healthcare workers from sars-cov-2 infection. design: during the covid-19 pandemic, 943 healthcare staff sent from guangzhou to wuhan to care for patients with suspected/confirmed covid-19 received infection precaution training before their mission and were equipped with level 2/3 personal protective equipment (ppe), in accordance with guidelines from the national health commission of china. we conducted a serological survey on the cumulative attack rate of sars-cov-2 among the healthcare workers sent to wuhan and compared the seropositive rate to that in local healthcare workers from wuhan and jingzhou. results: serial tests for sars-cov-2 rna and tests for sars-cov-2 immunoglobulin m and g after the 6-8 week mission revealed a zero cumulative attack rate. among the local healthcare workers in wuhan and jingzhou of hubei province, 2.5% (113 out of 4495) and 0.32% (10 out of 3091) had rt-pcr confirmed covid-19, respectively. the seropositivity for sars-cov-2 antibodies (igg, igm, or both igg/igm positive) was 3.4% (53 out of 1571) in local healthcare workers from wuhan with level 2/3 ppe working in isolation areas and 5.4% (126 out of 2336) in healthcare staff with level 1 ppe working in non-isolation medical areas, respectively. conclusions and relevance: our study confirmed that adequate training/ppe can protect medical personnel against sars-cov-2. the novel coronavirus sars-cov-2, associate disease, covid-19, has evolved as a major pandemic in less than three months because of the highly infectious nature of the virus and the current intensive social interaction which favors transmission of the virus. such an explosive pandemic has created unprecedented stress on the healthcare system globally. protecting healthcare workers is critical for functioning of the system and to prevent the workers serving as a vector for disease transmission. although china is a major supplier of personal protective equipment (ppe), the impact of covid-19 initially created a critical shortage of ppe. 1 the national health commission of china has previously issued technical guidance for prevention of airborne transmission diseases in healthcare facilities with three hierarchical levels of personal protection in 2017, which were further updated for prevention of the spread of covid-19 in february 2020. 2, 3 a chinese expert panel also reported a consensus on personal protection in medical institutions during the covid-19 epidemic. 4 the efficacy of such measures, however, was never tested in a real pandemic situation until covid-19. during the pandemic, the sudden surge in demand for healthcare called for unprecedented initiatives. china was building new temporary hospitals within 10 days and a large number of healthcare workers were called to wuhan. here, we describe the logistics behind some of the personnel efforts and whether or not the personnel protection strategy was effective. we enrolled a total of 8529 healthcare workers, including medical teams aiding hubei, local healthcare workers in wuhan and jingzhou of hubei province. employees in the participating hospitals, including those without direct patient care responsibilities, were invited to take a serological test for antibodies against sars-cov-2 and to submit a self-report of gender, age, division, occupation, history of confirmed covid-19, and history of working in the isolation area for covid-19 management . the serologic survey was performed between 20 march and 15 april 2020. the medical ethics committee of nanfang hospital approved the study and all participants signed the consent form. healthcare workers were classified into three groups according to their working areas during the epidemic. members of medical teams aiding hubei as well as local healthcare workers who had a self-reported history of working in the isolation medical area for covid-19 management were classified as working in the isolation medical area. healthcare workers who did not work in the isolation medical area but were directly involved in patient care (physicians, nurses, and technical staff) or those potentially exposed to infectious materials (sanitary workers, staff in the laundry/disinfection facilities) were classified as working in the non-isolation medical area. healthcare workers without direct patient care responsibility nor exposure to infectious material under the hospital settings (clerical staff or executives) were classified as working in the non-medical area. use of ppe for the healthcare workers was determined by their working area according to the protection guidelines issued by the national health commission of china (table 1 ). in brief, level 1 protection is required for healthcare workers working in routine or emergency patient care. ppe for level 1 protection includes disposable caps, surgical masks, white coats, and hand hygiene. n95/ffp (filtering facepiece, ffp), isolation gowns, and disposable gloves are used when necessary. level 2 protection is required for healthcare workers who need to enter the isolation medical areas where patients with suspected or confirmed infection are managed. in addition to ppe for level 1 protection, goggles and fullface shields, long sleeved, fluid repellent gowns, and shoe covers are used. for healthcare workers engaged in aerosol-generating procedures or management of biosamples from patients with infection, level 3 protection, including full face shields, eye protection, ffp masks, gloves, and fluid repellent sleeved gowns, is required. positive pressure helmets can be used when necessary. serum samples were collected at local hospitals. all samples were inactivated at 56 • c for 30 min and stored at −20 • c before testing. the antibodies against sars-cov-2 were measured at local hospitals using one of the commercialized assay kits approved by the national medical products administration of china. according to the manufacturers, the sensitivity of the assay kits ranged from 87.3% to 94.3%, and the specificity from 99.5% to 100%. the seropositive rate of the healthcare workers was expressed as a percentage and the corresponding confidence interval was calculated from binomial probabilities using wilson's method. for healthcare workers working in the non-isolation medical area, seropositive rates stratified by region and division were also estimated, and the top five divisions ranked by the lower boundary of the estimate were listed. we conducted a serological survey on the cumulative attack rate of sars-cov-2 in 8529 healthcare workers in hubei province, of which 943 were sent from guangzhou to wuhan to care for patients with suspected/confirmed covid-19; 4495 were local healthcare workers from wuhan, the epicenter in china, and 3091 were from jingzhou of hubei province, a city 200 km west of wuhan. among the healthcare workers, 71% were female and the median age was 33 years ( table 2 ). all 943 healthcare workers from guangzhou who were sent to assist wuhan to combat covid-19, tested negative for all four reverse transcription polymerase chain reaction (rt-pcr) performed on days 1, 2, 7, and 14. all also tested seronegative for both igg and igm for sars-cov-2 (10-11 days after they had contact with covid-19 patients/contacts) ( table 2 ). in contrast, among the local healthcare workers in wuhan and jingzhou of hubei province, 2.5% (113 out of 4495) and 0.32% (10 out of 3091) had rt-pcr confirmed covid-19, respectively. the seropositivity for sars-cov-2 antibodies (igg, igm, or both igg/igm positive) was 3.4% (53/1571) in local healthcare workers from wuhan with level 2/3 ppe working in isolation areas and 5.4% (126/2336) in healthcare staff with level 1 ppe working in non-isolation medical areas, respectively (table 3) . similar analysis for the jingzhou healthcare workers identified seropositivity of 0.3% for those working in the isolation area with level 2/3 ppe and 1.6% for those working in the non-isolation areas with level 1 ppe. note that for those staff who did not provide direct medical services (including sanitary workers, laundry/disinfection staff, elevator operators), 4.4% of the wuhan healthcare workers and 1.0% of the jingzhou area were antibodyseropositive, respectively (table 3) . for wuhan, the top five divisions with the highest estimated cumulative attack rate based on antibody-seropositivity were the hemodialysis unit (12/96, 12.5%), emergency department (6/40, 15%), endoscopy area (9/80, 11.3%), surgery department (40/586, 6.8%), and sanitary department (12/154, 7.8%) ( table 4 ). to the best of our knowledge, this is the largest serological survey on the accumulative rate of sars-cov-2 infection and the effectiveness of ppe use in healthcare workers. the healthcare staff sent from guangzhou to wuhan received infection precaution training before their mission and were equipped with level 2/3 ppe. serial tests for sars-cov-2 rna and tests for sars-cov-2 immunoglobulin m and g after the 6-8 week mission revealed a zero cumulative attack rate, confirming that adequate training/ppe can protect medical personnel against sars-cov-2. table 3 summarizes the guideline issued by the national health commission of china for personal protection in medical institutions during covid-19. 2, 3 note that this guideline was mainly designed for airborne transmitted pathogens and attention was focused on aerosol and contact transmission. also note that level 3 differs from level 2 with the addition of an isolation gown on top of the disposable coverall and potential use of a positive pressure helmet. in the wuhan situation, positive pressure helmets were generally not used. healthcare workers in wuhan city and the nearby jingzhou city (around 200 km away from wuhan, both are in hubei province) were updated regularly on the latest recommendations for their protection. the challenge in analysis of data from this group was that these healthcare workers could acquire the virus via patients/staff in the hospital but also through community transmission when not at work. for healthcare workers coming from outside hubei province whose primary role was to engage in direct patient care and clinical management patients with suspected or confirmed covid-19, an additional strategy was adopted for protection. for this study, our aim was to evaluate the clinical outcomes of this group. first, these workers were recruited, debriefed on the situation in wuhan, and written consent was obtained from them to participate as part of a medical team in the major hospitals in wuhan to assist in combating the epidemic. second, they were given personal protection training and as all would be summoned to care for patients with suspected/confirmed covid-19, they were all provided with level 2 or 3 protection (but no positive pressure helmets). third, it was arranged for all the workers to stay in designated hotels in which only medical staff were accommodated, and all were informed to practice social distancing, limit their exposure to the local community, and wear face masks whenever possible. finally, there was also a medical team to monitor the mental status of these healthcare workers. with the epidemic under control around 6-8 weeks after their deployment, the healthcare workers from outside hubei underwent the following procedures before heading home: around 4-5 days prior to leaving wuhan, they stopped working in the hospitals, ceased patient contact, and participated in a debriefing period, both to receive information on the next phase but also to give their input on how to improve the system. they were requested to wear face masks whenever possible. there were 943 healthcare workers sent to support wuhan from hospitals located in guangzhou. when they came back to guangzhou (on 20 march 2020), they were required to undergo 14 days of quarantine. they all had sars-cov-2 nucleic acid rt-pcr tests performed four times (upon arrival, and on day 2, day 7, and day 14) and serology for sars-cov-2 immunoglobulin (igg and igm) performed on day 6 (or 10 days after they stopped seeing patients or working in hospital in wuhan). these results were then compared with data from local healthcare workers from wuhan and jingzhou of hubei province. all rt-pcr and serology tests were performed in government-approved laboratories using protocols approved by the chinese fda as previously described. 5 this study identifies two important points. first, prior training on use of level 2/3 ppe, in conjunction with standard infection control practice, was very effective in protecting healthcare personnel from sars-cov-2 infection even though they were in direct contact with patients and were actively involved in management of patients with confirmed/suspected covid-19. this is in striking contrast to previous observations that ppe did not effectively protect healthcare workers from infection during the 2003 sars outbreak. 6, 7 one possible explanation is that the previous sars incidence had created a high alert and that current adherence to the personal protection protocol makes the difference. the second point was the relatively high seropositive rate for sars-cov-2 antibodies among the local healthcare workers with level 1 protection and those working in the non-medical area with no ppe. it is worth re-examining the need for additional training and ppe support for healthcare staff working in non-isolation medical areas, and even non-medical areas with an epidemic of an airborne highly infectious pathogen, especially if ppe supply is not limited. one potential limitation of this study was that enrollment of subjects for this study was based on voluntary participation (apart from the 943 medical staff from guangzhou which was mandatory), thus there might be potential bias in the volunteering participants being more eager to observe the rules. even with this limitation, the personnel protection strategy, coupled together with appropriate coaching and practice, was shown to protect the healthcare personnel sent from guangzhou to wuhan with zero cumulative attack rate in this sars-cov-2 epidemic. however, there is room for improvement in terms of staff with level 1 protection working in nonisolated areas and staff in non-medical areas. these data provide a framework to assist other countries that are still in the midst of combating this pandemic, and could be used to prepare for future epidemics/pandemics. our study confirmed that adequate training and ppe can protect medical personnel against sars-cov-2 infection. s.n., g.y.w., k.z. contributed to the study design, data analysis, and interpretation. j.y-n.l helped with the data analysis and preparation of the manuscript. k.z. and f.f.h. contributed to the study design, data analysis, and writing of the manuscript. all authors reviewed and approved the final version of the manuscript. sourcing personal protective equipment during the covid-19 pandemic national health commission of the people's republic of china. norms for hospital infection prevention and control of airborne diseases: ws/t 511-2016 national health commission of the people's republic of china. notice on printing and distributing the technical guidelines for the protection of medical staff during the new coronary pneumonia outbreak expert consensus on personal protection in different regional posts of medical institutions during covid-19 epidemic period seroprevalence of immunoglobulin m and g antibodies against sars-cov-2 in china which preventive measures might protect health care workers from sars? factors associated with critical-care healthcare workers' adherence to recommended barrier precautions during the toronto severe acute respiratory syndrome outbreak none declared. key: cord-344480-6tcush4w authors: zhou, guangbiao; chen, saijuan; chen, zhu title: back to the spring of wuhan: facts and hope of covid-19 outbreak date: 2020-03-14 journal: front med doi: 10.1007/s11684-020-0758-9 sha: doc_id: 344480 cord_uid: 6tcush4w nan since december 2019, an atypical pneumonia has been spreading from wuhan, a beautiful city located at the center of china (fig. 1) , to the whole country. this disease originated from the huanan seafood wholesale market that was closed on january 1, 2020. very rapidly, a novel coronavirus was isolated and named first the 2019 novel coronavirus (2019-ncov) [1] and subsequently severe acute respiratory syndrome coronavirus 2 (sars-cov-2) [2] , and is suggested to be named as human coronavirus 2019 (hcov-19) [3] . meanwhile, the disease is chronologically called pneumonia of unknown origin, novel coronavirus pneumonia (ncp), and coronavirus disease-2019 (covid-19) (fig. 2 ). superspreading events of this virus have also taken place on the diamond princess cruise off the coast of yokohama, japan [4] . the chinese central [5] and local governments [6] have been endeavoring unprecedented efforts to constrain the outbreak, and more than 30 000 medical professionals especially doctors and nurses outside wuhan have been joining the local ones to handle this emergency. in early december 2019, the first case was reported; by december 31, 104 cases were diagnosed [7] . the disease took 30 days to spread to all the 34 provinces/regions (including hong kong, macao, and taiwan) of china. the number of confirmed cases of covid-19 rose to 11 791 in chinese mainland as of january 31, including 259 deaths. the confirmed cases increased rapidly, and by february 21, 75 567 confirmed cases, 5206 suspected cases, and 2239 deaths, have been reported in china. the disease also spread to 26 countries, with 1151 confirmed cases and 8 deaths reported by february 21 [8] . by february 21, severe cases in wuhan, other regions of china, and the whole country were 9628 (21.2%), 2005 (6.6%), and 11633 (15.4%), respectively ( table 1 ). the reproduction number (r 0 ) is between 2.2 and 4.8 [9, 10] . the commonest symptoms of the covid-19 include fever, dry cough, fatigue, sputum, and shortness of breath, with a small proportion of patients (889/72 314, 1.2%) as asymptomatic and probably spreaders [7] . cytokine storm that is induced by virus particles, is associated with disease severity [11, 12] . a first histological examination of covid-19 patient showed diffuse alveolar damage with cellular fibromyxoid exudates, desquamation of pneumocytes and hyaline membrane formation, pulmonary edema with hyaline membrane formation, interstitial mononuclear inflammatory infiltrates, and multinucleated syncytial cells with atypical enlarged pneumocytes in the lungs [13] . these results shed insights into the pathogenesis of covid-19 and may help design therapeutic strategies against the disease. a previously unknown betacoronavirus was discovered from bronchoalveolar-lavage fluid samples of the patients, which is the seventh member of the family of coronaviruses that infect humans [1, 14] . the virus was most closely related to a group of sars-like coronaviruses (genus betacoronavirus, subgenus sarbecovirus) previously sampled from bats in china [14, 15] , and a virus with 99% sequence homology to the receptor-binding domain (rbd) and 90% to the sars-cov-2 genome was also found in malayan pangolins in southern china [16] . however, higher viral loads were detected in the nose than in the throat of symptomatic and asymptomatic covid-19, a pattern resembling that of influenza but not sars-cov [17] . human angiotensin-converting enzyme 2 (ace2) has been shown to be the putative receptor for the virus to enter into host cells [15, 18] , and biophysical and structural evidence shows that the sars-cov-2 spike glycoprotein binds ace2 with high affinity [19] . ace2 can also bind spike protein through association with b0at1 [20] . ace2 locates on the organs such as lung, heart, esophagus, kidney, bladder and ileum, and in particular on the cell types such as type ii alveolar cells, myocardial cells, proximal tubule cells of kidney, ileum and esophagus epithelial cells, and bladder urothelial cells, providing clues for further investigating the pathogenesis covid-19 [21] . so far, neither drug nor vaccine has been approved to treat the novel covid-19. while supportive treatment regimens including oxygen therapy are widely used, antivirus (oseltamivir) and anti-hiv (lopinavir/ritonavir) drugs are also applied in treating covid-19. some emerging therapeutics are being tested in clinical trials. for example, virally targeted agents, approved nucleoside analogs (favipiravir and ribavirin) and experimental nucleoside analogs (remdesivir and galidesivir), may have potentials against sars-cov-2 [22] . remdesivir has been shown to be able to block virus infection [23] and exert therapeutic efficacy in the first covid-19 case in the united states [24] . two phase iii trials have been initiated to evaluate remdesivir in covid-19. anti-malaria drug chloroquine shows activity in blocking sars-cov-2 infection [23] and is being evaluated in an open-label trial [22] . convalescent patient plasma that contain anti-sars-cov-2 antibody holds promise to beat this disease [25] . ace2 and spike protein represent two novel therapeutic targets for the disease [26] . an ongoing study using tocilizumab, a specific monoclonal antibody antagonist of interleukin-6 receptor (il-6r) which proved to be effective in alleviating cytokine release syndrome, showed preliminary positive effects [27] . traditional chinese medicine (tcm) plays an active role in fighting infectious disease, exemplified by ancient formula maxingshigan-yinqiaosan in the treatment of h1n1 influenza [28] . in combination with western medicine [29] or used alone, tcm is widely applied or being evaluated in clinical trials to treat covid-19. two and a half months have witnessed the great efforts that china has been endeavoring to control the outbreak of the covid-19. these include lockdown of wuhan and related cities, control of population mobility, and input of huge resource to the regions. china races against the clock to build virus hospitals, including huoshenshan hospital with 1000 beds built in 9 days and leishenshan hospital with 1500 beds completed in 15 days. more than 15 fangcang hospitals (with large open space and necessary anti-infection conditions) have been built with a capacity of more than 20 000 beds for the isolation and treatment of the patients. the updated genome sequence of sars-cov-2 has been shared to the public, clinical trials are undergoing, and scientists from china and overseas are working together to combat this public health emergency. with great contributions of our domestic selfless medical professionals and supports from public health scientists around the world [30] , by using smart but firm public health measures preventing spreadout of the virus and more specific combinatorial therapeutic strategies, such as the anti-viral convalescent plasma and drugs against cytokine storm for severe cases, as well as effective tcm drugs and technologies, we believe that the mankind will win this battle, and wuhan will be back to the spring. guangbiao zhou, saijuan chen, and zhu chen declare no conflict of interests. this manuscript does not involve a research protocol requiring approval by the relevant institutional review board or ethics committee. china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china severe acute respiratory syndromerelated coronavirus: the species and its viruses -a statement of the coronavirus study group a distinct name is needed for the new coronavirus epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-ncov) outbreak a novel coronavirus outbreak of global health concern china's local governments are combating covid-19 with unprecedented responses -from a wenzhou governance perspective novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in china databased analysis, modelling and forecasting of the novel coronavirus (2019-ncov) outbreak early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features of patients infected with 2019 novel coronavirus in wuhan, china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study pathological findings of covid-19 associated with acute respiratory distress syndrome genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding a pneumonia outbreak associated with a new coronavirus of probable bat origin identification of 2019-ncov related coronaviruses in malayan pangolins in southern china sars-cov-2 viral load in upper respiratory specimens of infected patients functional assessment of cell entry and receptor usage for lineage b β-coronaviruses, including 2019-ncov cryo-em structure of the 2019-ncov spike in the prefusion conformation structure of dimeric fulllength human ace2 in complex with b 0 at1 the single-cell rna-seq data analysis on the receptor ace2 expression reveals the potential risk of different human organs vulnerable to wuhan 2019-ncov infection therapeutic options for the 2019 novel coronavirus (2019-ncov) remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-ncov) in vitro washington state 2019-ncov case investigation team. first case of 2019 novel coronavirus in the united states 32 recovered patients donate plasma to others with coronavirus infection therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in wuhan, china. (version 2; peer review: 2 approved scientists target major cause of critically ill virus deaths. china daily oseltamivir compared with the chinese traditional therapy maxingshigan-yinqiaosan in the treatment of h1n1 influenza: a randomized trial combination of western medicine and chinese patent medicine in treating a family case of covid-19 in wuhan statement in support of the scientists, public health professionals, and medical professionals of china combatting covid-19 key: cord-027758-vgr6ht3a authors: wang, tianbing; wu, yanqiu; lau, johnson yiu-nam; yu, yingqi; liu, liyu; li, jing; zhang, kang; tong, weiwei; jiang, baoguo title: a four-compartment model for the covid-19 infection—implications on infection kinetics, control measures, and lockdown exit strategies date: 2020-05-28 journal: precis clin med doi: 10.1093/pcmedi/pbaa018 sha: doc_id: 27758 cord_uid: vgr6ht3a objective: to analyse the impact and repercussions of the surge in healthcare demand in response to the covid-19 pandemic, assess the potential effectiveness of various infection/disease control measures, and make projections on the best approach to exit from the current lockdown. design: a four-compartment model was constructed for sars-cov-2 infection based on the wuhan data and validated with data collected in italy, the uk, and the us. the model captures the effectiveness of various disease suppression measures in three modifiable factors: (a) the per capita contact rate (β) that can be lowered by means of social distancing, (b) infection probability upon contacting infectious individuals that can be lowered by wearing facemasks, personal hygiene, etc., and (c) the population of infectious individuals in contact with the susceptible population, which can be lowered by quarantine. the model was used to make projections on the best approach to exit from the current lockdown. results: the model was applied to evaluate the epidemiological data and hospital burden in italy, the uk, and the us. the control measures were identified as the key drivers for the observed epidemiological data through sensitivity analyses. analysing the different lockdown exit strategies showed that a lockdown exit strategy with a combination of social separation/general facemask use may work, but this needs to be supported by intense monitoring which would allow re-introduction/tightening of the control measures if the number of new infected subjects increases again. conclusions and relevance: governments should act early in a swift and decisive manner for containment policies. any lockdown exit will need to be monitored closely, with regards to the potential of lockdown reimplementation. this mathematical model provides a framework for major pandemics in the future. the novel coronavirus (sars-cov-2) and the infectionrelated disease (covid19) were declared a public health emergency of international concern by the world health organization in early 2020, and have since grown into a pandemic. 1,2 covid-19 has created an unprecedent global health problem, for which most healthcare systems were not well prepared. 3 policies such as case isolation, social distancing, travel restriction, and quarantine represent the key measures adopted by various governments to control the outbreak. [4] [5] [6] [7] however, such measures also carry significant impact to individual psychological well-being and social/economic costs. many epidemiological models [8] [9] [10] [11] have been proposed to describe the dynamics of the transmission and simulate the course of the outbreak. however, few studies have assessed the impact of the effectiveness of various measures in the control of viral spread. a four-compartment model was established to describe the sars-cov-2 infection, assess the potential effectiveness of various infection control measures, and make projections on the best approach to exit lockdown. the population is divided into the following states: susceptible subjects (s), had close contacts (c, those exposed to infected subjects/pathogen but not necessarily infected), latent (e, infected and infectious but asymptomatic), infected (i; and symptomatic), recovered (v), and dead (d) ( fig. 1 and supplementary data). the transmissibility of sars-cov-2 is modelled by two separate parameters-the social transmissibility factor β, which measures the probability of having close contact with infectious subjects, and the pathologic transmissibility σ , which measures the probability of an individual developing covid-19 upon contact with the pathogen. 12 the model also allows a predetermined portion of infected individuals to stay latent for the entire incubation period and then move directly to the removed states (recovered or deceased) while bypassing the infected (i) compartment. the model was established based on demographic and covid-19 epidemiological data in wuhan. data from italy, the united kingdom (uk), and the united states (us) fit well with our model, assuming that these countries were affected by multi-sources at around the same time. β in the community was estimated separately. all other parameters were set to the estimated parameters from wuhan data before 23 january 2020. the four-compartment model and the validation in our four-compartment susceptible-quarantined-infected-removed (sqir) model, the transmissibility of covid-19 is modelled by two factors, the per capita contact rate (β, social interaction factor, when multiplied by the ratio of infectious individuals in the population, describes the probability of a subject moving from status s to status c), and infection rate upon contact (σ , the viral transmission factor, the probability of a subject moving from status c to status e). together with the quarantine rates (κ c and κ e ), they make up the parameters that can be modified by public health policies to suppress the outbreak. all other parameters in the model are pathogenic/viral characteristics that would not be affected significantly by non-pharmaceutical interventions. the progression rates from latent to infected and from infected to recovered were based on published estimates of 0.1 and 0.06 13 , respectively, which should remain relatively constant throughout the outbreak. [14] [15] [16] the natural infection probability upon contact was set at 0.2. 12 the rate of covid-19-related death of all hospitalized cases was set at 4.5%. 17 our model was calibrated 18 using 32 583 laboratoryconfirmed covid-19 cases in wuhan, china between 8 december 2019 and 8 march 2020 19 (fig. 2a) . the date of the first human covid-19 latent infection (d 0 ) was set as 3 december 2019 (assuming 5 days before the first symptom of patient zero). the estimation of β was 5.8 under normal social circumstance, and 1.4 after lockdown, and σ was estimated to be 0.04 in the second and third periods, representing roughly a 2-fold decrease from 0.08 during the first period possibly related to the stringent compulsory facemask use policy. local government estimated that the effective quarantine rate after 31 january 2020 was from 35% to 75%. in italy, our model fits, assuming there were four effective sources in italy at around that time (fig. 2b ). 20 the estimated β was 5.5 before social distancing (slightly lower than wuhan, a metropolitan area densely populated). after nationwide lockdown, β was reduced to the population is divided into the following states: susceptible subject(s) (s), had close contact(s) (c, those that were exposed to the infected subjects/pathogen but not necessarily infected), latent (e, infected and infectious but asymptomatic), infected (i; and symptomatic), recovered (v), and dead (d). c m is the portion of the contact cases that are missed by contact tracing and will not be quarantined. individuals in states c, c m , and c q will progress to their respective latent groups e, e m (by contact tracing), and e q (quarantined). after the onset of symptoms, latent individuals will enter the infectious status i, and i q denoting the infected population treated in isolation wards. it was assumed that when the infected subjects have recovered, they will acquire immunity that does not wane during the timeframe of the analysis (i.e. of this season). 2.8 (starting 10 march) and further reduced to 1.4 (starting 23 march), suggesting that the stricter lockdown in italy achieved the same effect on β as in wuhan. our model assumed 10% effective facemask use compared to wuhan (σ = 0.076). for the uk, our model estimated that the number of effective sources was 6 and β was 4.6 ( fig. 2c ). nationwide lockdown was implemented on 23 march (β = 2.3, σ = 0.076) and strengthened on 31 march (β = 1.5, σ = 0.076). for the us, based on cdc data (5 days before the first illness onset), the estimated number of effective sources was 100 (fig. 2c) . note that the effective number of sources might come down to six, assuming the infection arrived in the us in mid-january 2020. 21 the recent report that the sars-cov-2 in washington state had the same genotype as wuhan, whereas northeast us had predominately the genotypes related to europe was consistent with our projection. 22 the estimates of β before and after the 'shelter in place' order were 5.2 and 2.05, respectively, indicating that us compliance was within reasonable limits and the big jump in numbers was likely related to the multiple sources of virus arriving in the us at the same time. this model projected that implementation of case isolation/quarantine is an important measure to control this pandemic. in wuhan, combining social distancing and compulsory facemask use capped the growth rate of infected cases per day, but not enough to reverse the trend. adding contact tracing and quarantine (and other measures including general use of facemask) 54 days after d 0 completely curbed the outbreak in 69 days. over the entire course, 32 583 individuals (0.3% of the population) were infected. the model projected that if no quarantine was taken and infection allowed to spread until herd immunity established, 10 111 537 individuals (91.1% of the wuhan population) would be infected (including crosses represent the cumulative numbers of cases observed. curves represent the model fitted to the observed data using mle. insets: the observed number of cases by date of illness onset (crosses) and the fitted curve in logarithmic scale. in wuhan, hubei, four distinct periods were defined: (a) before 23 january 2020 before major public health interventions, (b) between 23 january and 31 january, when there was a travel ban and cancellation of social gatherings [which would lower per capita contact rates (β)] and compulsory facemask use [which would lower the infection rate upon contact (σ )], (c) between 31 january and 17 february, when quarantine was in place, and (d) between 17 february and 18 april. in italy, three distinct periods were defined: (a) from 26 january 2020 (5 days before the first covid-19 confirmed in rome) to 9 march when the nationwide lockdown was implemented; (b) from 9 march to 22 march; and (c) after 22 march when stricter lockdown policies were implemented that halted all nonessential operations. in the uk, two periods were defined before and after the nationwide lockdown was implemented on 23 march. in the us, two periods were defined before and after the 'shelter in place' order in the san francisco area on 16 march. 4 494 017 being asymptomatic) at the end of 1 year. for comparison, the annual culminative attack rates of two common human coronaviruses 229e and oc43 were 2.8% and 26.0%, respectively. 23 to determine the sensitivity of each parameter, they were evaluated/matched to the observed outbreak data 24 (supplementary table 1 and supplementary fig. 1 ). only the control measures were found to significantly affect the outcome. assuming that 15%-25% of all hospitalized individuals needed critical care, 17, 25, 26 the model estimated that the uk's need for hospital beds would plateau after 17 april at around 23 000 and critical care beds around 4600, close to the estimates given by nhs england. for the us, the need for hospital beds and critical care units is still growing. our model estimated that on 18 april 2020, the us needed 98 702 hospital beds (30 per 100 000 people) and around 20 000 critical care beds, and by 15 may (as predicted by our model on 28 april 2020), the us would need an additional 183 320 hospital beds (55 per 100 000 people) and around 37 000 critical care beds. as of 18 april, cdc reported that the overall cumulative hospitalization rate was 29.2 per 100 000 people. by the world bank's estimation, the us currently has around 1 million hospital beds and 115 000 critical care beds, and, therefore, the covid-19 pandemic poses a heavy burden on the us healthcare system (the need for 20% more inpatient and 35% more critical care beds). the fact that covid-19 is very concentrated in new york city/new jersey suggests even higher projected needs there. the quarantine starting time after d 0 was identified and the effective quarantine rate had the most impact to the outcome ( supplementary fig. 2 ). sensitivity analysis of the quarantine rate of asymptomatic infected subjects (κ e ) showed a clear breakpoint between 40% and 50%. quarantine rates lower than 40% would lead to a completely uncontrollable outbreak. the impact of a delayed quarantine on the effectiveness of infection control was also significant (supplementary fig. 2) . by reducing the duration between d 0 and the start date of quarantine measures (assuming 80% quarantine rate) from 9 to 7 weeks reduced the overall attack rate from 0.3% to 0.029%. if quarantine measures started after 11 weeks, these measures would not control the outbreak. we evaluated the impact of lockdown by estimating the projected equivalence of lockdown/social distancing to quarantine ( supplementary fig. 3a) . a stringent lockdown reduced the average social contact by > 2-fold, equivalent to 18% effective quarantine rate. however, the breakpoint of lockdown (i.e. the β that can control the outbreak on its own) was between 0.5 and 1, much lower than the estimated β achieved by lockdown in italy, the uk, and the us. thus, the effectiveness of such policy in these countries was reduced as observed. in wuhan, compulsory facemask use reduced σ by 46%, equivalent to 19% effective quarantine rate (supplementary fig. 3b ). the breakpoint of general facemask use was beyond 100% (around 115%), indicating that general facemask use alone would be insufficient for complete control of the outbreak . this effect was witnessed in wuhan during the second period (23-31 january). only after compulsory facemask use was combined with lockdown and quarantine in the third and fourth period (after 31 january) did the number of new cases show a sharp downward trend ( fig. 2a, inset) . the combined effect of lockdown and general facemask use given different ranges of hospitalization (1%-30%) is given in fig. 3 . during the initial surge of the covid-19 outbreak in italy/uk/us, no disease control policy was in place (β = 6, σ = 0.08) and hospitalization rate (κ i ) was close to 5%, with the number of new cases per day doubling every 5 days. both lockdown and general facemask use could reduce the growth rate of new infections; and when combined give the best overall effect. for lockdown to be effective, β needs to be reduced from 6 to < 1.1. currently in italy/uk/us, σ is estimated to decrease only slightly from 0.08 to 0.076. with general facemask use at 50% compliance rate (σ = 0.06), β will need to be < 1.5 to reduce the number of new infections. this level of social distancing was achieved during lockdown in italy (estimated β = 1.44) and in the uk (estimated β = 1.5), but not yet in the us (estimated β = 2.05). with general facemask use (σ = 0.04), β will only need to be 1.99, which is slightly lower than the current us estimate (β = 2.05). if stricter lockdown and facemask use are implemented together (β = 1.5, σ = 0.04), the number of new cases would reduce by half every 16 days, even without quarantine. higher hospitalization rate puts more cases under isolation and thus may ease the need for general facemask use. at 15% and 30% hospitalization rate, strict lockdown and compulsory facemask use (β = 1.5, σ = 0.04) would reduce new infection by half in 12 days and 10 days, respectively. currently, most government advisers recommend continuation of lockdown till the outbreak is suppressed to an acceptable level ('wuhan approach'), a relatively safe approach. however, some governments are considering an exit to balance the sociopsychological impact of a long lockdown and the huge impact on economy. in italy, for lockdown to continue till zero new infection, it would have to continue until 6 january 2021 (fig. 4a) . for the uk, it would not be until 2023 before the number of new infections dropped to zero (fig. 4b) . the us is still not seeing a firm plateau in the number of new cases and thus it may be even longer until the projection of zero new infection (fig. 4c) . a more balanced approach would be to reduce the number of new infections to a considerably low level, then relax the infection control policies measures in a controlled fashion with intensive monitoring. based on our projection, either strict quarantine of contacts, or a combination of both a relatively strict lockdown and general facemask use may be sufficient. it is important to note that the latter approach would need to be used in combination because of (a) the non-linear nature of the effectiveness, and (b) the existence of breakpoints as described above. we predict that in italy, a quarantine policy with an effective quarantine rate of 12% starting on 24 may (18 weeks after d 0 ) in addition to the current implemented lockdown would reduce the incidence of new infections exponentially, reaching ≤ 100 in just 26 days (19 june) and zero in 62 days (24 july). the same infection suppression effect can also be achieved with no active quarantine, but by using the same lockdown as at present, and mandate compulsory facemask use (fig. 4a) . in the uk, lockdown and general facemask use starting on 24 may would bring the incidence of new infections to under 100 in 52 days (15 july) and to zero in 129 days (30 september) (fig. 4b) . this is almost equivalent to an effective quarantine rate of 10%. an effective quarantine rate of 20% would bring the incidence of new infections to under 100 in 35 days (28 june) and to zero in 70 days (2 august). in the us, general facemask use starting on 24 may would bring the incidence of new infections to under 100 in 152 days, which is equivalent to a quarantine effective rate of 9%. if the government can achieve 20% effective quarantine rate, the incidence of new infections will drop to around 100 in 65 days (28 july). implementing a monitoring-based, data-driven lockdown exit strategy is essential to sustain the containment of covid-19. based on our model, loosening the quarantine too early while there are still a significant number of latent cases may lead to an uncontrollable second outbreak. with daily active monitoring of new infection numbers, it is possible to adjust the infection control policies to maintain new infections within a band trending downwards. as discussed, lockdown should only be loosened to social distancing (β = 2.8) and general facemask use when daily new infections are reduced to a very low number (e.g. 100 cases) and re-implemented to an aggressive lockdown (β = 1.4, similar to the lockdown in italy) with general facemask use when daily new infections is rising (e.g. ≥1000 cases). this approach will provide the time for vaccine, drugs, or other pharmaceutical interventions to catch up while allowing economical activities to be less uninterrupted in regions with low numbers of new infections. for italy (fig. 4d) , if the quarantine is lifted after daily new infections drops to < 100 (june 19) with all infection suppression policies currently in place (β = 5.53, σ = 0.08), the number of new infections would quickly return to exponential growth. even with general facemask use (β = 5.53, σ = 0.04), a second wave of outbreak is still inevitable. thus, the quarantine should last till the incidence of new infections is close to zero (on 24 july), plus a 2-week wash out period (the estimated latent period) before implementing exit. in the uk, if quarantine is lifted after daily new infections drops to < 100 (15 july) along with all current infection suppression policies (β = 4.6, σ = 0.08), it would only take 36 days (20 august) for the incidence of new infections to reach 10 000. however, an extended lockdown and quarantine that lasts 129 days (until 30 september to eliminate new incidences) would also be less plausible economically and politically. thus, we recommend that after the outbreak is suppressed to an acceptable level, restrictions can be relaxed gradually to keep the infection under control, allowing economic activities to recover. various level of social distancing and facemask use and data-driven lockdown policies are considered, including: disease suppression measures completely lifted (β = β 0 , σ = 0.08), social distancing continues to apply (β = 2.8, σ = 0.08), stringent lockdown continues to apply (β = 1.4, σ = 0.08), social distancing and general facemask use continues to apply (β = 2.35, σ = 0.05), compulsory facemask use continues to apply (β = β 0 , σ = 0.04). data-driven lockdowns are also plotted: loosening of social distancing (β = 2.8, σ = 0.08) and completely loosened (β = β 0 , σ = 0.08). β 0 : per capita contact (β) rate of the normal social distance in each country. this model can be modified to adapt to different adjusted scenarios. in the us, to effectively reduce the size of the outbreak, quarantine should remain in effect at > 20% rate. with quarantine, the number of daily new cases is projected to be < 100 by 28 july. afterwards, a monitoringbased, data-driven approach can be implemented. the same level of lockdown or social distancing plus general facemask use should continue. it should be noted that a full cycle of loosening and re-implementation would span 53 days if during the loosening period, the infection control policies were completely lifted (β = 5.2), or 89 days if loosened to social distancing (β = 2.8). in this study a four-compartment mathematical model was established for the sars-cov-2 infection, which could be useful in the policy decision-making process. second, our model suggested that italy, the uk, and usa likely had multiple sources of infections to account for the observed early sharp rise in the number of infected subjects. third, effective and early implementation of quarantine were the two most important factors for control of the outbreak. fourth, the relative contributions of quarantine, lockdown, social distancing, and the general facemask use were estimated. finally, different strategies for lockdown exit were evaluated and challenges identified. our model allows examination of the issues unique to sars-cov-2 infection, the highly infectious nature of this pathogen, the potential of this infection to overwhelm the healthcare system, and the alternative containment strategy implemented for this pandemic. the sensitivity analyses showed that, in the time from the index patient to control measures and effective quarantine, measures were most effective when the majority of the infected carriers, mostly asymptomatic 27-31 , were put under quarantine. our data support the latest recommendation from the us cdc on the use of facemasks in public during this pandemic. once the outbreak is under control, quarantine can be lifted through a data-driven, monitoring-based dynamic disease mitigation policy. thus, general availability of a rapid viral diagnostic test is critical. a real challenge will be the potential to have both sars-cov-2 and other upper respiratory viral pathogens prevalent at the same time (e.g. this winter) when this pandemic is still ongoing. if this occurs, our model will require adjustment for two pathogens simultaneously. our data highlight the importance for governments to act swiftly and decisively for any containment policies. 32 also, any lockdown exit must be monitored closely with the potential for lockdown reimplementation. this four-compartment mathematical model describes sars-cov-2 infection, can be adjusted to reflect local transmission characteristics and public health capabilities, can help to determine the optimal local disease suppression strategy, and can help when making projections for the best local lockdown exit strategy. a novel coronavirus emerging in china -key questions for impact assessment a novel coronavirus outbreak of global health concern responding to covid-19 -a once-in-a-century pandemic? sars outbreaks in ontario, hong kong and singapore: the role of diagnosis and isolation as a control mechanism first-wave covid-19 transmissibility and severity in china outside hubei after control measures, and second-wave scenario planning: a modelling impact assessment the effect of travel 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characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china markov chain monte carlo: an introduction for epidemiologists association of public health interventions with the epidemiology of the covid-19 outbreak in wuhan, china spread and dynamics of the covid-19 epidemic in italy: effects of emergency containment measures first case of 2019 novel coronavirus in the united states phylogenetic network analysis of sars-cov-2 genomes clinical impact of human coronaviruses 229e and oc43 infection in diverse adult populations a methodology for performing global uncertainty and sensitivity analysis in systems biology clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study critical care utilization for the covid-19 outbreak in lombardy, italy: early experience and forecast during an emergency response. jama 2020.online ahead of print transmission of 2019-ncov infection from an asymptomatic contact in germany presumed asymptomatic carrier transmission of covid-19 epidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in china. pediatrics 2020. online ahead of print estimating the asymptomatic proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess cruise ship estimation of the asymptomatic ratio of novel coronavirus infections mass gathering events and reducing further global spread of covid-19: a political and public health dilemma we thank the volunteers who curated the number of cases in wuhan, us, uk, and italy. we thank members of lau, zhang, tong, and jiang groups for their assistance and discussions. supplementary data are available at pcmedi online. t. w., y. w., y. y., l. l., j. l., k. z., w. t., and b. j. collected and analysed the data. j.y.-n. l., developed the strategic approaches used for the analyses and helped to write the manuscript. t. w., k. z., w. t., and b. j. conceived and supervised the project and wrote the manuscript. all authors discussed the results and reviewed the manuscript. none declared. key: cord-338231-uni4aqxo authors: shi, puyu; ren, guoxia; yang, jun; li, zhiqiang; deng, shujiao; li, miao; wang, shasha; xu, xiaofeng; chen, fuping; li, yuanjun; li, chunyan; yang, xiaohua; xie, zhaofeng; wu, zhengxia; chen, mingwei title: clinical characteristics of imported and second-generation coronavirus disease 2019 (covid-19) cases in shaanxi outside wuhan, china: a multicentre retrospective study date: 2020-09-30 journal: epidemiology and infection doi: 10.1017/s0950268820002332 sha: doc_id: 338231 cord_uid: uni4aqxo the mortality of coronavirus disease 2019 (covid-19) differs between countries and regions. this study aimed to clarify the clinical characteristics of imported and second-generation cases in shaanxi. this study included 134 covid-19 cases in shaanxi outside wuhan. clinical data were compared between severe and non-severe cases. we further profiled the dynamic laboratory findings of some patients. in total, 34.3% of the 134 patients were severe cases, 11.2% had complications. as of 7 march 2020, 91.8% patients were discharged and one patient (0.7%) died. age, lymphocyte count, c-reactive protein, erythrocyte sedimentation rate, direct bilirubin, lactate dehydrogenase and hydroxybutyrate dehydrogenase showed difference between severe and no-severe cases (all p < 0.05). baseline lymphocyte count was higher in survived patients than in non-survivor case, and it increased as the condition improved, but declined sharply when death occurred. the interleukin-6 (il-6) level displayed a downtrend in survivors, but rose very high in the death case. pulmonary fibrosis was found on later chest computed tomography images in 51.5% of the pneumonia cases. imported and second-generation cases outside wuhan had a better prognosis than initial cases in wuhan. lymphocyte count and il-6 level could be used for evaluating prognosis. pulmonary fibrosis as the sequelae of covid-19 should be taken into account. in december 2019, a cluster of pneumonia cases of unknown cause occurred in wuhan city of china [1] . in early january 2020, a novel betacoronavirus was isolated [2] from the bronchoalveolar lavage samples of the infected patients, and the pathogen was named severe acute respiratory syndrome coronavirus 2 (sars-cov-2; previously known as 2019 novel coronavirus, 2019-ncov). in february 2020, the who officially designated the syndrome as coronavirus disease 2019 . due to human-to-human transmission [3, 4] , covid-19 has spread rapidly. as of 27 march 2020, a total of 82 078 cases have been confirmed in china and 509 164 cases have been reported in more than 200 countries and five continents [5] . the clinical spectrum of covid-19 appears to be wide, including asymptomatic infection, mild respiratory tract illness and severe pneumonia with respiratory failure and even death [6] . the mortality of covid-19 is different among countries and regions, for instance 4.02% in china, 0% in vietnam, 10 .14% in italy, 1.45% in usa, and 0.44% in australia [5] . so far, studies on the epidemic and clinical characteristics of covid-19 have mainly concentrated on initial or first-generation cases. information about imported and secondgeneration cases is limited. in this study, we focused on shaanxi province as a region with imported and second-generation cases and described the clinical and laboratory characteristics of 134 covid-19 cases in this province with a hope to provide some insight into the prevention and treatment of the disease in china and elsewhere. this retrospective study included 134 confirmed cases of covid-19 admitted and treated in 10 designated hospitals across nine cities (xi'an, ankang, baoji, hanzhong, weinan, xianyang, shangluo, yan'an and tongchuan) in shaanxi province from 23 january 2020 to 7 march 2020 (supplementary table s1 ). sars-cov-2 infection was defined in accordance with version 7.0 of the guideline issued by the national health commission of the people's republic of china [7] . the epidemiological, demographic, clinical, laboratory and radiologic characteristics as well as treatment and outcome data were collected from patients' electronic medical records using a standardised case report form. clinical outcomes were followed up until 7 march 2020. the data were reviewed by a trained team of physicians. if information was not clear, the research team contacted the doctor responsible for treating the patient for clarification. laboratory confirmation of covid-19 was performed immediately after admission and verified by the shaanxi provincial centre for disease control and prevention (cdc). a confirmed covid-19 case was defined as a positive result to high-throughput sequencing or real-time reverse-transcriptase polymerase chain reaction assay for nasal and pharyngeal swab samples or sputum specimens [8] . the date of disease onset was defined as the day when the symptom was noticed. fever was defined as axillary temperature above 37.3°c. ards was defined in accordance with the berlin definition [9] . acute kidney injury was identified based on the kidney disease: improving global outcomes definition [10] . cardiac injury was determined when the serum levels of cardiac biomarkers (e.g. troponin i/t) were above the 99th percentile upper reference limit or new abnormalities detected in electrocardiography and echocardiography [11] . ventilator-associated pneumonia was determined referring to the guidelines for treatment of hospital-acquired and ventilator-associated pneumonia [12] . severity of covid-19 was categorised into non-severe group (mild and moderate) and severe group (severe and critically ill) based on version 7.0 of the guideline issued by the national health commission of the people's republic of china [7] . the cohort of patients was divided into severe and non-severe cases. continuous and categorical variables were expressed as median (interquartile range (iqr)) and n (%), respectively. the mann-whitney test was used for continuous variables and χ 2 test or fisher's exact test (when the data were limited) was used for categorical variables to compare differences between severe and non-severe cases where appropriate. all statistical analyses were performed with spss software, version 23.0. a two-sided α of less than 0.05 was considered statistically significant. this study recruited a total of 134 confirmed covid-19 patients from nine cities in shaanxi province from 23 january 2020 to 7 march 2020. the median age of the patients was 46 years old (iqr 34-58), ranging from 4 to 89 years, and more than half (69, 51.5%) were female (table 1) . altogether 88 (65.7%) cases were non-severe and 46 (34.3%) were severe, including two critically ill cases (1.5%) with one patient unable to survive (0.7%) ( table 4 ). the ages of severe patients were significantly older than that of non-severe patients (median, 56 years vs. 41 years, p < 0.05). moreover, the proportion of patients aged 65 or older was higher (32.6% vs. 5.7%, p < 0.05), and the proportion of patients aged 14-30 was lower (4.3% vs. 21.6%, p < 0.05) in the group of severe patients than in non-severe patients ( table 1) . none of the patients had a history of exposure to the huanan seafood market or wild animals. the majority of the cases were community-infected and three cases were hospital-infected. of these patients, 59 (44%) resided in wuhan or had short trips to wuhan before the onset of covid-19; 40 (29.9%) had close contact with someone from wuhan; 20 (14.9%), including three (2.2%) medical staff, had exposure to covid-19 patients; 15 (11.2%) had no definite epidemiological history and 71 (53%) patients got infected as familial clustering (table 1) . of the 134 patients, 58 (43.3%) had one or more coexisting medical conditions, the most common of which was hypertension (14.9%), followed by diabetes (6.7%), cardiovascular disease (4.5%) and cerebrovascular disease (4.5%) ( table 1 ). the most common symptoms at onset were cough (96, 71.6%), followed by fever (87, 64.9%) ( table 2 ). the incidences of chest stuffiness and dyspnoea differed between severe and no-severe cases ( table 2 , both p < 0.05). the median interval from onset of symptoms to first hospital admission was 4.5 (iqr 3-7) days, and that to positive result of nucleic acid detection was 5 (iqr 3-9) days. the median duration from hospital admission to discharge was 17 days (iqr 14-20) ( table 1) . the incidences of temperature >38°c, respiratory rate >21 breaths per min, heart rate >100 beats per min and median systolic pressure showed difference between severe and no-severe cases (table 2, all p < 0.05). all of these were higher in severe cases compared to in non-severe cases. ninety-four per cent (126/134) of the patients showed abnormal chest computed tomography (ct) images, consisting of 26 cases (26/134, 19 .4%) of unilateral pneumonia and 100 cases (100/ 134, 74.6%) of bilateral pneumonia, with ground-glass opacity as the typical hallmark finding. among the patients, 26 patients (19.4%) showed multiple patchy shadowing, 26 cases (19.4%) showed subsegmental consolidation with air bronchogram (5, 3.7%), with two cases (1.5%) having progressed to 'white lung'. additionally, pleural effusion occurred in six patients (4.5%) and pneumothorax occurred in one patient (0.7%). when the shadow or consolidation was resolved, pulmonary fibrosis was found on later chest ct images of 69 (51.5%) patients (table 2) . moreover, the incidences of bilateral pneumonia, pleural effusion and pulmonary fibrosis were higher in severe cases than in non-severe cases (table 2, all p < 0.05). puyu shi et al. upon admission, 25 (18.7%) of the patients showed leucopoenia (white blood cell count <3.5 × 10 9 /l) and 51 (38.1%) showed lymphopoenia (lymphocyte count <1.1 × 10 9 /l). in most patients, leucocytes (107, 79.9%) and lymphocytes (82, 61.2%) were within the normal ranges. the median values of c-reactive protein (crp) (10.0, iqr 9.0-38.3 mg/l), erythrocyte sedimentation rate (esr) (38.5, iqr 17.8-74.8 mm/h), interleukin-6 (il-6) (8.1, iqr 5.0-23.0 pg/ml) and direct bilirubin (dbil) (4.9, iqr 3.3-7.5 μmol/l) elevated in the patients. the median partial pressure of oxygen level was 80 mmhg (iqr 67-92), and the median of oxygenation index (pao 2 :fio 2 ) was 255 mmhg (iqr 210-307) ( table 3) . a number of laboratory parameters showed higher values in severe patients as compared with non-severe patients (table 3) , including crp, esr, dbil, glucose, lactate dehydrogenase (ldh), hydroxybutyrate dehydrogenase (hbdh) and pro-brain natriuretic peptide (table 3 , all p < 0.05). in addition, lymphocyte count, albumin, pao 2 and pao 2 :fio 2 were comparatively neutrophil count ( × 10 9 /l) 1.8-6. epidemiology and infection lower in severe patients than in non-severe patients (table 3 , all p < 0.05). during hospitalisation, 15 (11.2%) of the patients had complications, including arrhythmia (4, 3.0%), acute respiratory distress syndrome (3, 2.2%), acute kidney injury (3, 2.2%), ventilator-associated pneumonia (2, 1.5%), multiple organ dysfunction syndrome (2, 1.5%) and shock (1, 0.7%). most of the complications (13 out of 15, 86.7%) occurred in the group of severe cases and the incidence of complications was comparatively higher in severe cases than in non-severe cases (28.3% vs. 2.3%, p < 0.05) ( table 4) . as for therapeutic management, 91 (67.9%) patients received oxygen inhalation, the two critical illness cases (1.5%) were treated with noninvasive ventilation, of whom one switched to invasive mechanical ventilation (imv), extracorporeal membrane oxygenation (ecmo) and continuous renal replacement therapy (crrt) as salvage therapy, and another one died before switching to imv (table 4) . of the 134 patients, 23 (17.2%) experienced a secondary bacterial infection, three (2.2%) were detected as positive for secondary fungus infection and six (4.5%) had other viruses infection (table 3) . empirical single antibiotic treatment, mainly moxifloxacin, was given to 103 patients (76.9%), with a median duration of 10 days (iqr 7-14). most patients (129, 96.3%) received antiviral therapy (median duration 13 days, iqr 8-17), including lopinavir/ritonavir (87, 64.9%), interferon alpha inhalation (68, 50.7%), arbidol (57,42.5%), ribaviron (44, 32.8%) and chloroquine (3, 2.2%). the median interval from onset of symptoms to antiviral therapy was 6.0 (iqr 4-9) days (table 4) . additionally, two patients (1.5%) received antifungal treatment (table 4) . glucocorticoid therapy (median duration 3 days, iqr 2.0-5.5) was performed in 41 patients (30.6%), the duration of which was remarkably longer in severe cases than in non-severe cases (median 5 vs. 3, p < 0.05). the median interval from onset of symptoms to glucocorticoid therapy was 6 days (iqr 5.0-10.3). in addition, 13 cases (9.7%) were supported with gamma globulin (median 4 days, iqr 3.0-7.0). significantly more severe cases were given oxygen inhalation, antibiotics, systematic corticosteroid and gamma globulin (all p < 0.05, table 4 ). by 7 march 2020, 123 (91.8%) of the 134 patients had been discharged and one critical patient (0.7%) had died. the remaining ten patients (7.5%) still under treatment were largely severe cases (8 out of 46 severe, 17.4% vs. 2 out of 88 non-severe, 2.3%, p < 0.05) ( table 4 ). fitness for discharge was based on abatement of fever for at least 3 days, significantly improved respiratory symptoms, and negative result for two consecutive respiratory pathogenic nucleic acid tests (sampling interval at least 1 day). to determine the major clinical features during covid-19 progression, the dynamic changes of six clinical laboratory parameters, namely, lymphocyte, il-6, crp, ldh, hbdh and dbil, were monitored every other day from day 1 to day 8 after hospital admission. by 7 march 2020, data of the complete clinical course from seven patients, including five randomly selected discharged patients, two critically ill cases (one managed with ecmo and one died) were analysed (fig. 1) . baseline lymphocyte count was significantly higher in survivors than in the non-survivor patient. in survivors, the lymphocyte count was lowest on day 5 after admission and increased gradually during hospitalisation, whereas, the non-survivor patient developed more severe lymphopoenia (0.19 × 10 9 /l) over time. the level of il-6 in survivors displayed a gradual decrease to normal range with the condition improved, but increased unexpectedly to a very high value (5001 pg/ml) before death in the non-survivor case. compared with those in the recovered patients, levels of crp, ldh, hbdh and dbil in the two critically ill patients were higher throughout the clinical course (fig. 1) . in the recovered patients, the levels of all the four markers reached the peak on day 3 after admission and decreased subsequently during recovery. in the two critically ill cases, the levels increased rapidly from day 3 with condition deterioration. fifty-six per cent of the patients enrolled in this multicentre study had never been to wuhan and had been infected outside wuhan. this suggests a gradual shift of initial infection to secondgeneration local infection which should be taken into account. the percentage of male patients in our data was 48.5%, different from the male patient predominance reported in two studies on wuhan cases (73% in huang et al. [13] and 68% in chen et al. [14] ). in this study, the male-female ratio was approximately 1:1.06, with no difference between severe and non-severe cases. this finding is contradicting to the previous conclusion that men were more susceptible than women to sars-cov-2 [14, 15] . this might be related to occupational exposures, for more men than women work as salesmen or market managers in seafood markets. as recorded, 66.0% of the patients in huang's report and 49% of the patients in chen's report had the history of exposure to the huanan seafood market, and most of the affected patients were male workers [13, 14] . in contrast, no patient in our study had such exposure. all of these indicated a change of transmission mode outside wuhan and that gender may not be a susceptible factor for covid-19. the median age of our patients was 46 years old, close to that of patients outside wuhan as reported by wu et al. p values indicate differences between severe and non-severe patients. p < 0.05 was considered statistically significant. (55 years) [14] . similarly, severe patients were much older than non-severe patients. this suggests that age may be an important risk factor for poor outcome. the role of age in covid-19 seems to be similar to its role in sars and mers, which has been reported as an independent predictor of adverse outcome [19, 20] . t-cell and b-cell hypofunction and excessive production of type 2 cytokines in older people could lead to defect in inhibition of viral replication and stronger host innate responses with sustained cytokine storm, potentially leading to poor outcome [21] . therefore, compromised immune function might be the major cause of higher mortality in older people infected by coronaviruses. the proportion of severe cases in shaanxi was close to that in wuhan as reported previously [13, 14, 22] , while the incidences of complications and mortality were considerably lower among shaanxi patients than among the initially infected wuhan patients [13, 14, 22] (supplementary table s2 , both p < 0.05). only two cases in our cohort needed mechanical ventilation, the incidence of which was much lower than that reported in wuhan cases [13, 14, 22] (supplementary table s2 , p < 0.05). this might indicate that patients outside wuhan had a much better prognosis than the first generation patients in wuhan. what's more, of the cases in wuhan, those initially identified had a higher mortality than those confirmed and treated later (15% [13] vs. 11% [14] vs. 4.3% [18] ). this phenomenon was similar to that during the transmission of mers-cov, in which the global mortality of the first-generation mers-cov was about 35.5%, while that of the second-generation was around 20% [23] . furthermore, the median interval from symptom onset to hospital admission in shaanxi cases was shorter than in wuhan cases (4.5 vs. 7 days) [13, 18] and the shaanxi patients were younger than those in wuhan (46 vs. 55-62 years) [14, 15, 18] . these may be reasons for the notable reduction in mortality in shaanxi cases. the percentage of cases having fever in our cohort was lower than that reported in wuhan [13, 14, 18] . in this regard, patients with normal temperature may be missed if the surveillance case definition focused heavily on fever detection. compared with non-severe patients, severe patients more commonly had symptoms and signs such as cough, sputum, chest stuffiness, dyspnoea, temperature above 38°c, respiratory rate above 21 breaths per min, and heart rate above 100 beats per min. the onset of symptoms and signs may assist physicians in identifying patients with greater severity. based on the radiological data, the incidences of bilateral pneumonia and pleural effusion were higher in severe cases than in non-severe cases, which suggested greater disease severity. similar to what was reported by sun et al. [24] , in 54.7% (69/126) puyu shi et al. of the pneumonia cases, pulmonary fibrosis was found in later chest ct images when shadowing had been resolved, and the phenomenon was more common in severe patients than in nonsevere patients. these findings consistently suggest that pulmonary fibrosis can be one of the sequelae of covid-19. it is necessary and important to explore how to prevent and reduce the occurrence of pulmonary fibrosis and how to manage the situation whenever it occurs in the treatment of covid-19. in terms of laboratory tests, different from cases in wuhan, most shaanxi patients had lymphocytes within the normal range, and only 38.1% showed lymphopoenia. the lymphocyte absolute count in our cohort of patients (1.1 × 10 9 /l) was higher than that reported in wuhan patients (0.6-0.8 × 10 9 /l) [13, 18, 25] . this may be another reason for the lower mortality of shaanxi cases as compared with of wuhan cases. in severe cases, the lymphocyte count was lower and the incidence of lymphopoenia was higher than in non-severe cases. these findings suggest that sars-cov-2 might mainly act on lymphocytes, especially t lymphocytes, and the severity of lymphopoenia might reflect the severity of the disease. furthermore, levels of inflammatory parameters, such as crp and esr elevated in covid-19 patients and were even higher in severe patients. the changes in these laboratory parameters illustrated that the virus invaded through respiratory mucosa and spread in the body, triggering a series of immune responses and inducing severe inflammation and cytokine storm in vivo [26] . few patients in our study had abnormal levels of alanine aminotransferase (alt), aspartate aminotransferase (ast) and indirect bilirubin (idbil). the median level of dbil in the patients elevated, and was even higher in severe patients. as reported, the potential mechanism of liver dysfunction in covid-19 could be that the virus might directly bind to ace2 positive bile duct cells [27] . therefore, the liver abnormality of covid-19 patients may not be caused by liver cell damage, but by bile duct cell dysfunction. in addition, elevated glucose, ldh, hbdh and pro-brain natriuretic peptide, as well as declined albumin, pao 2 and pao 2 :fio 2 , were more commonly seen in severe cases, suggesting greater disease severity. the dynamic changes of six laboratory markers showed that baseline lymphocyte count was significantly higher in survivors than in the non-survivor patient, and it increased as the condition improved, but declined sharply when death occurred. conversely, the il-6 level displayed a downtrend in survivors, but continually rose to a very high level in the non-survivor patient. hence, we assume that t cellular immune function might relate to mortality, and lymphocyte and il-6 should be used as indicators for prognosis. additionally, crp, ldh, hbdh and dbil levels decreased as the condition improved in recovered patients, but increased rapidly as the condition worsened in the two critically ill cases. these may be related to cytokine storm and bile duct cell dysfunction induced by virus invasion. most patients (96.3%) in our study received antiviral therapy, including lopinavir/ritonavir (64.9%), interferon alpha inhalation (50.7%), arbidol (42.5%), ribaviron (32.8%) and chloroquine (2%). until now, no specific treatment has been recommended for covid-19 infection except for optimal supportive care. currently, randomised clinical trials for lopinavir/ritonavir (chictr2000029308) and intravenous remdesivir (nct04257656, nct04252664) in treatment of covid-19 showed no benefit with lopinavir/ritonavir [28] or remdesivir treatment [29] beyond standard care. meanwhile, covid-19 vaccine is highly expected. ongoing efforts are needed to explore effective therapies for this emerging acute respiratory infection. this study has some limitations. first, as only covid patients in shaanxi were recruited, our conclusions need to be further verified by recruiting larger number of cases of other provinces or cities, outside wuhan. second, there were two critically ill cases with one nonsurvivor in our study, thus dynamic observations of laboratory parameters between non-survivor and survivor, recovered cases and critically ill cases were just descriptive analysis. larger number of critically ill cases are needed to verify our observation. in summary, the present study identified that the imported and second-generation covid-19 cases in shaanxi had a better prognosis in comparison with initial or first-generation cases in wuhan, with less complications and lower fatality. these differences may be related to the shorter interval from symptom onset to hospital admission, younger age and higher lymphocyte count of patients in shaanxi. lymphocyte count and il-6 level could be used as indicators for evaluating prognosis. crp, ldh, hbdh and dbil levels could help estimate the severity and development tendency of the disease. pulmonary fibrosis was found in later chest ct images in more than half of the pneumonia cases and should be taken into account. supplementary material. the supplementary material for this article can be found at https://doi.org/10.1017/s0950268820002332 a novel coronavirus outbreak of global health concern a novel coronavirus from patients with pneumonia in china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia world health organization (2020) coronavirus disease 2019 (covid-19) situation report -67 a review of coronavirus disease-2019 (covid-19) national health commission of the people's republic of china (2020) diagnosis and treatment protocol for novel coronavirus pneumonia world health organization (2020) laboratory testing for coronavirus disease (covid-19) in suspected human cases acute respiratory 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placebocontrolled, multicentre trial acknowledgments. we are grateful to all health-care workers involved in the diagnosis and treatment of covid patients. we thank all our colleagues who helped us during the current study. conflict of interest. the authors declare that they have no conflicts of interest.data availability statement. the datasets generated and/or analysed during the current study are available from the corresponding author on reasonable request. key: cord-278638-2dm54f6l authors: huang, ian; pranata, raymond title: lymphopenia in severe coronavirus disease-2019 (covid-19): systematic review and meta-analysis date: 2020-05-24 journal: j intensive care doi: 10.1186/s40560-020-00453-4 sha: doc_id: 278638 cord_uid: 2dm54f6l objective: clinical and laboratory biomarkers to predict the severity of coronavirus disease 2019 (covid-19) are essential in this pandemic situation of which resource allocation must be urgently prepared especially in the context of respiratory support readiness. lymphocyte count has been a marker of interest since the first covid-19 publication. we conducted a systematic review and meta-analysis in order to investigate the association of lymphocyte count on admission and the severity of covid-19. we would also like to analyze whether patient characteristics such as age and comorbidities affect the relationship between lymphocyte count and covid-19. methods: comprehensive and systematic literature search was performed from pubmed, scopus, europepmc, proquest, cochrane central databases, and google scholar. research articles in adult patients diagnosed with covid-19 with information on lymphocyte count and several outcomes of interest, including mortality, acute respiratory distress syndrome (ards), intensive care unit (icu) care, and severe covid-19, were included in the analysis. inverse variance method was used to obtain mean differences and its standard deviations. maentel-haenszel formula was used to calculate dichotomous variables to obtain odds ratios (ors) along with its 95% confidence intervals. random-effect models were used for meta-analysis regardless of heterogeneity. restricted-maximum likelihood random-effects meta-regression was performed for age, gender, cardiac comorbidity, hypertension, diabetes mellitus, copd, and smoking. results: there were a total of 3099 patients from 24 studies. meta-analysis showed that patients with poor outcome have a lower lymphocyte count (mean difference − 361.06 μl [− 439.18, − 282.95], p < 0.001; i(2) 84%) compared to those with good outcome. subgroup analysis showed lower lymphocyte count in patients who died (mean difference − 395.35 μl [− 165.64, − 625.07], p < 0.001; i(2) 87%), experienced ards (mean difference − 377.56 μl [− 271.89, − 483.22], p < 0.001; i(2) 0%), received icu care (mean difference − 376.53 μl [− 682.84, − 70.22], p = 0.02; i(2) 89%), and have severe covid-19 (mean difference − 353.34 μl [− 250.94, − 455.73], p < 0.001; i(2) 85%). lymphopenia was associated with severe covid-19 (or 3.70 [2.44, 5.63], p < 0.001; i(2) 40%). meta-regression showed that the association between lymphocyte count and composite poor outcome was affected by age (p = 0.034). conclusion: this meta-analysis showed that lymphopenia on admission was associated with poor outcome in patients with covid-19. coronavirus disease 2019 (covid -19) has been declared by the world health organization (who) as a global public health emergency due to its pandemicity [1] . since its first emergence in wuhan, china, more than 450,000 cases and 20,000 deaths have been recorded globally due to covid-19 [2] . while most patients with covid19 have mild influenza-like illness and may be asymptomatic, a minority of patients will develop severe pneumonia, acute respiratory distress syndrome (ards), multi-organ failure (mof), and death [3] . clinical and laboratory biomarkers [4] to predict the mortality and severity of covid-19 are essential in this pandemic situation of which resource allocation must be urgently prepared especially in the context of respiratory support readiness. since the first descriptive study in china regarding the covid-19 infection [5] , lymphocyte count has been a marker of interest. it has been associated with severe covid-19 [6, 7] , and non-survivors of covid-19 were reported to have a significantly lower lymphocyte count than survivors [7] . whether lower lymphocyte count and lymphopenia could really be predictor of severity of covid-19 was our main interest, since this laboratory tools are readily available even in the remote areas. therefore, in the present study, we conducted a systematic review and meta-analysis in order to investigate the association of lymphocyte count on admission and the severity of covid-19. we would also like to analyze whether patient characteristics such as age and comorbidities affect the relationship between lymphocyte count and covid-19. we included research articles concerning adult patients diagnosed with covid-19 that has information on lymphocyte count at admission, and clinical grouping or outcome of clinically validated definition of severe covid-19, death, or icu care. we exclude review articles, non-research letters, commentaries, case reports, animal studies, original research with samples below 20 or case reports and series, non-english language articles, and studies in pediatric populations (≤ 17 years old). we systematically searched pubmed, scopus, eur-opepmc, proquest, cochrane central databases, and google scholar with the search terms "covid-19" or "sars-cov-2" and "lymphocyte" (table s1 ). after initial search, duplicates were excluded. two independent authors (ih and rp) screened title and abstracts for potentially relevant articles. the full-text of the potential articles was assessed by applying inclusion and exclusion criteria. the literature search was finalized on march 25, 2020. the study was carried out in accordance with the declaration of helsinki and with the term of local protocol. this is a preferred reporting items for systematic reviews and meta-analyses (prisma)-compliant systematic review and meta-analysis data extraction was performed independently by two authors (ih and rp). we used standardized forms that included author, year, study design, age, gender, cardiac comorbidities, hypertension, diabetes mellitus, chronic obstructive pulmonary disease, smoking, lymphocyte count, lymphopenia, mortality, ards, icu care, and severe covid-19. the outcome of interest was composite poor outcome that comprised of mortality, ards, icu care, and severe covid-19. mortality and icu care was defined as death and admittance to icu during inhospital care, respectively. ards was defined according to the criteria from the world health organization (who) interim guidance for severe acute respiratory infection (sari) in covid-19, which includes the acuity of symptom onset, chest x-ray and origin of pulmonary infiltrates, and oxygenation impairment [8] . severe covid-19 was defined as patients who had any of the following features at the time of, or after, admission: (1) respiratory rate ≥ 30 breaths per min, (2) oxygen saturation ≤ 93% (at rest), (3) ratio of partial pressure of arterial oxygen to fractional concentration of oxygen inspired air (pao2 to fio2 ratio) ≤ 300 mmhg, or (4) specific complications, such as septic shock, respiratory failure, and or multiple organ dysfunction [9] . the meta-analysis of studies was performed using review manager 5.3 (cochrane collaboration) and stata version 16. to pool continuous variables, we used an inverse variance method to obtain mean differences (mds) and its standard deviations (sds). maentel-haenszel formula was used to calculate dichotomous variables to obtain odds ratios (ors) along with its 95% confidence intervals (cis). we used random-effects models for pooled analysis regardless of heterogeneity. all p values were two-tailed, and statistical significance was set at ≤ 0.05. subgroup analysis was performed for lymphopenia cutoff point at ≤ 1100 cells/μl. sensitivity analysis using a leave-one-out method was performed to single out the cause of heterogeneity. regression-based egger's test was used to assess smallstudy effects for continuous variables and harbord's test for binary outcome. restricted maximum likelihood randomeffects meta-regression was performed for age, gender, cardiac comorbidity, hypertension, diabetes mellitus, chronic obstructive pulmonary disease (copd), and smoking. we found a total of 150 records of which 132 remained after the removal of duplicates. a total of 105 records were excluded after screening the title/abstracts. after assessing 27 articles for eligibility, we excluded 4 in which lymphocyte count was unavailable. thereby, 23 studies remained for qualitative synthesis and meta-analysis ( fig. 1 ). there were a total of 3099 patients from 23 studies [5] [6] [7] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] . baseline characteristics are presented in table 1 . the reported mean age of the patients on these studies was 51 years old; 55% of the overall samples were men. most studies reported lymphocyte count on admission except for ruan sensitivity analysis showed that removal of one particular study [24] reduced the heterogeneity for icu outcome, but lymphocyte count was still lower in those that received icu care (mean difference − 503.51 μl [− 638.11, − 368.92], p < 0.001; i 2 0%, p = 0.41). removal of any single study did not significantly reduce heterogeneity for mortality, ards, and severe covid-19. meta-analysis showed that lymphopenia was associated with severe covid-19 (or 3.70 [2.44, 5 .63], p < 0.001; i 2 40%, p = 0.14) (fig. 2b) . subgroup analysis was performed for lymphopenia with definition of lymphocyte count ≤ 1100 μl, showing that lymphopenia was associated with severe covid-19 (or 3.27 [1.85, 5 .78], p < 0.001; i 2 55%, p = 0.08) ( figure s1 ). random-effects meta-regression analysis showed that the association between lower lymphocyte count in patients with composite poor outcome was affected by age (p = 0.034) (fig. 3a) , but not by gender (p = 0.109), cardiac comorbidity (p = 0.953) (fig. 3b) , hypertension (p = 0.065) (fig. 3c) , diabetes mellitus (p = 0.931), copd (p = 0.798), and smoking (p = 0.581). since the composite poor outcome was affected by age, we performed subgroup analysis by using 55 years old as cutoff point. funnel plot analysis showed asymmetrical shape for lymphocyte count and composite poor outcome (fig. 4) . the funnel plot was symmetrical for lymphopenia and severe covid-19. regression-based egger's test showed statistically significant small-study effects (p = 0.018) for the lymphocyte and composite poor outcome. trimand-fill method did not impute any study. regressionbased harbord's test showed no evidence of small-study effects (p = 0.086) for lymphopenia and severe covid-19 outcome. this meta-analysis showed that lower lymphocyte count was associated with increased mortality, ards, need for icu care, and severe covid-19. the association seemed to be stronger in younger patients compared to older patients. although the definition of lymphopenia differed among studies, a subgroup analysis using ≤ 1100 cells/μl cut-off point has showed a consistent outcome in four studies [10] [11] [12] 19] . we set a cut-off point of ≤ 1100 μl because there were 4 studies using it as a cutoff point. there were only 2 studies for ≤ 1000 μl, and 1 study for < 1200μl and ≤1500 μl, respectively. this subgroup analysis aimed to determine the magnitude of odds ratio at a specific cutoff point (not because of its superiority over the other cutoff points). based on the meta-regression result, subgroup analysis of age group by using 55 years old as the cutoff point was performed. by analyzing the bubble plot chart, the center of bubble plot is approximately 52 to 55 years old. hence, we chose 55 as the cutoff point to ensure the number of studies is almost equal in the left side and the right side of the bubble plot. if the number of studies was too small, the pooled effect estimate will be less reliable. interestingly, we found that the association between lymphopenia and severe covid-19 was stronger in younger patients compared to older patients. this was a novel finding which, as far as we know, has not been discussed in previous literature. although changes in the number and composition of lymphocytes are considered as hallmark of immunosenescence [30] , it could not fully explain this association. one possible hypothesis is that the aging of the immune system could contribute to a relatively "non-reactive" immune state, thereby causing a relatively stable reduced lymphocyte count, while in younger populations, the highly active lymphocyte kinetics may be influenced by a wide range of insults and comorbidities, thus contributing to a relatively higher mean difference between younger populations. this is further reflected by the sensitivity analysis which showed that upon removal of wang et al. study, heterogeneity can be reduced to 0% for the icu care outcome. this heterogeneity was attributed to the mean/median age; there were 3 studies for the icu care outcome, cao et al. pre-existing cardiac disease has been shown to increase mortality in patients with covid-19 [20] ; in this metaanalysis, cardiac comorbidity was not found to affect the association between lymphocyte count difference and composite poor outcome. angiotensin-converting enzyme (ace) inhibitor and angiotensin-receptor blocker (arb) have been hypothetically suggested to exacerbate covid-19 due to increase in angiotensin ii level [31] . these drugs are frequently used in patients with diabetes and hypertension, which was associated with poor outcome [32, 33] . although we did not have data on hypertensive medications in the present study, meta-regression showed that hypertension and diabetes did not significantly affect the lymphocyte count difference between poor and good outcome. our understanding of the pathogenesis of lymphocyte reduction in covid-19 might possibly be enlightened by studies of other similar beta-cov infection, including severe acute respiratory syndrome (sars)-cov and middle east respiratory syndrome (mers)-cov [34] . peripheral t lymphocytes, both cd4+ and cd8+, are rapidly reduced in acute sars-cov infection hypothetically due to lymphocyte sequestration in specific target organs [35] . although mers-cov and sars-cov are structurally similar, they bind to different receptors to facilitate entry. sars-cov attaches to angiotensinconverting enzyme 2 (ace2) to enter the host cells, while mers-cov attaches to a different receptor, namely dipeptidyl peptidase 4 (dpp4) [36] . although the mechanism of significant lymphocyte reduction in severe covid-19 remains unclear, there are hypothesis other than lymphocyte infiltration and sequestration in the lungs, gastrointestinal tracts, and or lymphoid tissues: (1) lymphocytes express the ace2 receptor and may be a direct target of sars-cov-2 infection [37] , and (2) an increase of pro-inflammatory cytokines in covid-19, especially il-6, could induce further lymphocyte reduction [34] . lymphopenia can be used as a marker for poor prognosis in covid-19 and in younger patients in particular. lymphopenia defined as lymphocyte count ≤ 1100 cells/μl is associated with threefold risk of poor outcome. the limitation of this systematic review and metaanalysis is the presence of publication bias. this is apparent in the lymphocyte count and composite poor outcome. most of the articles included in the study were published at preprint server of which are not yet peerreviewed. data curation from preprint server is crucial due to the novel and emergent nature of covid-19; most of the studies are not yet published in journals. most of the studies were exclusively from china; thus the possibility of the same patients reported more than once is high and may represent inaccurate scientific records. the included studies were also mostly retrospective in design. we encourage further studies to create prognostic model that include lymphopenia. this meta-analysis showed that lymphopenia on admission was associated with poor outcome in patients with covid-19. supplementary information accompanies this paper at https://doi.org/10. 1186/s40560-020-00453-4. additional file 1: table s1 . electronic search strategy. additional file 2: figure s1 . subgroup analysis performed for lymphopenia. world health organization. coronavirus disease (covid-19) outbreak world health organization. coronavirus disease 2019 (covid-19) situation report -79. world heal epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study elevated n-terminal pro-brain natriuretic peptide is associated 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hypertension is associated with increased mortality and severity of disease meta-analysis, and meta-regression hypothesis for potential pathogenesis of sars-cov-2 infection--a review of immune changes in patients with viral pneumonia significant changes of peripheral t lymphocyte subsets in patients with severe acute respiratory syndrome dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-emc high expression of ace2 receptor of 2019-ncov on the epithelial cells of oral mucosa publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations none authors' contributions ih and rp developed the concept and drafted the manuscript. ih and rp performed data acquisition, data analysis, and statistical analysis and approved the final version. availability of data and materials all data generated or analyzed during this study are included in this published article. corresponding author (r.p) can be contacted for more information.ethics approval and consent to participate not applicable the authors declare that they have no competing interests key: cord-342822-d7jx06mh authors: izadi, n.; taherpour, n.; mokhayeri, y.; sotoodeh ghorbani, s.; rahmani, k.; hashemi nazari, s. s. title: the epidemiologic parameters for covid-19: a systematic review and meta-analysis date: 2020-05-06 journal: nan doi: 10.1101/2020.05.02.20088385 sha: doc_id: 342822 cord_uid: d7jx06mh introduction: the world health organization (who) declared the outbreak to be a public health emergency and international concern and recognized it as a pandemic. the aim of this study was to estimate the epidemiologic parameters of novel coronavirus (covid-19) pandemic for clinical and epidemiological help. methods: four electronic databases including web of science, medline (pubmed), scopus and google scholar were searched for literature published from early december 2019 up to 23 march 2020. the "metan" command was used to perform a fixed or random effects analysis. cumulative meta-analysis was performed using the "metacum" command. results: totally 76 observational studies were included in the analysis. the pooled estimate for r0 was 2.99 (95% ci: 2.71-3.27) for covid-19. the overall r0 was 3.23, 1.19, 3.6 and 2.35 for china, singapore, iran and japan, respectively. the overall serial interval, doubling time, incubation period were 4.45, 4.14 and 4.24 days for covid-19. in addition, the overall estimation for growth rate and case fatality rate for covid-19 were 0.38% and 3.29%, respectively. conclusion: calculating the pooled estimate of the epidemiological parameters of covid-19 as an emerging disease, could reveal epidemiological features of the disease that consequently pave the way for health policy makers to think more about control strategies. keywords: epidemiologic parameters; r0; serial interval; doubling time; case fatality rate;covid-19 coronaviruses are a group of rna viruses that cause diseases among humans and animals (1) . the latest of coronavirus types as a novel coronavirus that was named severe acute respiratory syndrome coronavirus 2 (sars-cov2) or covid-19 occurred in wuhan, china in december 2019 with a human outbreak (2) . the world health organization (who) declared the outbreak to be a public health emergency and international concern and recognized it as a pandemic on 11 most covid-19 infected people (80.9%) are with mild to moderate respiratory syndromes, old people or patients with underlying diseases such as diabetes, cardiovascular disease, cancer, immune deficiency and respiratory disease are more at risk to develop sever (13.8%) and critical (4.7%) disease (6, 7) . knowledge regarding epidemiological characteristics and parameters of the infectious diseases such as, incubation period (time from exposure to the agent until the first symptoms develop), serial interval (duration between symptom onset of a primary case and symptom onset of its secondary cases), basic reproduction number (r 0 ) (the transmission potential of a disease) and other epidemiologic parameters is important for modelling and estimation of epidemic trends and also implementation and evaluation of preventive procedures (8) (9) (10) (11) . . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . https://doi.org/10.1101/2020.05.02.20088385 doi: medrxiv preprint about covid-19 pandemic parameters, there are many reports from different countries in the world. for example, about 25.6 % to 51.7% of patients have been reported to be asymptomatic or with mild symptoms (12) and 25-30% of them have been admitted to icu for medical care (13) . case-fatality rate was reported in china and other countries among old patients 6% (4-11% ranges) and 2.3 % in all ages (13, 14) . furthermore, the median incubation period was reported as so, for efficient estimation and forecasting of disease spreading, we need acceptable and real values of each parameter. the present study was conducted to provide a systematic assessment and estimation of parameters related to covid-19. this evaluation will help researchers with better prediction and estimation of current epidemic trends. the current study is a systematic review and meta-analysis to determine the epidemiologic parameters for covid-19. to find relevant studies, a comprehensive literature search of the web of science, medline . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 6, 2020. consistent with prisma guidelines, the standard meta-analysis techniques, we included studies. all of the extracted articles independently were screened by two researchers. abstract and full text of the articles were reviewed and duplicated studies were excluded and then relevant articles were selected for data extraction. all epidemiological studies designs (observational studies) including peer reviewed or not peer reviewed articles that provided the epidemiologic parameters of interest regarding the novel corona virus were included. in addition, irrelevant studies, letters and news and studies that didn't report epidemiologic parameters were excluded. all articles were reviewed independently by four researchers and information was extracted using designed checklist (appendix 1). extracted items were name of the first author, years and month of article published, duration of the study, location of study conduction, type of . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 6, 2020. . https://doi.org/10.1101/2020.05.02.20088385 doi: medrxiv preprint parameters, point estimate or mean/median and its confidence interval for epidemiological parameters and review status of articles (peer-reviewed or not). to assess the quality of included the peer-reviewed and not peer reviewed articles, we used the strobe quality assessment scale for observational studies. we assessed the quality of all studies and finally, studies with high and medium quality were included in the analyses. the "metan" command was used to apply a fixed or random effects model based on cochran's q-test results or a large higgins and thompson's i 2 value. forest plots were used for graphical description of the results. also, the "metacum" command was used for cumulative meta-analysis to determine trend of basic reproductive number (r 0 ). in studies that mortality rate was reported, because of the denominator was confirmed cases, it was considered a case fatality rate (cfr). in addition, for studies that reported the median and interquartile range (iqr), the median was considered equivalent to the mean and the iqr was converted to standard deviation using the "iqr/1.35" formula. stata 14 was used for all statistical analyses. having assessed the quality of relevant studies, 76 observational studies up to 23 march, 2020 were included in this study (follow diagram). the majority of studies were done in wuhan, china. detailed information of the eligible studies and their characteristics has been shown in appendix 1 (12,17,18,20-92). -the overall basic reproductive number (r 0 ) by country and peer review status total: the overall r 0 was 2.99 (95% ci: 2.71-3.27) for covid-19 ( table 1) . . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . https://doi.org/10.1101/2020.05.02.20088385 doi: medrxiv preprint country: the overall r 0 was 3.23, 1.19, 3.6 and 2.35 for china, singapore, iran and japan, respectively ( table 1) . the overall r 0 was 2.75 and 3.08 for peer reviewed and not peer reviewed articles, respectively ( table 1) . -the overall serial interval (si) by country and peer review status total: the overall si was 4.45 days (95% ci: 4.03-4.87) for covid-19. country: using random effect model, the overall si was 4.46 and 4.64 days for china and singapore, respectively (error! reference source not found.). peer review status: the overall si was 5.3 and 4.39 days for peer reviewed and not peer reviewed articles, respectively (error! reference source not found.2). -the overall doubling time by peer review status total: the overall doubling time was 4.14 days (95% ci: 2.67-5.62) for covid-19. peer review status: the overall doubling time was 3.33 and 4.64 days for peer reviewed and not peer reviewed articles, respectively (error! reference source not found.3). -the overall incubation period by peer review status total: the overall incubation period was 4.24 days (95% ci: 3.03-5.44) for covid-19. peer review status: the overall incubation period was 4.03 and 5.82 days for peer reviewed and not peer reviewed articles, respectively ( table 1) . the overall estimation for growth rate and case fatality rate for covid-19 were 0.38% and 3.29%, respectively (table 1 & fig 4) . in addition, the overall time from symptom onset to hospitalization was 5.09 days for covid-19 ( table 1) . . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. based on the cumulative meta-analysis, the trend of r 0 had been increasing at first and, then, decreasing in march. records screened based on title and abstract (n =111) . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . https://doi.org/10.1101/2020.05.02.20088385 doi: medrxiv preprint reviewed some published papers. therefore, we tried to calculate the pooled parameters by peer review status. it should be noted that, r 0 variations to some extent might be due to different methods calculations including exponential growth method, maximum likelihood, and bayesian timedependent method (93) (94) (95) . according to our results the pooled estimate of cfr 3.29% (95% ci: 2.78-3.81) is lower than sars-cov(96) and mers-cov (97) . health control policies, medical standard, and detection rate could affect cfr (35). moreover, cfr estimate in the early phase of the epidemic might be biased (overestimated). usually in the early phase, some subclinical cases and patients with mild symptoms may not be detected (detection bias) (98, 99) . pooled estimate of incubation period using 22 studies was 4.24 days (95% ci: 3.03, 5.44). valid and precise estimate of incubation period has a pivotal role for duration of quarantine (50) . in fact, knowledge about incubation period is useful for surveillance and control approaches, also modeling and monitoring activities (100). our estimate for overall doubling time-time for a given quantity to double in size or number at a constant growth rate was 4.14 days (95% ci: 2.67, 5.62). the doubling time has an important implication for predicting epidemic. generally, social distancing, quarantine, and active surveillance are needed to reduce transmission and consequently extend the doubling time (101) . moreover, the authors tried to estimate pooled measures for growth rate and serial interval. these two epidemiological parameters are used to estimate reproduction number (102) . as a limitation, all 76 studies (except for one, mirjam e kretzschmar et al) (103) have been conducted in asia, particularly in wuhan, china. some epidemiological parameters in europe, africa, and america could be different based on control strategies. hence, distribution of these . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . https://doi.org/10.1101/2020.05.02.20088385 doi: medrxiv preprint epidemiological parameters could be more globally. future studies to calculate more generalized pooled estimates, using studies all over the world, would be recommended. calculating the pooled estimate of the epidemiological parameters of covid-19 as an emerging disease, could reveal epidemiological features of the disease that consequently pave the way for health policy makers to think more about control strategies. we would like to appreciate all those researchers who helped us to conduct this study. this study was supported by school of public health and safety, shahid beheshti university of medical sciences grant number 23149. the funding agency did not play any role in the planning, conduct, and reporting or in the decision to submit the paper for publication. the authors declare that they have no competing interests. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 6, 2020. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. 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(2019-ncov) in wuhan estimation of the reproductive number and the serial interval in early phase of the 2009 influenza a/h1n1 pandemic in the usa. influenza and other respiratory viruses real time bayesian estimation of the epidemic potential of emerging infectious diseases the r0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks. bmc medical informatics and decision making epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in hong kong estimation of mers-coronavirus reproductive number and case fatality rate for the spring 2014 saudi arabia outbreak: insights from publicly available data methods for estimating the case fatality ratio for a novel, emerging infectious disease case fatality rate of coronavirus disease 2019 (covid-19) in iran-a term of caution the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application. annals of internal medicine high contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2. emerging infectious diseases transmission potential of covid-19 in iran effectiveness of isolation and contact tracing for containment and slowing down a covid-19 epidemic: a modelling study key: cord-351880-iqr419fp authors: fan, changyu; liu, linping; guo, wei; yang, anuo; ye, chenchen; jilili, maitixirepu; ren, meina; xu, peng; long, hexing; wang, yufan title: prediction of epidemic spread of the 2019 novel coronavirus driven by spring festival transportation in china: a population-based study date: 2020-03-04 journal: int j environ res public health doi: 10.3390/ijerph17051679 sha: doc_id: 351880 cord_uid: iqr419fp after the 2019 novel coronavirus (2019-ncov) outbreak, we estimated the distribution and scale of more than 5 million migrants residing in wuhan after they returned to their hometown communities in hubei province or other provinces at the end of 2019 by using the data from the 2013–2018 china migrants dynamic survey (cmds). we found that the distribution of wuhan’s migrants is centred in hubei province (approximately 75%) at a provincial level, gradually decreasing in the surrounding provinces in layers, with obvious spatial characteristics of circle layers and echelons. the scale of wuhan’s migrants, whose origins in hubei province give rise to a gradient reduction from east to west within the province, and account for 66% of wuhan’s total migrants, are from the surrounding prefectural-level cities of wuhan. the distribution comprises 94 districts and counties in hubei province, and the cumulative percentage of the top 30 districts and counties exceeds 80%. wuhan’s migrants have a large proportion of middle-aged and high-risk individuals. their social characteristics include nuclear family migration (84%), migration with families of 3–4 members (71%), a rural household registration (85%), and working or doing business (84%) as the main reason for migration. using a quasi-experimental analysis framework, we found that the size of wuhan’s migrants was highly correlated with the daily number of confirmed cases. furthermore, we compared the epidemic situation in different regions and found that the number of confirmed cases in some provinces and cities in hubei province may be underestimated, while the epidemic situation in some regions has increased rapidly. the results are conducive to monitoring the epidemic prevention and control in various regions. the outbreak of a new coronavirus (2019-ncov) has spread internationally since the initial report of cases by wuhan municipal health commission, china on 31 december 2019 [1] [2] [3] [4] . on 26 january 2020, who announced that there is a high risk of a 2019-ncov epidemic in china and at a global level [5] . the analysis object of this study was the floating population who have lived in wuhan for more than one month. short-term migrants and students were not included. distinct from other models of the dynamics of this epidemic, we used the information of the respondents from the cmds and their family members to further explore the origins of wuhan's migrant population, such as their returning destination, population characteristics, family structures and other metrics. this approach can provide practical solutions to prepare prevention strategies, and approaches to assess resources for treatment and containment of the epidemic. the national health commission of china released a report on 27 january 2020 that stated that 2019-ncov could be transmitted not only via respiratory droplets, but also via direct contact. 2019-ncov has now spread nationally and worldwide, and due to the lack of data on the size and origins of the floating population of wuhan, it has been difficult for the chinese government to arrange real-time medical resources and implement effective public health interventions. we used data from the wuhan floating population monitoring survey to estimate the size and origins of the migrant population in wuhan. we also described the socio-demographic characteristics of this population, and compared confirmed cases from different regions to estimate the epidemic with modelling techniques. we found that three-quarters of wuhan's floating population are from hubei province, and that nearly 85% migrated with nuclear families. the number of members per family is 3 to 4, and most individuals are migrant workers from rural areas with low education levels. by comparing the predicted and actual values obtained from the model, we analysed the profile of the epidemic in various regions since january 25, and found that the spread of the 2019-ncov has varied greatly between regions, and that the epidemic in some regions may be underestimated. there may also be unknowns, such as structural factors in some regions, that deserve further attention. the majority of the floating population left wuhan before the city was "closed off" by authorities, so our analysis will be useful for estimating the key geographic areas for prevention and control. the results indicate that the floating population of wuhan is centred in hubei province and the surrounding provinces, so local government must quickly and effectively take steps to prevent further spread of 2019-ncov. higher-level governments must also strengthen the assistance they are providing, such as sending medical workers and medical supplies to these areas to avoid 2019-ncov becoming a new pandemic. at the same time, it is important to increase surveillance in areas where the epidemic may be underestimated, and promptly identify prevention and control loopholes to reduce the burden of a new round of transmission. china has been deeply involved in the globalisation process, and even china's central and western regions have become important links in the global production and trade chain. therefore, while our research is aimed at china in the current era of migration, this research has practical implications for global public health and disease control, as floating populations are increasing in size all over the world and relationships between countries are becoming increasingly close. thus, other countries should pay attention to the epidemic situation in specific geographic areas of china to prevent secondary and international transmission of the 2019-ncov. the data used in this study are based on the 2013-2018 china migrants dynamic survey (cmds), and the tabulated data of 5 million migrants in wuhan recently released by the wuhan municipal government. this survey was carried out via a multi-stage stratified sampling method, and collected data with structured questionnaires. as survey data is limited to the mainland provinces, municipalities, autonomous regions, and hainan province, the population analysed in this study excluded the populations of hong kong and macao. a total of 11,999 samples of the resident floating population in wuhan from 2013 to 2018 were extracted from the survey dataset. according to the survey design, wuhan's floating population was defined as the population from other cities and districts, aged 15 and over, residing for more than one month in wuhan, and not registered in wuhan. in table 1 , the sample distribution of the resident population in wuhan over time is presented. the sample size was 1999 in the year 2013, and 2000 for other years. the outbreak is considered to have originated in the huanan seafood market, near hankou railway station in the jianghan district, wuhan, china. a severely infected area was concentrated in the urban areas of hankou. from the sample distribution in table 1 , the floating population of wuhan is seen to be concentrated in the urban area of hankou. the results indicate that the sample proportion of jianghan district and nearby jiang'an district, tongkou district, and dongxihu district is approximately 51.6%. therefore, the samples used in this study are suitably representative and thus acceptable for assessing the spread of the 2019-ncov outbreak among the floating population. total 1999 2000 2000 2000 2000 2000 11,999 hankou zone jiang'an 400 360 360 320 400 -1840 qiaokou 240 240 240 200 240 -1160 jianghan 280 240 200 200 160 -1080 dongxihu 200 160 200 320 200 -1080 huangpi 120 120 120 120 160 -640 xinzhou 0 0 40 40 0 -80 wuchang zone hongshan 239 240 240 240 200 -1159 wuchang 200 160 200 200 240 -1000 qingshan 80 160 120 80 40 -480 jiangxia 40 0 40 40 40 -160 hanyang zone hanyang 120 160 160 160 200 -800 hannan 40 120 80 80 80 -400 caidian 40 40 0 0 40 -120 all three zones -----2000 2000 we obtained data from the "dingxiangyuan" national real-time epidemic website on confirmed cases from 25 january to 31 january 2020 [6] . these data are compiled from open data released by authorities such as the national health commission, and the provincial and municipal health commissions. to ensure data comparability, we collected the data daily from 12:00 to 14:00 every day. using the information of the floating population and their family members in wuhan, we analysed their return destinations and their structural characteristics by descriptive statistical methods. in table 2 , the distribution of the origins of wuhan's floating population is presented, at the provincial level, over the past several years. the sample size is quite stable for each province over time. the province of origin for 75% of the floating population was hubei province, which contains the city of wuhan, and approximately 25% of the population originated in other provinces. the location information published in other historical survey data is limited to the province where household registration is located, due to a lack of data for 2019. the data provided by the hubei provincial health commission in 2017 includes more detailed information of prefectures, cities, districts and counties. the analysis was therefore divided into two parts; the first part comprised an analysis of the origin of wuhan's floating population at the provincial level using historical data. the second part comprised an analysis of the floating population within hubei province based on 2017 data. when analysing the floating population at the provincial level, we used all samples from the previous years-i.e., the mean of 6 years of data collection-to ensure the robustness of the results, in view of the stability of sample distributions in each province over time. total 1999 2000 2000 2000 2000 2000 11,999 hubei 1514 1508 1487 1465 1477 1547 8998 henan 113 134 109 159 170 125 810 anhui 59 58 55 53 56 46 327 hunan 57 46 68 54 41 36 302 jiangxi 58 40 53 57 49 34 291 chongqing 34 29 34 33 33 35 198 zhejiang 22 29 25 33 25 33 167 sichuan 22 30 45 21 22 27 167 fujian 14 17 16 15 39 19 120 jiangsu 38 13 16 19 13 11 110 shandong 12 18 11 13 8 12 74 guangdong 7 8 18 18 14 8 73 hebei 0 1 5 tianjin 1 0 0 1 0 1 3 shanghai 0 1 0 1 0 1 3 inner mongolia 1 0 0 0 1 0 2 xizang 0 0 1 0 0 1 2 ningxia 0 0 1 0 0 0 1 according to the current infectious features of 2019-ncov, which are that middle-aged and elderly people have a high risk of infection, and transmission can occur between individuals, families and communities, we assessed several main variables. these comprised age group, educational level, pattern of migration, number of migrating family members per household, type of household registration, and reasons for migration. we defined these variables in the following ways: (1) age group was classified as under 20, 21-30, 31-40, 41-50, 51-60, and over 60; (2) educational level was divided into junior high school and below, high school/secondary school, and college and above; (3) pattern of migration was divided into independent migration, nuclear family migration, and extended family migration; (4) number of migrating family members per household was classified as 1, 2, 3, 4, and 5 or more; (5) types of household registration were divided into rural and urban household registration; (6) reasons for migration were working and doing business, family relocation, or other reasons. the analyses assume a theoretical model of 2019-ncov transmission. we considered a floating population of 5 million in wuhan, who returned to their hometowns from 23 january 2020, as potential infected persons. moreover, we added factors of demographic characteristics, the situation of medical diagnosis, government prevention and control, the number of confirmed cases, and undisclosed data to our statistical model to estimate the dynamics of the epidemic. after controlling for certain factors, we analysed the factors that were not controlled, such as government intervention and the number of statistical reports. specifically, we first analysed the correlation between the size of the floating population in wuhan and the number of confirmed cases per day. then, we examined the differences among regions and proposed a transmission rate as a reference to compare the differences in regions. in the comparative analysis, we focused on the probably underestimated number of cases and the virus transmission rate to determine the likelihood of epidemics existing in different regions. finally, we predicted the floating population of wuhan using statistical methods and compared it with the number of 2019-ncov confirmed cases in each region, to identify regional differences of 2019-ncov infection. furthermore, we predicted the forthcoming epidemic trend at the prefectureand province-level based on the proportion of wuhan's floating population represented by people from these areas. human-to-human transmission of the 2019-ncov has been confirmed. four sets of factors that may influence regional differences appear to be involved: (1) demographic factors, such as short-term business travellers between wuhan and other regions, college students in wuhan returning to their homes in other regions, spring festival tourists from wuhan to other regions, and trans-regional floating populations for spring festival family reunions from or across wuhan; (2) intervention factors, such as medical treatments and governmental preventative measures; (3) information disclosure and the information release system; and (4) other unknown factors. we considered all these factors, and hypothesised the social environment of 2019-ncov transmission. first, although the government had taken the unprecedented measure of sealing off wuhan city on 23 january 2020, we assumed that, at that time, the entire floating population of wuhan, all short-term business travellers to wuhan and all college students in wuhan had returned to their hometowns throughout china, because 24 january 2020 was the spring festival's eve (normally, the 2020 spring festival holiday from january 24 to 30). moreover, this spring festival vacation period started at least a week before this date time, leaving plenty of time for these people to leave the city. however, the number of people in wuhan that travelled to reunite with their families in other cities during the spring festival vacation may be negligible, for the sealing-off of the city and other preventive measures taken across the country may have prevented their travelling. second, the influence of the college students in wuhan was an invariant factor, as college students are young and healthy, have fixed travelling routes, come from different regions evenly scattered across the country, and travelled to return home on or around january 10; we would assume their influence on virus transmission to different regions to be the same. third, the medical treatment ability of regional medical centres of hubei province would also be the same, as the breakout emerged so fast that these regional medical centres would have had the same level of emergency-preparedness. finally, the above factors will not change dramatically until the mass return of wuhan's floating population after the conclusion of the spring festival vacation. to estimate the floating population in the cities of hubei province and across the country, we must determine the floating population residing in wuhan in 2019. as the statistics compiled by the wuhan city government from 2019 have not been released, the data from previous years was used for this prediction. the prediction of floating population in wuhan based on the statistics from previous years is presented in table 3 , demonstrating that there were approximately 2.43 million migrants living in wuhan for more than six months in 2019. however, if the predictions of the statistical data were combined with survey data, which was used in this study to estimate the origin of wuhan's floating population that return to their hometowns, there would have been a problem with inconsistent statistical strength. this would have resulted from the fact that the floating population measured by the government statistics department reflects those who have lived in wuhan for more than 6 months, but the respondents in the survey have lived in wuhan for over one month. a shorter defined residence time would have therefore produced a larger estimate of the population, and thus the total floating population in wuhan, as determined from the cmds data, was larger than the population as determined by the government statistics department. on 22 january 2020, xinhua news agency (an official government media source) interviewed the mayor of wuhan and reported that more than 5 million members of the floating population had returned to their hometowns before the spring festival holiday. this number stated (over 5 million) was more than twice the predicted value in this study (2.43 million), indicating that the statistical strength of the news report was based on a shorter period of residence, and this was consistent with the data we used to determine the floating population residing in wuhan for over one month. thus, in the absence of more rigorous and authoritative total data, we used 5 million people as wuhan's floating population, from which to estimate the scale and distribution of those members of this population who returned to their hometown during the festival. based on sample survey data, in table 4 , the proportional estimation of the origins of wuhan's floating population at a provincial level is presented, as well as the results of statistical analysis based on a floating population of 5 million. estimation of population size is based on the total number of floating population in wuhan (about 5 million); ci = confidence interval. the national distribution of the migrants presents obvious spatial characteristics of circle layers and echelons at provincial level (table 4 and figure 1 ). (1) hubei province is the central area of origin of wuhan's floating population, accounting for 75% of the population, with a 95% confidence interval of (74.21, 75.76). based on a total population of 5 million people, wuhan's floating population with household registration in hubei province is approximately 3.75 million, with a 95% confidence interval of (3,710,227 to 3,788,125). (2) henan, anhui, jiangxi and hunan provinces belong to the first circle layer. henan province, home to a floating population of 337,000, had the highest proportion with respect to its total population, equating to approximately 6.7% and a 95% confidence interval of (315,401 to 360,712). based on the analysis of city data in 2017, xinyang, zhumadian, shangqiu, and nanyang cities in henan province accounted for 38.82%, 20.59%, 12.94%, and 10.59% respectively, of the floating population from henan living in wuhan, accounting for approximately 83% of the total. the floating population proportions of anhui, hunan, and jiangxi provinces were 2.7%, 2.5%, and 2.4%, respectively, with corresponding floating populations in wuhan of 136,000, 126,000, and 121,000 respectively. (3) chongqing, zhejiang, sichuan, fujian and jiangsu provinces are at the second circle layer, with 1.65%, 1.39%, 1.39%, 1.00% and 0.92% floating populations, respectively, with corresponding populations of approximately 83,000, 70,000, 70,000, 50,000 and 46,000 respectively. (4) shandong, guangdong, hebei, gansu, guangxi, heilongjiang, shaanxi, shanxi and guizhou provinces are at the third circle layer, with a proportion of 0.19% to 0.62% and a corresponding population of 10,000 to 30,000. (5) some provinces and municipalities, including qinghai, liaoning, yunnan, jilin and beijing, are located in the fourth circle layer, accounting for 0.08-0.16% of the floating population, equating to 4000-8000 people. (6) the remaining provinces and municipalities, such as hainan, xinjiang, tianjin, shanghai, inner mongolia, tibet and ningxia, are at the fifth circle layer, with a floating population proportion of less than 0.04%, corresponding to ≤2000 people. as presented in the table above, this population is mainly 21-40 years old, but the scale of the susceptible, high-risk and over 40 years old population is also very large. the distribution is as follows: (1) the susceptible and high-risk population is concentrated in hubei province. the size of the 41-50 age group is more than 800,000, that of the age group of 51-60 is 180,000, and the number of people over 60 is 40,000. (2) henan and anhui provinces have larger susceptible and high-risk populations, of more than 100,000 and nearly 40,000, respectively. (3) six provinces and municipalities, namely hunan, jiangxi, chongqing, zhejiang, sichuan and jiangsu, have a high-risk population of 41 to 50 years old, comprising 14,000-30,000 people. (4) in 10 provinces, namely fujian, shandong, guangdong, hebei, gansu, guangxi, shanxi, guizhou, qinghai and xinjiang, the susceptible and high-risk populations are also concentrated in the 41-50 age group, with a population of approximately 1500-6550. (5) the three provinces of northeast china, namely heilongjiang, jilin and liaoning, have large susceptible and high-risk populations, equating to approximately 7000 in heilongjiang and approximately 3000 in jilin and liaoning. infection of family members is a main means of transmission, and the distribution of the characteristics of floating population family migration at the provincial level are detailed in table 5 . the vast majority of the floating population migrates to wuhan in the form of nuclear families (84.42%), and most families comprise 3-4 members (71.44%). the distribution is as follows: (1) the number of nuclear family households in the wuhan floating population that originates from hubei province is 3.425 million, accounting for 62.85% of the total floating population of wuhan, and households with 3-4 family members number 2,693,500, accounting for 53.87% of the total. the high risk of 2019-ncov transmission within and by this population is self-evident. (2) families from henan, anhui, hunan and jiangxi provinces comprise a large proportion of those in the floating population of wuhan. those from henan total nearly 300,000 households, and the number of these households with 3-4 family members is more than 240,000. approximately 110,000 families from the remaining provinces are part of the floating population of wuhan, including nearly 100,000 3-4 family-member households from anhui and more than 80,000 from hunan and jiangxi. (3) the number of families in the floating population of wuhan from chongqing, zhejiang, sichuan, fujian and jiangsu municipalities and provinces is 40,000-80,000, and the number of households with 3-4 family members is 30,000-60,000. (4) the number of families in the floating population of wuhan that originate from 7 other provinces, namely shandong, guangdong, hebei, gansu, guangxi, heilongjiang and shaanxi, is 10,000-30,000 households, and the number of households with 3-4 family members is approximately 20,000. the remaining provinces comprise fewer than 10,000 households jiangxi. certain factors can easily spread the virus from homes to communities in rural areas, such as a lack of medical resources and investment, weak health prevention and control, low awareness of health, and insufficient awareness of infectious diseases. in table 5 , the floating population in wuhan is dominated by rural households (85.14%), and working or doing business is the main reason for their having travelled to wuhan (84.29%). therefore, epidemic prevention and control in rural areas is of critical importance. the distribution is as follows: (1) the joint distribution of the origins of wuhan's floating population within hubei province is 63.73%, equating to a population of 3,186,500, and 62.71% of these are migrant workers, equating to 3,135,500 people. (2) henan, anhui, hunan, and jiangxi province both have more than 100,000 households with rural household registers and migrant workers in wuhan, and the population of those from henan in wuhan's floating population is approximately 300,000. (3) chongqing, zhejiang, sichuan, fujian, jiangsu, shandong, guangdong, hebei, gansu, and guangxi provinces together have a population of 10,000-80,000 households with rural household registers in wuhan and less than 10,000 in the remaining provinces of china. notably, guangdong, gansu, heilongjiang and liaoning have a larger proportion of the population with urban household registers, and this is greater than the number of rural household registers in guangdong province. 0 0 1667 9167 1250 1667 1250 4167 4584 417 9584 2500 10,834 833 10,834 6251 2917 2917 guizhou 9584 417 5000 2500 1667 0 0 833 8751 0 833 1250 5417 2084 0 7501 2084 7084 2500 7084 5417 2084 2084 qinghai 7917 417 3750 2084 1667 0 0 0 7501 417 0 1667 3750 2084 417 7917 0 7084 833 7084 7501 417 0 liaoning 7084 0 1667 2917 1250 1250 0 1667 5000 417 1667 1667 3334 417 0 2500 4584 6251 417 6251 1667 1667 3750 yunnan 4584 833 2917 833 0 0 0 417 3750 417 417 833 2084 833 417 4167 417 3334 1250 3334 2917 417 1250 beijing 4167 0 417 833 2917 0 0 833 3334 0 833 1667 1250 417 0 1250 2917 4167 0 4167 1250 1667 1250 jilin 3750 417 1250 1250 833 0 0 1667 2084 0 1667 0 2084 0 0 833 2917 3334 417 3334 1250 0 2500 hainan 2084 0 1250 417 0 417 0 833 1250 0 833 0 1250 0 0 833 1250 1667 417 1667 417 833 833 xinjiang 2084 0 833 0 1250 0 0 417 1667 0 417 0 417 1250 0 2084 0 1667 417 1667 1250 417 417 tianjin 1250 417 417 417 0 0 0 417 833 0 417 417 0 417 0 833 417 833 417 833 417 0 833 shanghai 1250 0 833 0 0 0 417 417 833 0 417 833 0 0 0 0 1250 1250 0 1250 0 417 833 inner mongolia 833 0 417 417 0 0 0 0 833 0 0 0 833 0 0 417 417 417 417 417 0 417 417 xizang 833 0 0 417 0 0 417 0 833 0 0 417 417 0 0 417 417 417 0 417 417 417 0 ningxia 417 0 417 0 0 0 0 0 417 0 0 0 417 0 0 417 0 417 0 417 417 0 0 virus transmission is related to individual health awareness, which is affected by an individual's educational level, so we also examined the educational level of the floating population in wuhan. in table 5 , 60% of the population was educated to junior middle school and below, 26% had senior high school or technical secondary school education, and 14% had college education and above, indicating that the overall education level of this population was low. specifically: (1) in the provinces of qinghai, chongqing, jiangxi, anhui, henan, yunnan, guangxi and xinjiang, 60% or more of the population was educated to junior high school level or below. (2) approximately 50-60 % of the population of the provinces of hubei, sichuan, hebei, fujian, jiangsu, hunan, guizhou, shandong, shanxi, tibet and gansu was educated to junior high school level or below. (3) the population in three municipalities, including beijing, tianjin and shanghai, have a high level of education, with over 66% receiving tertiary education. the population of the remaining provinces had a medium-to-high educational level. above all, these data indicated that there is a large middle-aged and older high-risk floating population in wuhan. their social characteristics include having travelled to wuhan in a nuclear family of 3-4 members, being on a rural household register, and often having a lower educational level. these characteristics are consistent with conditions favouring the wide spread of 2019-ncov. according to the foregoing analysis, 75% of wuhan's floating population have registered households in hubei province, equating to approximately 3.75 million people. that such a large proportion of the floating population of wuhan originate from elsewhere in hubei province has reduced the possibility of the epidemic spreading across the country, but all regions in hubei province are facing tremendous pressure from the spread of the epidemic. therefore, we used the 2017 cmds data to analyse the distribution of the floating population in regions within hubei province. table 6 and figure 2 present the distribution of the origins of wuhan's floating population within hubei province. the proportion of the floating population gradually decreases from east to west across hubei province, and there are great differences between cities. the distribution is as follows: (1) xiaogan, wuhan, and huanggang are in the first echelon. the proportion of the floating population who originate from these cities is high, accounting for 23.4%, 19.6%, and 14% of the total, respectively. they are a cross-regional floating population of 734,000 and a 95% confidence interval of (65.89, 81.30). the analysis of districts and counties indicates that the members the floating population who originate from the outskirts of huangpi district and xinzhou district flow into the main urban area of hankou, so the epidemic situation in the outskirts of huangpi district and xinzhou district needs special attention. secondly, the members of wuhan's floating population who originate from xiaogan comprise the largest proportion, equating to approximately 788,000 people and a 95% confidence interval of (79.81, 96.25). members of wuhan's floating population who originate from huanggang comprise the third proportion, equating to approximately 52,549 people and a 95% confidence interval of (46.06, 59.58). (2) the three directly managed by province (dmp) cities (xiantao, qianjiang, and tianmen) and jingzhou belong to the second echelon, each comprising approximately 330,000 people, and each accounting for approximately 9% of the floating population of wuhan, with a 95% confidence interval of (28,39). (3) jingmen, suizhou, xianning, and huangshi belong to the third echelon, accounting for 3-5% of the floating population of wuhan, equating to 130,000-170,000 people. (4) xiangyang, ezhou, yichang, enshi, and shiyan belong to the fourth echelon, accounting for less than 3% of the floating population of wuhan, equating to fewer than 100,000 people. overall, the suburbs of wuhan surrounding xiaogan, huanggang, and the three dmp cities are the origins of the largest proportion (66%) of the floating population of wuhan, equating to approximately 2.475 million people. we used district-and county-level variables to estimate the floating population within hubei province, and the results are presented in table 7 . the survey covered 94 districts and counties, including huangpi, xinzhou, jiangxia, caidian, and hannan in wuhan, as well as cross-region active migrants in some major urban areas. the top 10 districts and counties of hubei province in terms of floating population are huangpi, hanchuan, xiantao, xinzhou, hong'an, yunmeng, honghu, macheng, xiaonan, and xiaochang. that is, ≥100,000 people from each of these districts and counties are part of the floating population of wuhan, with the top 3 districts and counties, huangpi, hanchuan and xiantao, having ≥200,000 people in wuhan's floating population. these top 10 district and counties of hubei province are followed by jingshan, yingcheng, dawu, guangshui, tianmen, lishui, jianli, anlu, jiangxia and caidian, which each have 60,000-100,000 people in wuhan's floating population. the third tier is huangmei, yangxin, daye, gongan, tongshan, jiayu, zhongxiang, qianjiang, songzi, huarong, zengdu, enshi, liangzihu, zaoyang, dongxihu, wuxue, huangzhou, hannan, xian'an, xiangzhou, zhijiang, echeng, luotian, badong, chibi, chongyang, hongshan, shayang, shishou, suixian, tuanfeng, gucheng and xiangcheng. these districts and counties each have 10,000-50,000 people in wuhan's floating population. the remaining districts and counties have fewer than 10,000 people in wuhan's floating population. in general, these members of wuhan's floating population originate from certain districts and counties of hubei province. the cumulative percentage of the top 30 districts and counties exceeds 80% of these areas' total population, showing a clear exponential distribution trend. we then analysed the social characteristics of the migrants in hubei province by age, type of migration, number of migrants, type of household registration, and reasons for traveling to wuhan to become part of its floating population. from table 8 (please see the last page), we observe that in terms of susceptible and high-risk groups over 40 years old, there are approximately 300,000 people in xiaogan, approximately 180,000 people in wuhan (cross-region migration), and approximately 150,000 people in huanggang. there are also approximately 100,000 people in the dmp cities and jingzhou respectively, and 30,000-50,000 people in jingmen, suizhou, xianning, and huangshi. fewer than 30,000 people from each of xiangyang, ezhou, yichang, enshi and shiyan have travelled to wuhan. the migration characteristics of the floating population of wuhan from hubei province are detailed in table 8 . migration with a nuclear family is the main pattern, accounting for nearly 80% of the total, or 2.985 million households. the proportion of households with 3-4 family members (i.e., nuclear families) is approximately 67%, or 2.53 million households. specifically, 740,000 nuclear families originate from xiaogan, 400,000-600,000 nuclear families originate from the inner suburbs of wuhan and huanggang, and approximately 260,000 nuclear families originate from the dmp cities and jingzhou. more than 100,000 nuclear families originate from jingmen, suizhou, xianning, and huangshi, while fewer than 100,000 nuclear families originate from xiangyang, ezhou, yichang, enshi and shiyan. the distribution of households with 3-4 members is similar to that of nuclear families. it also presents the distribution of the origins of wuhan's floating population who originate from within hubei province. according to the statistical results, rural household registers account for 83%, equating to a population of approximately 3.12 million. the proportion of the group who was working and doing business in urban areas is 77%, and the population is 2.89 million. the size of the population distribution in each city is similar to the aforementioned migration types and other variables, and is not reported here. in table 8 , the overall educational level of those members of wuhan's floating population who originate from hubei province is higher than the national level, with approximately 52% having been educated to junior high school level and below, approximately 29% to high school/secondary school level and below, and approximately 19% to college and above. however, in those members of wuhan's floating population who originate from the surrounding cities of wuhan, which contribute a large number of people to the floating population of wuhan, namely xiaogan, huanggang, huangshi, suizhou, dmp cities, xianning, and ezhou, >50% of people have an educational level of junior high school and below, with this being >60% in xiaogan. this means that the awareness of health protection and timely treatment may be low in this section of the floating population of wuhan, which will heighten the risk of large-scale transmission of 2019-ncov. the floating population in wuhan will serve as a sound predictor for the trend of the 2019-ncov outbreak. the pearson's correlation coefficient between the proportion of the floating population in wuhan who originate from a certain region of hubei and the number of confirmed 2019-ncov cases in each region increased from 0.65 on 25 january 2020 to 0.84 on 31 january 2020 (table 9 ). this indicates that when a region contributes a higher number of people to the floating residential population of wuhan, more confirmed cases will emerge in this region. table 6 ); 3 ratio = confirmed cases (on 2020/1/31)/floating population from wuhan (unit: 10,000 people); 4 dmp (directly managed by the province) cities includes xiantao, qianjiang and tianmen; 5 the pearson's correlation coefficient is calculated from the number of floating populations in wuhan and the number of confirmed cases per day. we assumed that the effect of the floating population on the transmission of the 2019-ncov is consistent across hubei province, and selected three prefectures that contribute the greatest number of people to the floating population of wuhan (xiaogan, huanggang and jingmeng) as the reference prefectures to predict the epidemic trend of the 2019-ncov at prefecture level. those prefectures can be divided into three groups since 28 january 2020 ( the floating population of wuhan originated from outside hubei province may have promoted the spread of 2019-ncov. table 10 compares the number of individuals travelling from wuhan to other provinces and the daily number of confirmed cases for those other provinces. analysis revealed that the correlation coefficient at the provincial level was lower than at the prefecture level within hubei province, but the correlation coefficient increased from 0.4 on 25 january 2020 to 0.63 on 31 january 2020. table 10 also shows the ratio of confirmed cases in each province to the proportion of people in the floating population in wuhan who originate from each of these provinces, on 28 january 2020. we divide provinces into two categories based on their short-term travel populations in wuhan, and wuhan's travelling population to other provinces during the spring festival holiday. the first category comprises those provinces that have large-scale short-term business trips or tourist populations in wuhan during the spring festival holiday, namely beijing, shanghai, tianjin, and hainan. obviously, such a high level of inter-provincial population mobility may exacerbate the spread of 2019-ncov. for example, the high ratio of confirmed cases in guangdong province may be due to the large short-term travel populations visiting shenzhen and guangzhou and wuhan, while the high ratio of confirmed cases in hainan province may result from the outbound tourist population from wuhan to hainan during the spring festival holiday. in table 10 , the results are divided into two parts: the correlation coefficient of the first category of provinces, which reaches a maximum of 0.96, and the correlation coefficient of the second category of provinces, which increased from 0.56 to 0.7. this abovementioned second category comprise the other 25 provinces that have small short-term business trip groups or tourist populations in wuhan during the spring festival holiday. we assumed that the effect of the floating population on the spread of 2019-ncov was consistent across the country. the other 25 provinces are divided into three groups since 25 january 2020 ( figure 4) : (1) provinces with a rapid increase in the number of confirmed cases, namely zhejiang, shandong, guangxi, shaanxi, liaoning, and yunnan; (2) provinces with a moderate increase in the number of confirmed cases, namely hunan, chongqing, sichuan, fujian, jiangsu, hebei, gansu, heilongjiang, shaanxi, guizhou, qinghai, jilin, xinjiang, inner mongolia, tibet, and ningxia; and (3) provinces with a small increase in the number of confirmed cases, namely henan, anhui, and jiangxi. in table 10 , if we exclude the data of henan province and zhejiang province from the second category, we find that the correlation coefficient on 31 january 2020 is 0.93. we selected four provinces (henan, hunan, sichuan, and zhejiang) as the reference provinces to predict the epidemic trend of 2019-ncov in each province. we found that: (1) the epidemic growth model of henan province does not fit the situation in most other provinces. that is, except in anhui and jiangxi, the actual number of outbreaks in other provinces was higher than that predicted by the henan model. as these provinces have large floating populations in wuhan, the rapid increase in the number of confirmed cases in henan, anhui and jiangxi may result from effective measures that have been taken to control the spread of 2019-ncov, or the lack of sufficient diagnostic capabilities to detect suspected cases. (2) the epidemic growth model for hunan and sichuan province predicts a rapid increase in the number of confirmed cases in henan, anhui and jiangxi provinces. thus, if the epidemic pattern in hunan and sichuan follows a typical evolutionary pattern, the current numbers of confirmed cases in the three provinces of henan, anhui, and jiangxi are greatly underestimated. for example, the number of confirmed cases in henan on 31 january 2020 would be between 860 and 889, but the number in official announcements was only 168. in contrast, the number of confirmed cases in zhejiang, shandong, guangxi, shaanxi, liaoning, and yunnan provinces were higher than the predicted number, which may be affected by uncontrollable local factors that need further investigation. (3) the epidemic growth model for zhejiang province predicts a rapid increase in the number of confirmed cases in most provinces, especially jiangsu and fujian provinces that are adjacent to zhejiang. it is important to investigate why there were so many confirmed cases in zhejiang, and whether the outbreak in jiangsu and fujian province was not detected in a timely manner, or whether all possible cases have not yet occurred. overall, the predicted epidemic pattern for hunan and sichuan provinces fits best to the actual epidemic trend of the 2019-ncov outbreak. however, the current number of confirmed cases in henan, anhui, and jiangxi provinces is likely to be underestimated, especially given that these contain extensive rural areas with large populations and limited medical resources. the higher actual number of confirmed cases in zhejiang, shandong, guangxi, shaanxi, liaoning, and yunnan provinces may be affected by other unknown factors or uncontrollable random factors that need further investigation. to prevent or mitigate the spread of an emerging infectious disease and its negative effects, public health interventions mainly aim at three types of population, namely the population in the source area, the floating population leaving the source area, and the population travelling from the infected area to other areas. the spring festival in 2020 is much earlier than in previous years. at this time, the possibility of human-to-human transmission of a new coronavirus had just been discovered. when the wuhan municipal government decided on 23 january 2020 to "close the city" to control the outflow of population, more than 5 million people had already left wuhan on the spring festival holiday, and it was too late to control the entire potentially infected population in the epidemic area. at present, china's high-speed railway and expressway transportation network has experienced great development. this fast and convenient transportation has led to a floating population that can leave the source area to quickly reach every part of the country, which makes it very difficult to quarantine the floating population leaving the source area through transportation stations. in addition, there is an incubation period after human infection, further increasing the difficulty of quarantine at traffic stations, which is also an important reason for the implementation of "city closure" control policies in many cities across the country. after 2019-ncov was confirmed as being capable of transmitting from human to human, the chinese government implemented top to bottom national mobilisation. it fully investigated and isolated the population of wuhan, and also publicised the severity of the epidemic, and also increased awareness of the prevention of infectious diseases and raised people's vigilance through messages on television, mobile communications and the internet. in addition, according to the latest epidemic surveillance, the incubation period of the coronavirus is 3 to 7 days, with an upper limit of 14 days. for this reason, the central government has issued an executive order to extend the spring festival holiday from 30 january to 2 february 2020. many provinces are even requiring firms to not restart work until 9 february, except those necessary for social operations related to the national economy and people's livelihood. extending the holiday is needed to avoid the returning people leaving home early and returning to work, so as to minimise the risk of the epidemic spreading again due to population fluctuations. there are limitations to this study. first, our analysis did not include other large-scale populations. for example, some are college students, because wuhan is the city with the largest number (>1 million) of college students in china and the world. the other parts include short-term business travellers, transit passengers and tourists. official media reported that the size of the populations during the spring festival holiday would reach more than 30 million. this can be confirmed from the daily-confirmed cases of 2019-ncov infection. although there is a small permanent population in wuhan whose household register belongs to provinces and cities such as beijing, shanghai, tianjin, hainan, and guangdong (in fact, shenzhen and guangzhou are two megacities), these provinces and cities still have large-scale temporary floating populations from and to wuhan because of the large population and well-developed economy. therefore, the number of confirmed cases of 2019-ncov infection in these areas is far ahead of that in most other provinces that have a large floating population in wuhan. second, our sample has a certain deviation. the data on the origin of wuhan's floating population does not include hong kong, macao, or international migrants, which makes our research unable to estimate the population size of these regions. at present, some cases have been confirmed in surrounding asian countries, europe, north america and australia. third, limited to interdisciplinary research capabilities, our model does not include infectious disease analysis models such as sir to further analyse the potential and scale of 2019-ncov spread, which may reduce the value of this research in the prevention and control of 2019-ncov infections. finally, the results of the study are mainly applicable to the end of the spring festival holiday, and after the large-scale population comes back to work or study, the spread of the epidemic will be more complicated. we believe that the abovementioned limitations can be overcome. using big data such as location information of transportation and mobile internet, short-term floating populations can be included in the study to maximise the estimated population flotation and scale in wuhan. unfortunately, thus far we have not seen a rigorous study using big data to analyse the outflow of populations in the epicentre of an epidemic. this means that there is still a long way to go for the research and application of big data in the field of national and global public health. at the time of writing this paper (29 january 2020), all provinces in china have reported confirmed or suspected cases of 2019-ncov, every prefecture and city in hubei province has confirmed cases of 2019-ncov, and transmission of 2019-ncov has spread from imported to inter-regional. due to the fact that 5 million migrants had left wuhan before the "closure of the city", our research reveals a high correlation between the number of wuhan's floating population and the number of confirmed cases. fortunately, the origin of wuhan's floating population is highly concentrated in hubei province and its surrounding provinces, of which the migrants with hubei household registers account for 75%, and more than 80% of the population is concentrated in the top 30 districts and counties. this means that some areas will face a very high risk of epidemic outbreaks, but it is also conducive to centralised resources enabling prevention and control of the epidemic to avoid large-scale spread in other regions. more than 5 million of wuhan's floating population have returned to their hometowns as potential carriers of the virus and may become carriers of the virus's re-transmission. due to china's urban and rural dualistic structure, most of these people are rural migrant workers with low levels of education. the results find that 85% of the migrants have rural household registers. these people, who frequently work outdoors or work overtime are more likely to be susceptible because of their poor diet and nutrition. at the same time, most of these people travel with 3-4 family members, and the susceptible and high-risk population over 40 years old accounts for a large proportion of this floating population, which provides ideal conditions for the transmission of 2019-ncov within families. to make matters worse, the rural areas where these people return to have very limited medical and public health services, and gatherings during the spring festival aggravate the risk of virus transmission in the community. so far, confirmed cases of 2019-ncov continue to increase every day across china. the results of our model analysis indicate that, on the one hand, the correlation between the size of the floating population and the number of confirmed cases in wuhan has continued to increase over time, and by 28 january, the correlation coefficient of these factors in hubei province had reached 0.78, which means that the size of the floating population in wuhan is an important parameter for predicting the epidemic. on the other hand, we also found that the effect of the size of the floating population in wuhan is heterogeneous across regions. some areas have a large floating population in wuhan, including henan, anhui, and jiangxi provinces, and xiaogan city, jingzhou city, and the three county-level cities directly under the provincial government, and yet the number of confirmed cases of 2019-ncov is apparently relatively small. however, we believe that the epidemic situation in these areas may be underestimated. considering the serious consequences of delays in diagnosis and loopholes in infection control in suspected or confirmed cases of sars in the sars epidemic in 2003, it is necessary to strengthen surveillance in these areas to determine the causes of the fewer confirmed cases of 2019-ncov in these areas. author contributions: l.l. conceived and proposed research ideas, c.f. and c.y. collected the data, c.f. undertook the main research work such as research methods, data analysis, and manuscript writing. c.f., l.l., w.g., a.y., c.y., m.j., m.r., p.x., h.l. and y.w. participated in draft review, contributed to data interpretation, and approved final manuscript. all authors have read and agreed to the published version of the manuscript. data sharing and outbreaks: best practice exemplified china coronavirus: what do we know so far? bmj 2020 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sars-cov to wuhan 2019-ncov outbreak: similarity of early epidemic and prediction of future trends a novel coronavirus emerging in china-key questions for impact assessment another decade, another coronavirus report 1: estimating the potential total number of novel coronavirus cases in wuhan city report 2: estimating the potential total number of novel coronavirus cases in wuhan city modelling the epidemic trend of the 2019 novel coronavirus outbreak in china clinical features of patients infected with 2019 novel coronavirus in epidemic situation of the novel coronavirus in guangdong province published on 23 xinhua news agency. 15 chinese medical workers confirmed infected with coronavirus the chinese new year travel rush-the world's largest annual human migration wuhan municipal people's government. wuhan implements restriction to curb the spread of the epidemic real-time update on coronavirus outbreak internal migration and health in china the new york times. china grapples with mystery pneumonia-like illness health status and access to health care of migrant workers in china. public health rep acknowledgments: thanks to the national health committee for the migrant population data; the youth project of national social science foundation and the youth teacher project of central china normal university 2019 for support on previous construction of floating population database; binbin tang and junyue qian for their selfless help in the process of thesis writing. the authors declare no conflict of interest. key: cord-326804-5psqro9d authors: wei, chen; wang, zhengyang; liang, zhichao; liu, quanying title: the focus and timing of covid-19 pandemic control measures under healthcare resource constraints date: 2020-04-19 journal: nan doi: 10.1101/2020.04.16.20067611 sha: doc_id: 326804 cord_uid: 5psqro9d generalizing covid-19 control strategies in one community to others is confounded by community′s unique demographic and socioeconomic attributes. here we propose a tailored dynamic model accounting for community-specific transmission controls and medical resource availability. we trained the model using data from wuhan and applied it to other countries. we show that isolating suspected cases is most effective in reducing transmission rate if the intervention starts early. having more hospital beds provides leverage that diminishes with delayed intervention onset. the importance of transmission control in turn increases by 65% with a 7-day delay. furthermore, prolonging outbreak duration by applying an intermediate, rather than strict, transmission control would not prevent hospital overload regardless of bed capacity, and would likely result in a high ratio (21% ~ 84%) of the population being infected but not treated. the model could help different countries design control policies and gauge the severity of suppression failure. fixing the average period of infectivity at 2.4 days, which based on current evidence 6 , was too low and likely resulted in an over-estimation of the transmission rate. the study further assuming a flat 0%/50%/75% drop in transmissibility following wuhan city lockdown. transmission models with more sophisticated assumptions have since been proposed 7, 8 , including ones with time-dependent control policies 9 or non-markovian transmission dynamics 10 . but these studies rarely made use of data beyond the confirmed number of cases such as the number of suspected cases. another key factor that shall not be neglected in modelling is the real-time healthcare system capacity. while some studies have considered its impact 11 , few have incorporated such a factor dynamically in their transmission models. the availability of a complete set of data and detailed records of adopted control policies from wuhan enables us to construct and test an epidemic model that accounts for the factors deciding an outbreak profile, including the control policy's evolution through time as well as the healthcare system capacity. we also dissected the effect of the proactive case isolation strategy adopted in wuhan. the model validated with data from wuhan is potentially applicable to other countries. subsequently manipulating the parameters corresponding to control strategies opens a window to evaluate the effectiveness of each policy under certain healthcare system capacity constraints. we gauged the required npi strength and timing for other 6 representative countries, namely us, italy, france, germany, japan and korea, with different hospital bed availability. a modified seir model ( figure 1 ) with time-dependent transmission rate control, timedependent case isolation and testing rate, non-markovian patient discharge was proposed (see methods for details). the model also imposes a hospital bed upper limit. data from wuhan between january 10, 2020 and march 11, 2020 was used to fit the model parameters. as shown in figure 2a , the combined effect of increases in npi and case isolation explained the successful outbreak suppression in wuhan. specifically, the transmission rate in wuhan was estimated to have been reduced to 31.0% of pre-lockdown level 5 days after january 23, 2020 and approaching an asymptote of 27.3%. furthermore, the daily proportion of symptomatic cases being isolated in medical facilities was estimated to have increased from a starting estimate of 0.017 on january 10, 2020 to 0.081 on january 28, 2020. the daily proportion of isolated cases being confirmed was estimated to have started at 0.092 and increased to 0.22 by january 28, 2020. the basic reproduction number, corresponding to the initial stage of the outbreak, was estimated to be 3.48. subsequently, the synergistic effect of increasing transmission control and isolation rate effectively reduced the daily reproduction number (see suppression success in methods) to be below 1 by feb 28, 2020, subsequently resulting in a suppressed covid-19 transmission ( figure 2b ). the estimated number of early cases until january 18, 2020 combing both the symptomatic and asymptomatic was 5,101, which was in line with the number of 4,000 (95% ci [1, 000, 9, 700] ) independently estimated from the number of covid-19 cases exported from wuhan internationally via air 4 . throughout the outbreak, the highest bed occupancy attributed to covid-19 (including both suspected and confirmed cases, see methods) was estimated to be 40,710, which was below the reported maximum bed capacity of 44,000 in wuhan. alternatively, we simulated that without proactive isolation, the daily reproduction number would have been reduced to 1 on january 30, 2020, 2 days later than reality ( figure 2d ). in this case, wuhan's bed capacity would have been marginally saturated for 2 days between february 22,2020 and february 23, 2020 ( figure 2c ). however, since the daily reproduction number would have been way below 1 at the time of hospital bed saturation, suppression would still have been achieved. through cross-validation (see model evaluation in methods), it was shown that the timedependent model, which assumed exponentially decreasing transmission rate and isolation delay, had lower prediction error (mean δrmse = -779. 16 , p(δrmse < 0) = 0.758, figure s2b ), compared to the null model that assumed those factors to be constant. in addition, the time-dependent model would make increasingly better predictions than the null model for future time points with accumulating evidence ( figure s2a ). we further estimated the effects of onset timing of control policy on outbreak suppression. the utility of isolating suspected cases was evaluated based on its influence on the npi strength threshold required for successful suppression. the criterion for a successful suppression was to reduce the daily reproduction number to 1 before all beds would have been occupied. as seen in figure 3a , the threshold for successful suppression clearly defined the resulting number of total infections. the number of total infections exhibited a noticeably discontinuous jump around the suppression threshold. while successful suppressions would cause a small percentage (median = 0.46%) of the population to be infected, failed suppressions would lead to much more infections (median = 96.6%). naturally, the further delayed had the implementation of controls been, the harder it would have been to achieve suppression. compared against the alternative strategy of only hospitalizing confirmed cases ( figure 3b ), wuhan's strategy of hospitalizing both confirmed and suspected cases won a margin worth a 1.4% decrease in relative requirement ( figure 3c&e ). nevertheless, fitting results showed that wuhan's npi strength and timing would have been adequate to put the city well above the suppression threshold even without proactive isolation ( figure 3b ). the benefit would have been the largest if actions had been taken as early as possible and would otherwise have been diminished by january 29, 2020, only 6 days later than the actual onset of intervention. should suppression fail, however, the isolation strategy would have had a negative impact on the total number of infected cases. at most an extra 1.2% of the population would have been infected (onset = +6 days, relative = 0.20) given proactive isolation ( figure 3c ). furthermore, increasing hospital bed limit from 4.8 beds (the real number in wuhan) to 8.0 beds per 1,000 population would have provided a further cushion for transmission rate reduction, but such an advantage would also have been diminished if the intervention had been postponed for 9 days ( figure 3d&e ). since most countries did not perform proactive isolations, the model without the isolation cohort was further examined. we manipulated hospital bed capacities estimated from . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . their national averages, and searched for the suited transmission control measures for certain communities. both the duration of healthcare system overload and the final proportion of infected population were the measurements used to evaluate outbreak outcomes. the two measurements showed the same steep jump in value, indicating suppression failure ( figure 4a , b, d&e). this jump was well captured by the suppression threshold derived from the daily reproduction number (the blue curves in respective panels). compared to the hospital capacity in us, the high hospital bed capacity in germany would yield a higher threshold for suppression ( figure 4c , relative ∆β = 0.10). but such an advantage would be greatly reduced if interventions were delayed by a week ( figure 4f , relative ∆β = 0.065). by regressing the threshold-level relative on the log-transformed number of beds per 1,000 population for a range of intervention onsets ( figure 5a ), we found that hospital bed capacity would play the most important role with the intervention onset 2 days later than wuhan. but having an advantage in hospital bed capacity would be less relevant if the onset was further delayed ( figure 5b ). specifically, the relative utility of transmission control in relation to bed capacity would be increased by 64.9% with a 7-day onset delay (slope shifted from 9.50 to 5.76). the duration of hospital overload followed closely the total outbreak duration (+0 onset: in an attempt to evaluate the seriousness of suppression failure, we examined scenarios where relative was at threshold level. a community with germany level of healthcare capacity (8.0 beds per 1,000 population) and acting as promptly as wuhan (0 days onset delay) would have a high relative threshold. but if transmission control requirements were relaxed too much, it would still see 83.3% of the population infected but untreated ( figure 4c , right). to generalize, we simulated such scenarios with 0 to 7 days of onset delay and 2.8 to 8.0 beds per 1,000 population (see figure s3 ). the results suggested that transmission control levels just short of suppression requirement, not only would yield the . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . longest outbreak durations, but also would result in the size of untreated patients amounting to anywhere between 21.9% and 83.7% of total population. our model allowed retrospective analyses and counterfactual reasoning on wuhan's control policies. wuhan's strategy to proactively isolate all suspected cases, effectively removed patients from the infectious pool; otherwise waiting for confirmation would lead to heavier reliance on the laboratory testing capacity and thus leaving more infectious cases in the community. serving as a buffer between the symptomatic cohort and the confirmed cohort, wuhan's strategy bought extra time for the culmination of medical resources in all departments, including extra-provincial medical staff dispatch, test kit production and new hospital construction. our model showed that such a strategy in wuhan was implemented soon enough (6 days until the advantage diminished) to provide a relieved npi strength required for suppression. moreover, proactive isolation in wuhan was also beneficial in reducing peak hospital bed occupancy (from 44,000 to 40,710). as long as the transmission control had been strong enough, such positive outcomes would have been warranted regardless of the timing of npi. however, if control measures had not been sufficiently strong to suppress the outbreak, isolating all suspected cases would have had a negative outcome due to imposing extra stress on the healthcare system. more generally speaking, increasing npi strength and hospital bed capacity both contribute to successfully suppressing the outbreak. however, the trade-off between investing in stronger npi and larger healthcare system capacity depends on how promptly a community responds. as suggested in figure 4 , when the control measures are delayed and the early window is missed, not only does the overall difficulty to suppress become higher, advantages in healthcare system capacity also quickly diminish. delaying intervention renders investing in npi increasingly more efficient than boosting healthcare system capacity ( figure 5b ). failing to suppress would cost countries even with the world's more abundant hospital beds a steep increase in the number of untreated infections. meanwhile, said communities would suffer an extended duration of healthcare system overflow. the "flattening the curve" notion was first illustrated by us centers for disease control and prevention (cdc) 12 and later popularized on social media. it advocates for a level of transmission . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint control that would be enough to lower the peak of patient number by prolonging the outbreak duration and thus preventing healthcare system overflow. however, our simulation proved this strategy to be flawed regarding covid-19 ( figure 4 ). successful suppressions are featured by greatly reduced outbreak size and duration. in contrast, prolonged outbreak durations indicate inadequate transmission control, in which case healthcare system overload is unavoidable ( figure 4c&f ). consequently, the number of untreated infections (and thus the death toll) would outgrow that of the treated by orders of magnitude ( figure 4f ). either consequence would be in violation of the goals behind the "flattening the curve" strategy. a similar conclusion has been drawn 11 the timing for lifting control policies and the potential for a rebound in transmission thereafter were not explicitly investigated in this study. under a given situation of successful suppression where the majority of the population was not infected, herd immunity would have to be established by population-wide vaccination 11, 17 . until an effective vaccine is developed, a partial relaxation of transmission control policies while maintaining suppression would nonetheless be potentially achievable by ensuring a close monitoring of the daily reproduction number. the reason behind it was evident in figure . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint 3&4 where the daily reproduction number at the time of hospital overload proved to be a clear indicator of suppression success. giving up transmission control to achieve herd immunity might be adopted by some communities. such a proposal could turn out even more ineffectual in the wake of the outbreak depending on sars-cov-2 immunity duration. herd immunity achieves reproduction number reduction by removing individuals from the susceptible pool. based on an estimated basic reproduction number of 3.48 by our model, 71% of the population would need to build and sustain immunity for sars-cov-2; otherwise, the reintroduction of the pathogen would cause the disease to circulate again. another issue for herd immunity strategy is the duration of immunity. although conclusions varied, evidence from sars suggested a significant antibody reduction 2 years after infection [18] [19] [20] . in this case, longitudinal studies on this topic for covid-19 would be crucial for designing vaccination strategies. as much as it has been used to describe the intrinsic properties of coivd-19, the basic reproduction number 0 is a function of the transmission rate 0 that depends that the frequency of human contact. an 0 estimated from wuhan is thus most suited to be transferred to a community with a similar level of social interactions. this is especially true when trying to describe the early transmission dynamics when no controls are in place. subsequent description of control policy strength using relative introduces flexibility by accounting for all factors influencing transmission rate. another caveat to the current study is that we neglected the inter-community traffic in the model, rendering the model most fitting to apply on a community on total lockdown. at the city level, discussions have started regarding locking down certain hot spots. at the country level, many have closed their borders to non-citizens. as the number of internationally imported cases grew, china announced that it would follow suit starting on march 28, 2020. partial inter-city traffic reduction only has been estimated to be not effective in preventing inter-community spread 5,21 , thus the impact of travel on epidemic development through increasing both numbers of susceptible and infectious individuals would need to be carefully evaluated for future decision-making when reassessing lockdowns. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint daily data from january 10, 2020 to march 11, 2020 by examining the evolution of the suspected case count on days preceding february 12, 2020, we concluded that the spike on february 12, 2020 was a delayed lump report of cases being cumulatively confirmed since the new criterion was implemented 22 . thus, in order to better represent the historical trend of the testing capacity growth and maintain the cumulative count on february 12, 2020, the newly confirmed cases officially reported on february 12, 2020 were retrospectively assigned to 9 days between february 4, 2020 and february 12, 2020 by assuming a linear increase in daily confirmed cases through clinical diagnosis ( figure s1) a modified seir model was proposed and coded in python. all citizens are assumed to belong to the susceptible cohort ( ) at the beginning of the outbreak. equation (1) asserts the susceptible to be infected by coming into contact with the asymptomatic cohort ( ) as well as the symptomatic cohort ( ) at a time-dependent rate of transmission ( ). the latent cohort was set to be 50% as infectious, according to previous literature 2429 . the . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint asymptomatic cases are converted to the symptomatic, at an average rate of 1/ as seen in equation (2) (7) specifies an exponential decrease in isolation delay starting on january 10, 2020 ( 0 ), while the decrease in testing delay in equation (8) follows the same exponential trend as that in isolation delay, reflecting a synchronization in resources utilized by either process (e.g. medical staff). the constraint of healthcare system capacity, an upper limit of , limits the combine beds occupied by i ( ) and c ( ) in equation (3) and equation (4) . the number of days a patient remains hospitalized until discharged are distributed uniformly amongst a 14-day time span centered at c , shown in equation (5) . the exponential decay of ( ) in equation (6) describes the joint effect of the npi measures from january 23, 2020 ( 1 ) including traffic control, homeisolation, social distancing, disinfection and public use of personal protective equipment etc. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint (2) (3) . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16 the full profile of cumulative confirmed cases in wuhan from january 10, 2020 to march 11, 2020 is used to estimate all free parameters except for c , for these parameters only concern the inflow of infections while c exclusively determines the outflow. a dual simulated annealing procedure is performed with 10,000 iterations using the scipy package 31 in python. subsequently, with the other parameters fixed, c is estimated from the number of currently hospitalized confirmed cases in wuhan using the same dual simulated annealing procedure. all parameters are summarized in table 1 . the time-dependent model is compared to a null model with a constant rate of transmission and a constant rate of isolation/confirmation. a cross validation method is applied to verify the improvement in prediction performance through a bootstrapping procedure described below 32, 33 . data from january 15, 2020 to march 11, 2020, 56 days in total, are involved in the analysis. the first 28 days are regarded as the training set and the later as the test set. the model is trained by the data sampled from the training set, and then tested the data sampled from the test set. in this way, it can avoid the bias due to the testing data immediately follow the training data. to ensure sufficient data for training, the samples of training data vary from 14 to 28, whereas the samples of testing data span 1 to 28. each model was optimized with the training set data. root mean squared error (rmse) in the predictions make by each . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint model were then calculated on the testing set. in total, 120,000 sample pairs were drawn to construct distributions for prediction errors by the two models as well as that for the difference between the two errors. a successful suppression is judged based on the reproduction number. the reproduction number is defined as the average number of new infections each patient generates. when the reproduction number is less than 1, the number of new cases decreases. if the reproduction number is greater than 1, the number of new cases would increase until the susceptible pool runs out 34 . at the beginning of an outbreak when every individual is susceptible, the basic reproduction number 0 can by calculated from equation (12), given that the asymptomatic cases are not infectious. with the current model specifying timedependent parameters and 50% asymptomatic transmissibility, the average time of contact for the symptomatic and asymptomatic cohort is computed respectively in equation (13) and equation (14) . a daily reproduction number is then computed as in equation (17) . whether the average daily production numbers during healthcare system overload is below 1 is the criterion for successful suppression. the strength of npi was quantified as the relative transmission rate calculated from ∞ / 0 . the threshold level of relative was linearly regressed on that of the log-transformed bed per 1,000 population to quantify the relative importance of the two. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the datasets generated during and/or analysed during the current study as well as the code used are available from the corresponding author on reasonable request. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint in figure 3a&b&c , relative increased from 0.0 to 0.5 (step=0.01); lockdown onset increased from -8 to 22 days (step = 1 day, jan. ). the other parameters were kept fixed. in figure 4a&b&d&e , relative increased from 0.0 to 0.5 (step=0.01) and number of beds per 1,000 population increased from 2.0 to 12.0 (step=0.2). lockdown onsets were +0 and +7 respectively. in figure 4c&f , the duration of outbreak was defined as the number of days from jan 10 until the number of confirmed cases went to 0. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint figure s1 . the cumulative confirmed data was adjusted to reflect updated diagnosis criteria. . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint a b . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint . cc-by 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04. 16.20067611 doi: medrxiv preprint who. report of the who-china joint mission on coronavirus disease estimating the potential total number of novel coronavirus cases in wuhan city nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study modified seir and ai prediction of the epidemics trend of covid-19 in china under public health interventions effect of non-pharmaceutical interventions for containing the covid-19 outbreak: an observational and modelling study an updated estimation of the risk of transmission of the novel coronavirus (2019-ncov) a time delay dynamic system with external source for the local outbreak of 2019-ncov impact of non-pharmaceutical interventions (npis) to reduce covid19 mortality and healthcare demand community mitigation guidelines to prevent pandemic influenza -united states clinical characteristics of coronavirus disease 2019 in china clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan, china estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china potential association between covid-19 mortality and health-care resource availability herd immunity": a rough guide duration of antibody responses after severe acute respiratory syndrome longitudinal profiles of immunoglobulin g antibodies against severe acute respiratory syndrome coronavirus components and neutralizing activities in recovered patients lack of peripheral memory b cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak hospital beds and discharge rates. in health at a glance covert coronavirus infections could be seeding new outbreaks a covid-19 transmission within a family cluster by presymptomatic infectors in china a familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period transmission of 2019-ncov infection from an asymptomatic contact in germany presumed asymptomatic carrier transmission of covid-19 estimating the generation interval for covid-19 based on symptom onset data viral dynamics in mild and severe cases of covid-19 scipy 1.0: fundamental algorithms for scientific computing in python consistent cross-validatory model-selection for dependent data: hvblock cross-validation evaluating time series forecasting models: an empirical study on performance estimation methods the mathematical theory of infectious diseases and its applications key: cord-254968-czrgzyr3 authors: zhang, qiang; zhang, huajun; gao, jindong; huang, kun; yang, yong; hui, xianfeng; he, xinglin; li, chengfei; gong, wenxiao; zhang, yufei; zhao, ya; peng, cheng; gao, xiaoxiao; chen, huanchun; zou, zhong; shi, zheng-li; jin, meilin title: a serological survey of sars-cov-2 in cat in wuhan date: 2020-09-17 journal: emerging microbes & infections doi: 10.1080/22221751.2020.1817796 sha: doc_id: 254968 cord_uid: czrgzyr3 covid-19 is a new respiratory illness caused by sars-cov-2, and has constituted a global public health emergency. cat is susceptible to sars-cov-2. however, the prevalence of sars-cov-2 in cats remains largely unknown. here, we investigated the infection of sars-cov-2 in cats during covid-19 outbreak in wuhan by serological detection methods. a cohort of serum samples were collected from cats in wuhan, including 102 sampled after covid-19 outbreak, and 39 prior to the outbreak. fifteen sera collected after the outbreak were positive for the receptor binding domain (rbd) of sars-cov-2 by indirect enzyme linked immunosorbent assay (elisa). among them, 11 had sars-cov-2 neutralizing antibodies with a titer ranging from 1/20 to 1/1080. no serological cross-reactivity was detected between sars-cov-2 and type i or ii feline infectious peritonitis virus (fipv). in addition, we continuously monitored serum antibody dynamics of two positive cats every 10 days over 130 days. their serum antibodies reached the peak at 10 days after first sampling, and declined to the limit of detection within 110 days. our data demonstrated that sars-cov-2 has infected cats in wuhan during the outbreak and described serum antibody dynamics in cats, providing an important reference for clinical treatment and prevention of covid-19. in december, 2019, an outbreak of pneumonia of unknown cause occurred in wuhan, china. the pathogen was soon identified to be the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), and the disease was designated coronavirus disease 2019 (covid-19) by world health organization (who) [1, 2] . the clinical symptoms of covid-19 mainly include asymptomatic infection, mild-tosevere respiratory tract illness, and even death [3] . compared with sars-cov, sars-cov-2 has the higher basic reproduction number, representing more transmissibility [4] . within a very short period of time, covid-19 has quickly become a very serious threat to travel, commerce, and human health worldwide [5] . by 24 july 2020, a total of 15,012,731 confirmed cases, including 619,150 deaths, involving 216 countries, areas, or territories, have been reported globally by who (https://www.who.int/emergencies/ diseases/novel-coronavirus-2019). the outbreak of covid-19 was first confirmed in wuhan, china, possibly associated with a seafood market. however, so far, there is no evidence that the seafood market is the original source of sars-cov-2 [6] . before sars-cov-2, four types of beta coronaviruses can infect humans, including sars-cov and mers-cov which are highly pathogenic and both originated from bats [7, 8] . genome analysis showed that sars-cov-2 has 96.2% overall genome sequence identity with bat cov ratg13, indicating that sars-cov-2 could also originate from bats [9] . the transmission of sars-cov-2 from bats to humans was suspected to via the direct contact between humans and intermediate host animals [6] . although several coronaviruses related to sars-cov-2 were isolated from pangolin, the molecular and phylogenetic analyses showed that sars-cov-2 hardly emerged directly from this pangolin-cov-2020 [10] . at present, it remains largely unknown which animals were the intermediate host of sars-cov-2. our previous study showed that sars-cov-2 uses the same cell entry receptor, angiotensin converting enzyme ii (ace2), as sars-cov [9] , suggesting that sars-cov-2 has the same host range as sars-cov. previous report demonstrated that sars-cov can infect ferrets and cats [11] , implying that they might be also susceptible to sars-cov-2. in fact, the recent reports have shown that sars-cov-2 can indeed infect cats, but not cause any obvious symptoms [12] [13] [14] . cat is one of the most popular pets and often has close contact with humans. thus, the prevalence of sars-cov-2 in cats is very important to investigate, especially in outbreak regions. here, we investigated the serological prevalence of sars-cov-2 in cats by an indirect elisa and virus neutralization tests (vnt), and monitored the serum antibody dynamics of cats infected sars-cov-2, providing a basis for further understanding the infection of sars-cov-2 in cats. a total of 102 cats were sampled in wuhan between jan. and mar. 2020 with three sources: (1) 46 abandoned cats were from 3 animal shelters, (2) 41 cats were from 5 pet hospitals, and (3) 15 cats were from covid-19 patient families. all cats in shelter and hospital were live in relatively close cages. blood samples were collected via leg venipuncture and sera were separated and stored at −20°c until further processing. nasopharyngeal and anal swabs were collected and put into tubes containing viral transport medium-vtm (copan diagnostics, brescia, italy) [15] . all samples were collected under full personal-protective equipment, including head covers, goggles, n95 masks, gloves, and disposable gowns. a set of 39 cat sera were retrieved from the serum bank in our lab, which were collected from wuhan between mar. and may, 2019. hyperimmune sera were obtained from neuropathy pathogen laboratory, huazhong agriculture university, with neutralization titres of 1/640 and 1/1280, respectively, against type i and ii feline infectious peritonitis virus (fipv). the convalescent serum of a covid-19 patient was collected from jiangxia tongji hospital with the consent of the patient and a neutralization titre 1/1280. sars-cov-2 (ivcas 6.7512) was isolated from a covid-19 patient as previously described [9] . vero e6 was purchased from atcc (atcc® crl-1586 ™ ). antibody was tested by indirect elisa with the sars-cov-2 rbd protein (sino biological inc., china) and peroxidase conjugated goat anti-cat igg (sigma-aldrich, usa). briefly, elisa plates were coated overnight at 4°c with rbd protein (1 μg/ml, 100 μl per well). after blocked with pbs containing 5% skim milk for 2 h at 37°c, the plates were added with sera at a dilution of 1: 40. after incubation for 30 min at 37°c, the plates were washed five times with washing buffer (pbs containing 0.05% tween-20). a 1:20,000 diluted anti-cat igg was added and incubated for an additional 30 min. after another 5 washes, tmb substrate (sigma-aldrich, usa) was added and incubated for 10 min. then the reaction was stopped, and optical density (od) was measured at 450 nm. as the judgment method described previously [16, 17] , those sera were considered positive if the od values were twice higher than the mean od of the 39 sera collected between mar. and may, 2019. for virus neutralization test, serum samples were heatinactivated by incubation at 56°c for 30 min. each serum sample was serially diluted with dulbecco's modified eagle medium (dmem) as two fold or three fold according to the od value and the sample quality, mixed with equal volume of diluted virus and incubated at 37°c for 1 h. vero e6 cells in 24-well plates were inoculated with the sera-virus mixture at 37°c; 1 h later, the mixture was replaced with dmem containing 2.5% fbs and 0.8% carboxymethylcellulose. the plates were fixed with 8% paraformaldehyde and stained with 0.5% crystal violet 3 days later. all samples were tested in duplicate and neutralization titres were defined as the serum dilution resulting in a plaque reduction of at least 50% [18] . the total protein concentration of purified and inactivated sars-cov-2 was determined by bradford protein assay [19] . 4 μg protein was subjected to 8% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) and transferred on to nitrocellulose membrane. then viral proteins were blotted with cat sera or human convalescent serum. protein bands were visualized by incubation with a goat anti-cat igg or mouse anti-human igg and then detected using the ecl system (amersham life science, arlington heights, il, usa). cat serum samples were detected with an indirect elisa based on recombinant rbd protein. from the 39 prior-to-outbreak sera, whose optical density (od) varied from 0.091 to -0.261, we set the cut-off as 0.32. the positive samples of 102 cat sera were screened according to this standard. as shown in table 1 and figure 1 , 15 (14.7%) cat sera collected during the outbreak were positive, with five strong positive ones with od more than 0.6. of which, cat#14 and cat#15 were from the same owner who was covid-19 patient. both type i and ii fipv hyperimmune sera showed no cross-reactivity with sars-cov-2 rbd protein. to further confirm the presence of sars-cov-2 specific antibody in cats, all of 15 elisa-positive sera were subjected to vnts for sars-cov-2. among them, 11 (10.8%) had sars-cov-2 neutralizing antibodies with a titre ranging from 1/20 to 1/1080 (table 1 and figure 2(a) ). however, 4 sera including #12, which was elisa strong positive with od of 0.852, showed no neutralizing activity, most likely because of recognition of non-neutralizing epitopes. another elisa strong positive one, #10, had very weak neutralizing activity. but strong neutralization was observed for the other three elisa strong positive sera, namely #4, #14 and #15, with neutralizing titre of 1/360-1/1080. consistent with the high neutralizing titre, the owners of cat#4, cat#14 and cat#15 were diagnosed as covid-19 patients. cat#1, cat#5∼9 was from pet hospitals, while cat#2, cat#10∼13 were initially abandoned cats and kept in animal protection shelters after the outbreak. again, both type i and ii fipv hyperimmune sera were negative for vnt. the sera of infected cats can specifically bind the s and n proteins of sars-cov-2 western blot assay was also performed to further verify the existence of sars-cov-2 specific igg in cat serum. as shown in figure 2 (b), s and n proteins of the purified sars-cov-2 were successfully detected with #4, #14 and #15 sera after diluted 100 folds, as well as human convalescent serum [20] . conversely, the elisa negative cat serum and healthy human serum did not probe the protein bands, thereby demonstrating the existence of sars-cov-2 specific igg in cat serum. fortunately, we had access to two cats, cat#14 and cat#15, for a long time, which gave us the opportunity to track the dynamic of antibody. we continuously sampled cat#14 and cat#15 every 10 days over 130 days. as shown in figure 3 (a), rbd antibodies of these two cats reached the peak at the second sampling, when both showed od>1.0 for elisa. after that, rbd antibodies turned down and decreased to detection limit in 110 days. accordingly, neutralizing antibodies showed similar trend (figure 3(b) ). in this study, we detected the presence of sars-cov-2 antibodies in cats in wuhan during the covid-19 outbreak with elisa, vnt and western blot. a total of 102 cats were tested, 15 (14.7%) were positive for rbd based elisa and 11 (10.8%) were further positive with vnt. these results demonstrated that sars-cov-2 has infected cats in wuhan, implying that this risk could also occur at other outbreak regions. in fact, it has been indeed successively reported that sars-cov-2 infected cats under natural conditions [14, 21] . retrospective investigation confirmed that all figure 2 . virus neutralization test and western blot assay of cat serum samples for sars-cov-2 (a) cat#14, cat#15 and cat#4 sera were 3-fold serially diluted and mixed with sars-cov-2; after incubated at 37°c for 1 h, the mixture was used to infect vero e6 cells, and replaced with semi-solid media 1 h later. the plates were fixed and stained 3 days later. all samples were tested in duplicate. (b) western blot of purified sars-cov-2 with cat or human sera. all sera were diluted 100 folds. c-n, negative cat serum. h-p, human convalescent serum. h-n, healthy human serum. of elisa positive sera were sampled after the outbreak, suggesting that the infection of cats could be due to the virus transmission from humans to cats. certainly, it is still needed to be verified via investigating the sars-cov-2 infections before this outbreak in a wide range of sampling. at present, there is no evidence of sars-cov-2 transmission from cats to humans. however, a latest report shows that sars-cov-2 can transmit between cats via respiratory droplets [12] . over all, some preventive measures are necessary for blocking the human-to-cat transmission or preventing the potential transmission risk of cats to other animals or humans. through analysing the background of the tested cats, we found that 4 of abandoned cats (9.8%), 4 of cats from pet hospitals (8.7%), and 3 of cats with patient owners (20%) were positive with vnt. although the positive rate among different source cats had no significant differences, the three cats with the highest neutralization titres (1/1080, 1/360, and 1/360, respectively) were owned by covid-19 patients. on the contrary, the sera collected from pet hospital cats and stray cats had neutralizing activity of 1/20-1/80, indicating that the high neutralization titres could be due to the close contact between cats and covid-19 patients. in addition, our data demonstrated that the duration of neutralizing antibody against sars-cov-2 is relatively transient in the infected cats. so, the low neutralization titres could also be due to the long-time interval between sample collection and actual infection date. although the infection in stray cats was not fully understood, it is reasonable to speculate that these infections are probably due to the contact with sars-cov-2 polluted environment, or covid-19 patients who fed the cats. the antibody-mediated humoral response is crucial for preventing viral infections, of which the neutralizing antibody can reduce the entry of the virus into an infected cell via blocking the interaction between virus and cell [22] . so, the neutralizing antibody is an important indicator that can reflect the host antiviral ability. although numerous reports have indicated that the infection of sars-cov-2 can induce the production of neutralizing antibody, the understanding about the dynamics of sars-cov-2 neutralizing antibody remains largely unknown. here, we continuously monitored the dynamics of binding antibody and neutralizing antibody against sars-cov-2 in the infected cats. we found that both these two antibodies can be induced with a relatively high level, however the duration of peak titre was very short, and decreased to the limit of detection within 110 days. it was worth noting that, these two cats were from the same owner who presented with fever and cough in mid-february, and was diagnosed and segregated as covid-19 patient on february 21. then these two cats were fostered in pet hospital and were also segregated. combined with the dynamic characteristic and timeline of antibody response, we speculated that these two cats should be infected at the same time. in addition, considering that the two cats were constantly in segregation, we believed that our data represented the antibody dynamic characteristic of primary infection. importantly, this transient antibody response induced by sars-cov-2 resembles those observed in seasonal coronavirus infections, implying that the convalescent cats after sars-cov-2 infection remain the risk of re-infection. in fact, this similar transient antibody response has also been observed in human antibody [23, 24] , suggesting that cat has a great potential as an animal model for assessing the characteristic of antibody against sars-cov-2 in human. our data provided a very important reference for the clinical treatment and prevention of covid-19. in addition, we also collected nasopharyngeal and anal swabs of each cat, and conducted sars-cov-2 specific qrt-pcr using a commercial kit which targeted orf1ab and n genes. seven samples from five cats were n gene single positive with ct ranging from 34.9 to 36.7, but no double gene positive sample was detected (according to the manufacture instruction in which ct value less than 37 was deemed as positive). the reason might be (1) that the viral rna load is too low to be detected; (2) the period that cat shed sars-cov-2 may be very short [21] , along with asymptomatic infection, we didn't catch the moment of acute infection; (3) there may be variants in the genomic sequences in cats, leading to the failure in amplification in cat samples. in conclusion, our study provided serological evidence for sars-cov-2 infection in pets, and described the dynamic characteristic of serum antibody in cats. further research is needed to investigate the transmission route of sars-cov-2 from 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coronavirus spike proteins and host ace2 receptors predict potential intermediate hosts of sars-cov-2 a pneumonia outbreak associated with a new coronavirus of probable bat origin are pangolins the intermediate host of the 2019 novel coronavirus (sars-cov-2)? virology: sars virus infection of cats and ferrets susceptibility of ferrets, cats, dogs, and other domesticated animals to sarscoronavirus 2 transmission of sars-cov-2 in domestic cats severe acute respiratory syndrome coronavirus 2-specific antibodies in pets in wuhan middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation detection of antibodies against dna polymerase of hepatitis b virus in hbsag-positive sera using elisa development of a novel rapid micro-neutralization elisa for the detection of neutralizing antibodies against chandipura virus vaccinia virus h3l envelope protein is a major target of neutralizing antibodies in humans and elicits protection against lethal challenge in mice inactivation efficacy of nonthermal plasma-activated solutions against newcastle disease virus effectiveness of convalescent plasma therapy in severe covid-19 patients first detection and genome sequencing of sars-cov-2 in an infected cat in france perspectives on therapeutic neutralizing antibodies against the novel coronavirus sars-cov-2 the production of antibodies for sars-cov-2 and its clinical implication longitudinal evaluation and decline of antibody responses in sars-cov-2 infection we acknowledge jiangxia tongji hospital for providing the convalescent serum of covid-19 patient. we thank professor guiqing peng (huazhong agriculture university) for providing the hyperimmune sera against type i and ii fipv. we are particularly grateful to wuhan national biosafety laboratory running team, including engineer, biosafety, biosecurity, and administrative staff. no potential conflict of interest was reported by the author(s). key: cord-347204-cafr7f38 authors: yuan, zheming; xiao, yi; dai, zhijun; huang, jianjun; zhang, zhenhai; chen, yuan title: modelling the effects of wuhan’s lockdown during covid-19, china date: 2020-07-01 journal: bull world health organ doi: 10.2471/blt.20.254045 sha: doc_id: 347204 cord_uid: cafr7f38 objective: to design a simple model to assess the effectiveness of measures to prevent the spread of coronavirus disease 2019 (covid-19) to different regions of mainland china. methods: we extracted data on population movements from an internet company data set and the numbers of confirmed cases of covid-19 from government sources. on 23 january 2020 all travel in and out of the city of wuhan was prohibited to control the spread of the disease. we modelled two key factors affecting the cumulative number of covid-19 cases in regions outside wuhan by 1 march 2020: (i) the total the number of people leaving wuhan during 20–26 january 2020; and (ii) the number of seed cases from wuhan before 19 january 2020, represented by the cumulative number of confirmed cases on 29 january 2020. we constructed a regression model to predict the cumulative number of cases in non-wuhan regions in three assumed epidemic control scenarios. findings: delaying the start date of control measures by only 3 days would have increased the estimated 30 699 confirmed cases of covid-19 by 1 march 2020 in regions outside wuhan by 34.6% (to 41 330 people). advancing controls by 3 days would reduce infections by 30.8% (to 21 235 people) with basic control measures or 48.6% (to 15 796 people) with strict control measures. based on standard residual values from the model, we were able to rank regions which were most effective in controlling the epidemic. conclusion: the control measures in wuhan combined with nationwide traffic restrictions and self-isolation reduced the ongoing spread of covid-19 across china. coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2), was first identified in december 2019 in wuhan, the capital city of hubei province of china. 1 on 30 january 2020 the world health organization declared the covid-19 epidemic a public health emergency of international concern. by 1 march 2020, the overall number of people confirmed with covid-19 in china had reached 80 174 and a total of 2915 people had died of the disease. 2 current knowledge about sars-cov-2 is that the virus has diverse routes of transmission and there are also now reports of virus transmission from asymptomatic individuals. 3, 4 early estimates of the basic reproductive number (r 0 ) of covid-19 were 2.2 (95% ci: 1.4 to 3.9), 5 2.68 (95% ci: 2.47 to 2.86), 6 3.6 to 4.0, 7 and 3.77 (range 2.23 to 4.82). 8 a later estimate of r 0 was 6.47 (95% ci: 5.71 to 7.23). 9 these values showed that sars-cov-2 is highly contagious and it was projected that without any control measures the infected population would exceed 200 000 in wuhan by the end of february 2020. 10 other researchers estimated infected numbers of 191 529 (95% ci: 132 751 to 273 649) by 4 february 2020. 11 in the absence of an effective vaccine, 12 social distancing measures were needed to prevent transmission of the virus. 13, 14 the chinese government therefore implemented a series of large-scale interventions to control the epidemic. the strictest control measures were applied in wuhan with a complete lockdown of the population. starting at 10 a.m. on 23 january 2020, wuhan city officials prohibited all transport in and out of the city of 9 million residents. within the rest of china, the interventions included nationwide traffic restrictions in the form of increased checkpoints at road junctions to reduce the number of people travelling and self-isolation of the popula-tion at home to reduce outside activities. hundreds of millions of chinese residents had to reduce or stop their inter-city travel and intra-city activities due to these measures. 15 following the interventions in wuhan, estimates show that the median daily r 0 value of covid-19 declined from 2.35 on 16 january 2020 to 1.05 by 30 january 2020 16 and the spread of infection to other cities was deferred by 2.91 days (95% confidence interval, ci: 2.54 to 3.29). 15 however, other researchers have suggested that travel restrictions from and to wuhan city are unlikely to have been effective in halting transmission across china. despite an estimated 99% reduction in the number of people travelling from wuhan to other areas (663 713 out of 670 417 people), the number of infected people in non-wuhan areas may only have been reduced by 24 .9% (1016 out of 4083 people) by 4 february 2020. 11 these large-scale public health interventions have caused significant disruption to the economic structure in china and globally. 14, 17 questions remain whether these interventions are necessary or really worked well in china and how to assess the performance of public health authorities in different regions in mainland china in controlling the epidemic. we present a simple model based on online data on population movements and confirmed numbers of people infected to quantify the consequences of the control measures in wuhan on the ongoing spread of covid-19 across mainland china. we also aimed to make a preliminary assessment of the efforts of the public health authorities in 29 provinces and 44 prefecture-level cities during the epidemic. the chinese transport commission does not release detailed data on population movements between cities. we therefore used data from baidu migration (baidu inc., beijing, china), a largescale data set based on an application that tracks the movements of mobile phone users and publishes the data in real time. 18 we extracted data on interand intra-city population movements from 1 january 2020 to 29 february 2020 in mainland china, including data for the same period in 2019 from 12 january to 12 march (based on the lunar calendar). the baidu platform represents the inter-city travel population of each city by the immigration and emigration indices. the intensity of intra-city population movements in each city is the ratio of the number of people travelling within a city to the number of residents in the city. to determine the number of people represented by the migration index per unit, we used data on population movements during the 2019 spring festival travel rush in china (over 40 days from 21 january 2019 to 1 march 2019). we extracted the actual number of people entering and leaving beijing and shanghai cities, and the number of people leaving foshan, nanjing, qingdao, shenzhen and wuhan cities from the official website of the local municipal transport commissions. [19] [20] [21] [22] [23] [24] [25] we constructed a simple regression equation with a constant term of 0, with the y coordinates representing the number of travellers and x coordinates representing the baidu migration index. we estimated that each unit of the baidu migration index was about equivalent to 56 137 travellers (fig. 1 data sources: we obtained the migration index from the baidu migration website 18 and the number of travellers from the websites of the municipal transportation commissions. [19] [20] [21] [22] [23] [24] [25] notes: the annual 40-day spring festival travel rush dates were 21 january to 1 march 2019. the municipal commissions of transport in beijing and shanghai released the numbers of people leaving and entering the cities, but other cities only released the number of people leaving. the migration index is the ratio of the number of people travelling within a city to the number of residents in the city. we obtained data on the number of people with confirmed (clinically defined) covid-19 in each province and prefecture-level city from the national health commission of china and its affiliates. 2 we used the cumulative number of confirmed cases of covid-19 on 1 march 2020 as the final values, because after that there were few locally confirmed cases in china except in wuhan. in addition, on 5 february 2020 the chinese national health committee issued its protocol for the diagnosis and treatment of pneumonia with novel coronavirus infections (5th trial version), 26 and counted clinically diagnosed cases as confirmed cases in hubei province. more than 10 000 additional confirmed cases were therefore added to the total in hubei province on 12 january 2020. our model needed to consider factors affecting the final cumulative numbers of confirmed cases in areas outside wuhan. we analysed data from 44 regions in mainland china, which accepted travellers from wuhan city, including 15 prefecture-level cities in hubei province and 29 other provinces in mainland china (tibet was excluded since only one confirmed case was reported). the data are available in supplementary data 1 in the data repository for this article. 27 we noticed that the number of confirmed cases of covid-19 in cities within hubei province and in other provinces outside hubei were closer in the early period of the epidemic (supplementary data 2 in the data repository). 27 for example, the cumulative number of confirmed cases by the end of 26 january 2020 in chongqing municipality and xiaogan city (hubei province) were 110 and 100, respectively. however, the cumulative number of confirmed cases in chongqing and xiaogan by the end of 27 february were 576 and 3517, respectively. we surmise that this was partly because xiaogan city had received more cases of infection from wuhan than from chongqing after the risk of human-to-human transmission of covid-19 was confirmed and announced on 20 january 2020. this surmise was confirmed by fig. 2 (see also supplementary data 3 in the data repository). 27 the proportion of travelnotes: actual scenario was the intervention in wuhan city. basic control was few people leaving wuhan; strict controls was nobody allowed to leave wuhan. i n refers to the actual total number of people travelling out of wuhan on the nth day of january 2020. lers from wuhan city to other cities in hubei province compared to the total travellers from wuhan increased rapidly from 70% (288 000 of 414 000 people) before 19 january 2020 to 74% (390 000 of 526 000 people) on 20 january 2020, and over 77% (28 000 of 37 000 people) after 26 january 2020. we therefore concluded that the first key factor (x 1 ) affecting the final cumulative number of confirmed cases in cities outside wuhan on 1 march 2020 was the sum of people travelling out of wuhan during 20-26 january 2020 (there were few population movements after 27 january 2020 because of the control measures). these people had a higher probability of being infected but lower transmission ability because of the epidemic control measures. the second key factor was the sum of the number of infected people travelling from wuhan city to other areas before 19 january 2020. according to later reports, there is a mean 10-day delay between infection and detection of infection, comprising a mean incubation period of about 5 days and a mean delay of 5 days from symptom onset to detection of a case. 5, 7, 8 so the second key factor (x 2 ) can be represented by the cumulative number of confirmed cases at the end of 29 january 2020. these seed cases had higher transmission ability because no protection measures were yet in place for susceptible people. we constructed a binary regression model based on these two key factors and used a standardized regression coefficient (coeff) to evaluate the importance of the independent variables x 1 and x 2 : where y is the number of cumulative confirmed cases by 1 march 2020, x 1 is the sum number of people leaving wuhan during 20 -26 january 2020, x 2 is the number of cumulative confirmed cases by 29 january 2020, where y is the dependent variable, x j is the jth independent variable, b j is the regression coefficient of x j . s xj is the standard deviation of x j and the s y is the standard deviation of y. to evaluate the effect of the lockdown in wuhan, we assumed that the number of cumulative confirmed cases by 29 january 2020 (x 2 ) was fixed, and we revised the sum of travellers from the city during 20-26 january 2020 (x 1 ) up or down according to the strength of interventions applied. the baseline intervention was lockdown on 23 january 2020. we defined two levels of travel control measures: basic (few people leaving wuhan) and strict (nobody allowed to leave wuhan). we then modelled three alterative scenarios: (i) lockdown starting 3 days earlier (on 20 january) with basic controls; (ii) lockdown starting 3 days earlier (on 20 january) with strict controls; and (iii) lockdown starting 3 days later (on 26 january) with basic controls ( table 1) . the final cumulative number of confirmed cases for the three alterative scenarios are predicted by the binary regression model (equation 1). as shown in table 1 we used the predicted final cumulative confirmed cases by this model to assess regional efforts to control the spread of covid-19. when the predicted value is greater than the true value, it indicates that the region has a better prevention and control effect; when it is lower than the true value it means that the prevention and control effect is poor. we calculated the standard residual (sr) for each region as the quantitative evaluation index for this comparison as follows: (2) where y i is the true final cumulative number of confirmed cases in region i, ŷ i is the predicted number of confirmed cases in region i, s e is the standard devia-tion of the residuals. based on the value of the standard residual, we classified regions arbitrarily by five grades of effectiveness of interventions (excellent: sr < −1.0; good: sr −1.0 to −0.5; neutral: sr −0.5 to 0.5; poor: sr 0.5 to 1.0; very poor: sr > 1.0). we constructed all the regression models using the regress function of matlab software, version r2016a (mathworks, natick, united states of america). more than 9 million residents were isolated in wuhan city after the epidemic control measures started on 23 january 2020. according to data from baidu migration, only 1. 27 in response to the government's call to reduce travel, the mean intensity of intra-city population movements for 316 cities in mainland china was only 2.61 per day during 24 january 2020 to 15 february 2020 according to data from baidu migration. population activity was greatly reduced compared with the same period in 2019 (4.53 per day) and the first 23 days of january 2020 (5.25 per day), respectively ( fig. 5 ; supplementary data 3 in the data repository). 27 we constructed the following simple regression model to explain the final cumulative number of confirmed cases (y) in regions other than wuhan: where x 1 is the sum of the number of people travelling out of wuhan during 20-26 january 2020 and x 2 is the cumulative number of confirmed cases by 29 january 2020 for 15 prefecture-level cities in hubei province and 29 other provincial regions (supplementary data 1 in the data repository). 27 the standard regression coefficients calculated from equation 1 of x 1 and x 2 were 0.657 and 0.380 respectively, indicating that x 1 is more important than x 2 for determining the final cumulative number of confirmed cases. the true and fitted values of the cumulative confirmed cases by 1 march 2020 in the 44 non-wuhan regions are shown in fig. 6 . based on the interpretative model (equation 3), we predicted the final cumulative confirmed cases of the 44 non-wuhan regions for the three modelled intervention plans. the results are shown in supplementary data 1 in the data respository. 27 even starting lockdown with only 3-days delay, the estimated total cumulative number of confirmed cases of covid-19 by 1 march 2020 in non-wuhan regions was 41 330, an increase of 34.6% compared with the actual numbers (30 699 cases). in contrast, even with lockdown starting 3 days earlier we estimated 21 235 and 15 796 people infected under basic and strict controls, respectively: 30.8% and 48.6% reductions, respectively, compared with the actual intervention. when predicting confirmed cases of covid-19 in wuhan, x 1 is the number of residents in the city. there were around 9 480 000 residents in wuhan around 26 january 2020 according to a press release from the wuhan government. the cumulative number of confirmed cases of covid-19 (x 2 ) were 2261 by 29 january 2020. based on equation 3, we therefore predicted that at least 56 572 people in wuhan were infected (70.3535 + (0.0054 × 9 480 000) + (2.3484 × 2261)). the true and predicted final cumulative numbers of confirmed cases of covid-19 in 29 provincial regions and 44 prefecture-level cities outside hubei based on the interpretative model are listed in table 2 and table 3 . more details of the data are available in supplementary data 1 in the data repository. 27 based on the values of the standard residual, we graded guizhou, henan and hunan provinces as having an excellent level of effectiveness against the spread of covid-19 (sr: −2.06, −1.85 and −1.13, respectively), whereas heilongjitable 3 ). we and, so far, our estimate is closer than other estimates to the official report of 50 333 confirmed cases. 29 many of the virus transmission control measures taken by china went beyond the requirements of the international health regulations for responding to emergencies, 30 setting new benchmarks for epidemic prevention in other countries. we found that the lockdown in wuhan combined with nationwide traffic restrictions and self-isolation measures reduced the ongoing spread of covid-19 across mainland china. as shown in fig. 7 , data from baidu migration showed that the number of newly diagnosed cases of covid-19 just in wuhan city far exceeded the total number of cases in non-wuhan regions of mainland china because of the early lack of attention to the epidemic. our method enabled us to assess the efforts of public health authorities in different regions of mainland china during the early stage of the epidemic. we found that the authorities of guizhou, henan and hunan provinces did the best job of prevention and control of the epidemic, whereas heilongjiang, guangdong, shandong, sichuan and jiangxi provinces performed relatively poorly compared with other provinces. the four cities of huanggang, xianning, enshi and jingmen performed well and ezhou, suizhou, xiaogan and yichang cities performed relatively poorly. our model was able to assess the impact of the lockdown in wuhan city on the epidemic in mainland china, and it confirmed that preventing the movement of people in and out of an area was an important measure to contain the epidemic. however, the baidu migration index does not fully accurately represent the real number of migration, so there may be errors in model estimation, and our model is not applicable to other regions and countries to assess the ongoing efforts of public health authorities in controlling disease transmission. as of may 2020, the epidemic of sars-cov-2 was still growing rapidly worldwide. we believe that the international community can learn from the strict interventions applied in wuhan and the experience from china. ■ objetivo diseñar un modelo sencillo para evaluar la efectividad de las medidas que se adoptaron para prevenir la propagación de la enfermedad causada por el coronavirus 2019 (covid-19) en diferentes regiones de china continental. métodos se obtuvieron datos sobre los movimientos de la población a partir de un conjunto de datos de una empresa de internet y el número de casos confirmados de la covid-19 a partir de fuentes gubernamentales. el 23 de enero de 2020 se prohibieron todos los viajes de entrada y salida de la ciudad de wuhan para controlar la propagación de la enfermedad. se modelaron dos factores clave que afectan al número acumulado de casos de la covid-19 en las regiones fuera de wuhan para el 1 de marzo de 2020: (i) el número total de personas que salieron de wuhan entre el 20 y el 26 de enero de 2020; y (ii) el número de casos iniciales de wuhan antes del 19 de enero de 2020, que representa el número acumulado de los casos que se confirmaron el 29 de enero de 2020. se elaboró un modelo de regresión para predecir el número acumulado de casos en las regiones fuera de wuhan mediante tres escenarios hipotéticos de control de la epidemia. resultados si se hubiera retrasado la fecha de inicio de las medidas de control por solo tres días, los 30 699 casos confirmados de la covid-19 que se estimaban para el 1 de marzo de 2020 en las regiones fuera de wuhan habrían aumentado en un 34,6 % (a 41 330 personas). si los controles se hubieran adelantado tres días, se habrían reducido las infecciones en un 30,8 % (a 21 235 personas) con medidas de control básicas o en un 48,6 % (a 15 796 personas) con medidas de control estrictas. por lo tanto, se pudo clasificar las regiones más efectivas en el control de la epidemia según los valores residuales estándar del modelo. conclusión las medidas de control en wuhan, junto con las restricciones de tráfico en todo el país y el autoaislamiento, redujeron la propagación actual de la covid-19 en toda china. clinical features of patients infected with 2019 novel coronavirus in wuhan new coronavirus pneumonia diagnosis and treatment plan (trial version 6) transmission and epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infected pneumonia (covid-19): preliminarily evidence obtained in comparison with 2003-sars the novel coronavirus, 2019-ncov, is highly contagious and more infectious than initially estimated early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study report 1: estimating the potential total number of novel coronavirus cases in wuhan city, china epidemiological and clinical features of the 2019 novel coronavirus outbreak in china covid-19 epidemic control measures, mainland china zheming yuan et al estimation of the transmission risk of the 2019-ncov and its implication for public health interventions phase adjusted estimation of the number of 2019 novel coronavirus cases in wuhan, china novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions optimal covid-19 epidemic control until vaccine deployment smallpox and bioterrorism how will country-based mitigation measures influence the course of the covid-19 epidemic? lancet early evaluation of transmission control measures in response to the 2019 novel coronavirus outbreak in china centre for mathematical modelling of infectious diseases covid-19 working group. early dynamics of transmission and control of covid-19: a mathematical modelling study modified seir and ai prediction of the epidemics trend of covid-19 in china under public health interventions beijing held the 2020 spring festival mobilization meeting beijing municipal commission of transport shanghai spring festival wraps up successfully shanghai municipal commission of transport spring festival has come to a safe end! foshan region sent 21.0348 million passengers the 2019 spring festival in nanjing have send 11.673 million passengers qingdao's 2019 spring festival comes to a successful conclusion shenzhen: shenzhen municipal commission of transport 40 days, 14.68 million people! what makes them so persistent? wuhan municipal commission of transport beijing ; national health commission supplementary webappendix: a simple model to assess wuhan lockdown effect and region efforts during covid-19 epidemic in mainland china epidemic size of novel coronavirus-infected pneumonia in the epicenter wuhan: using data of five-countries' evacuation action beijing : baidu; 2020 geneva: world health organization zy competing interests: none declared. key: cord-340369-y8o5j2be authors: zhang, juanjuan; litvinova, maria; liang, yuxia; wang, yan; wang, wei; zhao, shanlu; wu, qianhui; merler, stefano; viboud, cecile; vespignani, alessandro; ajelli, marco; yu, hongjie title: age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in china date: 2020-03-20 journal: medrxiv : the preprint server for health sciences doi: 10.1101/2020.03.19.20039107 sha: doc_id: 340369 cord_uid: y8o5j2be strict interventions were successful to control the novel coronavirus (covid-19) outbreak in china. as transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection and disease, and covid-19 dynamics remains unclear. to answer these questions, we analyze contact surveys data for wuhan and shanghai before and during the outbreak and contact tracing information from hunan province. daily contacts were reduced 7-9 fold during the covid-19 social distancing period, with most interactions restricted to the household. children 0-14 years were 59% (95% ci 7-82%) less susceptible than individuals 65 years and over. a transmission model calibrated against these data indicates that social distancing alone, as implemented in china during the outbreak, is sufficient to control covid-19. while proactive school closures cannot interrupt transmission on their own, they reduce peak incidence by half and delay the epidemic. these findings can help guide global intervention policies. also estimate age differences in susceptibility to infection and clinical disease based on contact tracing information gathered by the hunan provincial center for disease control and prevention (cdc), china. based on those findings, we develop a mathematical transmission model to disentangle how transmission is affected by age differences in the biology of covid-19 infection and disease, and altered mixing patterns due to social distancing. in turn, we project the impact of social distancing and school closure on covid-19 transmission. to estimate changes in age-mixing patterns associated with covid-19 interventions, we performed contact surveys in two cities, wuhan, the epicenter of the outbreak, and shanghai, one of the largest and most densely populated cities in southeast china. shanghai experienced extensive importation of covid-19 cases from wuhan as well as local transmission (3) . the surveys were conducted from february 1, 2020 to february 10, 2020, as transmission of covid-19 peaked across china and stringent interventions were in place. participants in wuhan were asked to complete a questionnaire describing their contact behavior (4, 5) on two different days: i) a regular weekday between december 24, 2020 and december 30, 2020, before the covid-19 outbreak was officially recognized by the wuhan municipal health commission (used as baseline); and ii) the day before the interview (outbreak period). a similar survey was conducted in shanghai to obtain information on contacts during the covid-19 outbreak period; contacts for the baseline period were based on a survey using the same design conducted in the same city in 2017-2018 (6) . details are given in the supplementary material. we analyzed a total of 1,245 contacts reported by 636 study participants in wuhan, and 1,296 contacts reported by 557 participants in shanghai. in wuhan, the average daily number of contacts per participant was significantly reduced from 14.6 for a regular weekday (weighted mean contacts by age structure: 14.0) to 2.0 for the outbreak period (weighted mean contacts by age structure: 1.9) (p<0.001). the reduction in contacts was significant for all stratifications by sex, age group, type of profession, and household size, except for pre-school children aged 0-6 years old (tab. 1). a larger reduction was observed in shanghai, where the average daily number of contacts declined from 20.6 (weighted mean contacts by age structure: 21.7) to 2.3 (weighted mean contacts by age structure: 2.1). although an average individual in shanghai reported more contacts than one in wuhan on a regular weekday, this difference disappeared during the covid-19 outbreak period. the typical features of age-mixing patterns(5, 6) emerge in wuhan and shanghai when we consider the regular baseline weekday period ( fig. 1a and 1d ). these features can be illustrated in the form of age-stratified contact matrices (provided as ready-to-use tables in the supplementary materials), where each cell represents the average number of contacts that an individual has with other individuals, stratified by age groups. the bottom left corner of the matrix, corresponding to contacts between school age children, is where the largest number of contacts is recorded. the contribution of contacts in the workplace is visible in the central part of the matrix, while the three diagonals (from bottom left to top right) represent contacts between household members. in contrast, for the outbreak period where strict social distancing was in place, much of the above-mentioned features disappears, essentially leaving the sole contribution of household mixing ( fig. 1b and 1e ). in particular, contacts between school-age individuals are fully removed, as highlighted by differencing baseline and outbreak matrices ( fig. 1c and 1f ). overall, contacts during the outbreak mostly occurred at home with household members (94.1% in wuhan and 78.5% in shanghai), thus the outbreak contact matrix nearly coincides with the within-household contact matrix in both study sites and the assortativity by age feature observed for regular days almost entirely disappear (see supplementary materials). all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 20, 2020. . to understand the interplay between social distancing interventions, changes in human mixing patterns, and outbreak dynamics, we also need to consider potential age differences in susceptibility to infection. this is currently a topic of debate, as little information on the age profile of asymptomatic cases is available (7, 8) . to this aim, we analyzed contact tracing information from detailed epidemiological field investigations conducted by the hunan cdc (supplement). we calculated the age-specific relative risk of infection for close contacts of confirmed covid-19 index cases. briefly, all close contacts of covid-19 cases reported in hunan province were placed under medical observation for 14 days and were tested using real-time rt-pcr. those who developed symptoms and tested positive were considered as symptomatic confirmed cases, while contacts who tested positive without exhibiting symptoms were considered as asymptomatic infections. the total of symptomatic and asymptomatic infections was used to estimate the relative susceptibility to infection by age. the ratio of symptomatic cases to total infections was used to estimate the relative probability of developing symptoms (see supplementary material). we found age differences in susceptibility to sars-cov2 infection, where young individuals (aged 0-14 years) had a lower risk of infection than individual ages 65 years and over (or=0.41 (95%ci: 0.18-0.93), p-value=0.026). there was a weak non-significant trend towards lower susceptibility in middle-aged adults, relative to seniors (or=0.76, 95%ci: 0.46-1.24, tab. 2). these findings are in contrast with a previous study in shenzhen, where susceptibility to infection did not change with age (7). moreover, we found that the relative probability of developing symptoms also increased with age, however the difference was not statistically significant (tab. 2). based on the estimated age-specific mixing patterns and susceptibility to covid-19 infection, we developed a sir model of sars-cov-2 transmission and tested the impact of social distancing measures on disease dynamics. in the model, the population is divided into three epidemiological categories: susceptible, infectious, and removed (either recovered or deceased individuals), stratified by 14 age groups. susceptible individuals can become infectious after contact with an infectious individual according to the estimated age-specific susceptibility to infection. because we did not see age differences in the probability of developing symptoms upon infection, we assumed equal infectivity across all age groups. the rate at which contacts occur is determined by the estimated mixing patterns in each age group. a key parameter regulating the dynamics of the model is the basic reproduction number (r0), which corresponds to the average number of secondary cases generated by a primary case in a fully susceptible population. the mean time interval between two consecutive generations of cases was taken to be 5.1 days (2) . details are reported in the supplementary materials. for baseline r0 values in the range 2.0-3.5 associated with a regular weekday contact patterns (corresponding to the early phase of covid-19 spread in wuhan (9-15)), we find that the profound alteration of mixing patterns of the magnitude observed in wuhan and shanghai leads to a drastic decrease in r0. when we consider contact matrices representing the outbreak period, keeping the same baseline disease transmissibility as the pre-intervention period, the reproductive number drops well below the epidemic threshold both in wuhan and shanghai ( fig. 2a) . in an uncontrolled epidemic (without intervention measure, travel restriction, or spontaneous behavioral response of the population), we estimate the mean infection attack rate to be in the range 64%-92% after a year of sars-cov-2 circulation, with slight variation between wuhan and shanghai (variations of about 5%-12%, fig. 2b ). on the other hand, if we consider a scenario where social distancing measures are implemented early on, as the new virus emerges, the estimated r0 remains under the threshold and thus the epidemic cannot take off in either location. furthermore, we estimate that the magnitude of interventions implemented in wuhan and shanghai would have been enough to bring the reproduction number below 1.0 for baseline r0 up to ~7 in wuhan and ~11.5 in shanghai (fig. 2a) . we also conduct sensitivity analyses on assumptions about the susceptibility profile of infections, since there is still uncertainty about this parameter (see supplementary material). our conclusions are robust to assuming equal susceptibility in all age groups. finally, armed with a carefully calibrated model, we turn to assess the impact of a preemptive mass school closure. we used the same estimates of relative susceptibility to infection by age as in our main analysis (see supplementary material for a sensitivity analysis assuming equal susceptibility to infection). we considered two different contact pattern scenarios, based on data from shanghai: contacts estimated during vacations period (6) and contacts estimated during regular weekdays, after all contacts occurring in school settings have been removed (6) . either one of these scenarios represent a simplification of a school closure strategy as during vacations children can still attend additional education, while removing all contacts in the school setting does not take into account that, for instance, parents may need to leave work to take care of children. we estimated that limiting contact patterns to those observed during vacations would interrupt transmission for baseline r0 up to 1.5 (fig. 2c) . removing all school contacts would do the same for baseline r0 up to 1.2. if we apply these interventions to a covid-19 scenario, assuming a baseline r0 of 2 -3.5, we can achieve a noticeable decrease in infection attack rate and peak incidence, and a delay in the epidemic, but transmission is not interrupted (fig. 2d ). for instance, for baseline r0=2.5 and assuming a vacation mixing pattern, the peak daily incidence is reduced by about 57%. in the corresponding scenario where school contacts are removed, we estimate a reduction of about 20%. overall, school-based policies are not sufficient to entirely prevent a covid-19 outbreak but they can have a significant impact on disease dynamics, and hence on hospital surge capacity. this study suffers from several limitations. first, the estimated mixing patterns for a regular weekday in wuhan may be affected by recall bias since contacts were assessed retrospectively. for shanghai, we relied on a survey conducted in december 2017 -may 2018, using the same design as the one conducted during the outbreak period, thus avoiding recall bias. it is also important to note that changes in contact patterns were measured in a context where social distancing was applied together with rapid isolation of infected individuals (including suspected cases) and quarantine of close contacts for 14 days. only a small portion of the population in the two study sites was affected by contact tracing and quarantine, thus having little to no effect on the average contact patterns of the general population. however, in reconstructing the observed epidemics in wuhan and shanghai, it is not possible to separate the effects of case-based strategies from population wide social distancing. in our simulation model, we estimated the effect of social distancing alone; combining social distancing and case-based interventions would have a synergistic effect to further reduce transmission. further, our estimates of age differences in susceptibility to infection and probability of developing symptoms are based on active testing of contacts of 57 primary confirmed cases. these data suffer from the usual difficulties inherent to identifying epidemiological links and index cases. seroepidemiology studies are currently lacking but will be essential to fully resolve the population susceptibility profile of covid-19. while the age patterns of contacts were not significantly different between the two study locations during the covid-19 outbreak period, these patterns may not be fully representative of other locations in china and abroad, where social distancing measures may differ. modeling results may possibly be underestimating the effect of social distancing interventions as our results account for a decreased number of contacts but ignore the impact of increased awareness of the population, which may have also affected the type of social interactions (e.g., increased distance between individuals while in contact, or use of face mask (16, 17) ). finally, our school closure simulations are not meant to formulate a full intervention strategy, which would require identification of epidemic triggers to initiate closures and evaluation of all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 20, 2020. . different durations of intervention (5) . nonetheless, our modeling exercise provides an indication of the possible impact of a nation-wide preemptive strategy on the infection attack rate and peak incidence. to generalize these findings to other contexts, location-specific age-mixing patterns and population structures should be considered. our study provides evidence that the interventions put in place in wuhan and shanghai, and the resulting changes in human behavior, drastically decreased daily contacts, essentially reducing them to household interactions. assuming the same scale of contact-distancing measures were to be put in place in other locations, human mixing patterns could be captured by data on within-household contacts, which are available for several countries around the world (4) (5) (6) (18) (19) (20) . further research should concentrate on refining age-specific estimates of susceptibility to infection, disease, and infectivity, which are instrumental to evaluating the impact of school-and work-based control strategies currently under consideration worldwide (21, 22). all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 20, 2020. coronavirus disease 2019 (covid-19) situation the novel coronavirus pneumonia emergency response epidemiology team proc. natl. acad. sci transmissibility of 2019-ncov report of the who-china joint mission on coronavirus disease age group 0-6 y key: cord-349276-viq01q8l authors: shaw, rajib; kim, yong-kyun; hua, jinling title: governance, technology and citizen behavior in pandemic: lessons from covid-19 in east asia date: 2020-04-30 journal: progress in disaster science doi: 10.1016/j.pdisas.2020.100090 sha: doc_id: 349276 cord_uid: viq01q8l abstract corona virus (codid-19) was first reported in wuhan in december 2019, then spread in different parts of china, and gradually became a global pandemic in march 2020. while the death toll is still increasing, the epicenter of casualty has shifted from asia to europe, and that of the affected people has shifted to usa. this paper analyzes the responses in east asian countries, in china, japan and south korea, and provides some commonalities and lessons. while countries have different governance mechanism, it was found that a few governance decisions in respective countries made a difference, along with strong community solidarity and community behavior. extensive use of emerging technologies is made along with medical/health care treatment to make the response more effective and reduce the risk of the spread of the disease. although the pandemic was a global one, its responses were local, depending on the local governance, socio-economic and cultural context. it is now widely acknowledged that the corona virus (covid-19, as formally known) was first reported in wuhan, china in december 2019, and was recognized by chinese authorities as a new virus in january 2020. who (world health organization) declared this as a pheic (public health emergency of international concern) in the end of january 2020. after the initial delay in the source point (wuhan), chinese authorities took utmost efforts to control the spread of the disease, however, it has already started impacting other parts of china as well as other countries during mid to end of january. a term "infodemic" has been used by the who director general at the initial stage of the spread of the disease (during mid-january 2020: [1] in lancet), which seems to be still valid while writing the paper in the end of march 2020. who colleagues have warned the tsunami of information, especially with social media, which many times call for panic situation. we have observed this in several countries, as well as fake news spreading through social media. on 11th of march 2020, who has declared this as a global pandemic, and as of 23rd of march 2020, the virus has affected 172 out of 195 countries. while the statistics of infected people, casualties changing rapidly overtime, it is very difficult to put a number. as of 29th of march, there are more than 30,000 death reported, while more than 23,000 people are in critical conditions globally. more than 650,000 people are affected. although it is early to make any comment on the nature of its spread, a few characteristics can define this new virus as follow: -high rate of spread: within three months the virus has spread globally and is considered as a global pandemic. the rate of its spread is high, which happened due to higher mobility of people in a globally interconnected world. it can be said that people to people transmission rate of very high. -aged and low immune people more vulnerable: data shows that the aged population [2] and people with low immunity (with diabetes or other chronic disease) are more vulnerable to this virus. -differential recovery rate: while the global average of recovery rate is relatively low (like 28 to 30%), different countries have differential recovery rate. while china, korea, japan has relatively high recovery rate, europe, iran, usa showed relatively lower recovery rate. of course, this is constantly changing, and hopefully gets better soon. over last few weeks, there are several words which got significant attention like: "community spreading", "social distancing (physical distancing)", "self-isolation", "14 days quarantine", "lockdown," "break the chain" etc. all these are used for one purpose, which is to stop spreading the virus. although there are reported use of medicines from different countries (without proper confirmation); there is no confirmed medicines used to cure this virus, or no vaccine available for covid-19 as of march 23, 2020 . thus, the only way to stop the spread is to isolate us from social gathering or masses, and isolate confirmed people for quarantine. this process needs a combination of strong governance, use of existing and next technologies in innovative ways, and strong community participation and solidarity. anderson et al. [3] made interesting analysis on how the country-based mitigation measures influence the course of epidemic (while they wrote the paper, the covid-19 status was not a pandemic). while acknowledging that governance, citizen participation/awareness, penetration of technology varies from country to country, this paper makes a modest effort to analyze the experiences of china, japan and korea as east asian cluster. time series analysis of the key governance decision is made and its correlation with the spread of the virus within these three countries are observed. a few common lessons are drawn, which have larger implications to the society in this critical phase of covid-19 global pandemic. who beijing office got the first information of an unknown virus on 31st of december 2019. from that point, three months are passed. in this section, a few global measures (mainly excluding east asia, which will be described later), especially the role of who is narrated. within two weeks from the first report in who beijing office, first overseas case was reported in thailand on 13th of january 2020. who director general met chinese president on 28th january and declared it as pheic (public health emergency of international concern) on 30th january. on the following day, italy declared a national emergency with two case reported there. the virus spread continued in china as well as overseas after that, and on 11th february who has named the virus as covid-19. a united nations cmt (crisis management team) was formed with who as the coordinating agency. who has appointed a few prominent persons as their covid envoy on 21st of february to provide advices to different countries. a series of missions were organized by who team: one in italy (24th february), one joint mission in china (25th february), and one in iran (2nd march). 24th february was the time when the global epicenter has started shifting from china to other countries, with number of affected people outside china crossing that within china. two major clusters were observed, apart from kore and japan: one in iran and the other in europe (northern italy). early march showed steady growth of affected people globally. who declared its research road map on 6th of march, and on 7th of march, it was found that the virus has affected 100 countries, and more than 100,000 people. this prompted who to declare covid-19 as a global pandemic on 11th of march, and usa declared national emergency on 13th of march. fig. 1 shows the number of affected people globally with key who decisions stated above. the above description shows that within two months (from 13th of january, when first case was reported in thailand, outside china to 13th of march, when usa declared emergency), the virus has taken a significant number of lives, affected a large number of people, and brought down many countries, including the economic hubs under lockdown. several countries have made travel bans, lock down of cities and provinces, which has also impacted significantly the local as well as global economy. as of 27th february 2020, a report by mckinsey [6] has identified six global clusters as follow: mature propagation (china complex), early propagation (east asia and middle east complex), new propagation (western europe), and no propagation (africa and america complex). however, one month has changed the scenario, where western europe complex has become the new epicenter, and america has observed a significant propagation. based on the simulation, mckinsey [6] proposed three global scenarios of quick recovery, global slowdown and global pandemic and recession. this would affect differentially the second and third quarter of the year. while the base scenario talks on the control of spread in east asia in europe in early second quarter, the early recovery predicts that it would be in late first quarter, while the recession/pandemic scenario talks about middle to late second quarter. fig. 2b shows the same on daily increase in these three countries. in both of figures, since the numbers in china exceeds that in korea and japan by a significant percentage, the values are provided to show the highest numbers in china. china sees a sharp increase in number of confirmed cases from the third week of january, while a sharp increase in both recovered and death from the first week of february. korea saw a sharp increase in number of cases from third week of february, while japan saw an increase in the first week of march. detailed time series analysis of china is presented in hua and shaw [7] , where the responses have been divided into five phases: 1) very early phase (up to 31st of december 2019), 2) investigation phase (up to 20th of january 2020), 3) early intensification phase (up to 31st of january 2020, 4) criticism, agony and depression phase (up to 14th of february 2020) and 5) positive prevention and curative control phase (up to 29th february 2020). this paper also looks at the other events in march until 25th of march 2020. while looking at the key policy decisions taken over the course of action, a few clusters can be observed as follow (fig. 3) . cluster 1 (20-25 january 2020): on 20th january 2020, dr. zhong nan shan made official announcement in cctv about the new type of virus identified in wuhan, followed by announcement of emergency in hubei province on 22nd of january, and decision on constructing new hospitals on 23rd and 25th of january. during this cluster the source area went under lockdown, and emergency response started officially. based on these key decisions, emergency supplies including goods and medical teams arrived in wuhan from different parts of the country. cluster 2 (2-5 february 2020): on 3rd of february 2020, city sanitization started with public spaces, parks etc. on 5th of february, a major decision was taken on "no one will be spared", which enabled the government officials to enter into people's house and check virus symptoms. this was a key turning point to identify new cases of affected people. a sharp increase in the number is also observed as a result of policy decision taken in cluster 1 and 2 (fig. 3) . to stop spread of the disease, it was important to identify all possible sources. thus, the strict decisions taken in cluster 1 and 2 were crucial. qr code was introduced for all residents on february 18, and this was a good check to distinguish between the affected and non-affected people. the next couple of weeks were devoted to implement the policy decisions and be vigilant for its violation. in case of taiwan, the time series analysis points out an early preparation. as early as 31st of december 2019, taiwan announced medical advisory (14 days self-vigilance, wearing mask, temperature check etc.) to inbound visitors on the wuhan and started medical test. specific warning was issues to all in-bound people from wuhan on 6th of january, and was repeated four times (10th, 11th and 17th january). a team of experts was dispatched to wuhan on 6th of january to identify the new disease spread. there was an early warning issued on restraining and legal actions on fake news spread, which was also repeated several times (11th, 17th, 21st and 23rd january). first confirmed case was reported on 21st january in taiwan, which also prompted some other key decisions. to protect panic buying, the government bought masks, and started its own distribution system through national insurance card. number of masks entitled per insurance card was strictly monitored, and masks were distributed free of charge in the rural areas. this system started at the early stage (3rd of february), and system was developed and customized based on the need and supply of masks, and finally the online shopping system started on 12th of march. other measures in taiwan include: 1) introduction of health declaration card at entry points (airports and ports) on 11th february, 2) pre-entry electronic health declaration on 14th of february, 3) issuing travel advisory to mainland china (in january), korea and japan (on 22nd february), 4) provide special allowance to all medical staffs (from 23rd of february), 5) provide financial assistance to family of affected people (on 11th of march), and 6) provision of free medical treatment of the affected people not having medical insurance in taiwan. the entry from europe and middle east was restricted on 11th march, and total travel ban was announced on 19th of march to be effective from 24th of march to 7th of april. on 25th march, all night entertainment was banned, and gathering more than 100 people in one place was prohibited. experience of taiwan points out that an early level of risk identification, risk understanding and risk control and mitigation are key to prevent the spread of the disease. prior experience of sars may have been utilized to take early decision making, along with the inputs from the experts. japan reported the first case of covid-19 between 10 and 15 january 2020 from a chinese national who travelled from wuhan. the second and third cases were reported on 24 and 25th january. it gradually spread through tourism industry (like bus driver, tour guide etc.). during 28th january to 17th february, japan evacuated more than 800 japanese national from wuhan through five chartered flight. a detailed description of appearance of different cases in japan can be found in wiki [8] . here, a few critical issues on japan's approach is described below: diamond princess experiences: the cruise ship "diamond princess" arrived at the port of yokohama on 3rd february 2020 and received world attention due to reported confirmed case in the ship. on 5th february, after a report of confirmed case, passengers were asked to stay in their rooms in the ship for quarantine and to avoid spread. at that time, there were 3711 individuals, which includes 1045 crew members. although there was an initial delay in testing, disaster infection control team (dict) under the japanese society for infection prevention and control started conducted test in the ship along with dmat (disaster medical assistance team) [9] . dict team comprised of approved infection control doctors, approved infection management nurses, as well as experts from university hospitals and other institutions. the crew members were provided with personal protective equipment (ppe) and instructed on appropriate ipc (infection prevention and control) practices. the passengers were given thermometers and asked to record their body temperatures. those passengers with lab-confirmed covid19 were disembarked and transferred to an isolation ward at healthcare facilities [10] . there was a zoning planned in the ship for the infected areas, as well as to store the infection prevention gears. with regards to the passengers, guidance was given through the in-cruise announcement repeatedly, and the video on the appropriate ways to remove masks and to sanitize fingers, created by the dict, was delivered to the smart phones provided to each passenger for public awareness. as of 18th february, there have been 531 confirmed cases (14.3% of all individuals on board on 5 february), including 65 crew and 466 passengers. based on the number of confirmed cases by onset date, there is clear evidence that substantial transmission of covid-19 had been occurring prior to implementation of quarantine on the diamond princess on 5 february [10] . the disembarkation of all passenger was completed on 27th february. border control phase to infection spread phase: japan has been doing border control measures (mizugiwa taisaku in japanese) to control the spread of infections in japan. the measures in diamond princess is the reflection of that. also, japan had put specific measures to control inbound visitors from hubei province and asking for filling up health forms, as well 14 days quarantine. however, from 15th of february, there have been reports of transmission cases for which routes could not be identified. in such situation, the focus shifted from boarder control to infection spread control phase [11] . as of february 20, three deaths have been reported, and severe cases have started to be reported in the elderly and patients with underlying diseases. as per the experts, during the epidemic phase, the treatment of the serious patients was required. border control measures continued with quarantine restrictions on travel of passengers from china and korea on 5th of march, which gradually extended to other high-risk countries also. once the disease started spreading, it was essential to identify the clusters from where it started spreading, which is stated below. cluster approach: the analysis by tohoku university virology professor hitoshi oshitani, who is on a government panel of medical experts, comes as japan ramps up contact tracing efforts with a focus on "active epidemiological investigation". on 25th february, mhlw prepared "cluster response section," in accordance to the basic policies for novel coronavirus disease control. the cluster approach targeted to identify the cluster to spread the disease, and quickly take actions to stop the spread from the clusters. japan has identified 15 coronavirus clusters nationwide in its first "cluster map", released on 16th march. although the data changes over time, in the map, the biggest cluster, which accounts for more than 80 cases, involves four live music venues in osaka. another live house in sapporo was also identified as a cluster [8] . keeping in mind the increasing growth of affected patients, as well as identification of clusters, the governor of hokkaido had announced "a state of emergency" in hokkaido on 28th of february and urged the residents to stay indoor over the weekend. temporary closure of schools across nation: prime minister shinzo abe had requested for the voluntary closure of school in the last week of february, and as a result, most of the schools across nations were closed from 3rd of march 2020. this apparently abrupt decision drew criticism from many schools, teachers and parents since it was announced with little preparation. however, this decision was on the crucial trigger to increase the urgency in people's understanding and actions. the only effective way at the moment to prevent the spread of this novel coronavirus is decrease personal contact among people and to increase personal hygiene, such as hand-washing [8] . basic policies for covid-19: on 25 february, the abe administration adopted the "basic policies for novel coronavirus disease control" based on the advice that it received from the expert meeting. first, the new policies advised local medical institutions that it is better for people with lighter, cold-like symptoms to rely on bed rest at home, rather than seeking medical help from clinics or hospitals. the policy also recommends people at a higher risk of infection -including the elderly and patients with pre-existing conditionsto avoid hospital visits for such non-treatment purposes as completing prescription orders by letting them fill the forms over the telephone instead of in person. second, the new policies allow general medical facilities in areas of a rapid covid-19 outbreak to accept patients suspected of infection. before this, patients could only get tested at specialized clinics after making an appointment with consultation centers to prevent the transmission of the disease. third, the policy asks those with any cold symptoms to take time off from work and avoid leaving their homes. government officials urged companies to let employees work from home and commute at offpeak hours. the japanese government also made an official request to local governments and businesses to cancel large-scale events. telework has been promoted very strongly with the private and public companies. however, in spite of several appeals, it was found that only 13% of are doing telework, while 38% who wish to do telework could not due to several issues, including technical problems [12] . the survey was conducted between 9 and 15 march with 21,000 company employees. on 5 march 2020, prime minister abe introduced a draft amendment to the "special measures act to counter new types of influenza of 2012". this would allow the prime minister to declare a "state of emergency" and mandate the prohibition of large-scale gatherings and the movement of people during a disease outbreak. the basic countermeasures of covid-19 is presented in the fig. 4 (mohw, [13] ). there are three phases considered in this approach: 1) domestic spread prevention, 2) prevent spread of infection, and 3) prevent severe spread. it seems that japan is currently in the second phase, which aims at preventing spread of infection. the key target is to reduce the number of affected people by lowering the peak, and strengthening medical system. the crucial in this phase is to prevent the outbreak and control the speed of infection, so as to provide enough time to the medical facilities to get prepared. this can be done also with strengthening other countermeasures like border control, identifying key clusters, closing of school, promoting telework, and avoiding gathering of people in public places like abandoning key sports events, festivals (like cherry blossoms viewing) etc. (1) the occurrence of first confirmed case and subsequent successful initial management: from the beginning of the covid-19 situation, the korean government, centered around the korea centers for disease control and prevention (kcdc), has shared information with related organizations and established an effective response system. when reports were received of pneumonic patients arising from an unknown origin in wuhan, china, in december 2019, the kcdc strengthened the quarantine process for people entering korea from the wuhan region in cooperation with chinese health authorities and the world health organization (who). after a 36-year-old woman of chinese nationality was classified as suspected of hosting the novel disease and quarantined on january 8, 2020, the korean government issued a blue alert level (the lowest among the 4 alerts along the national crisis management system) and established a joint response system by sharing immigration information among the kcdc, the ministry of interior and safety (mois), the ministry of justice (moj) and other related agencies. on january 20, 2020, the kcdc confirmed the first imported case of covid-19. the case was a 30-year-old chinese woman living in wuhan, china, and four days later confirmed the second imported case; a 55-yearold korean male working in wuhan. on the same day, the korean government raised the alert level from blue (level 1) to yellow (level 2) and set up the central discharge countermeasures headquarters (cdchqs) to initiate the 24-hour emergency response system [14] . in addition, the kcdc began to conduct a thorough survey of all visitors from the wuhan region to prevent the influx of potentially infected people, and to strengthen the quarantine and public relations efforts to prevent the spread of covid-19 during the lunar new year holiday season; a time when millions of people are on the move. accordingly, president moon emphasized that the government should mobilize all available resources to prevent the spread of covid-19 and conduct a thorough investigation on all visitors from wuhan, leading to a transparent disclosure of processes and results [15] . on january 30 and 31, 2020, the ministry of foreign affairs, mois, and related ministries worked together to transport koreans residing in wuhan, china, back to korea. mois formed a joint government support group to ensure the returnees were regularly monitored while adhering to a 14-day quarantine at the government facilities in asan city and jincheon city. thanks to the government's transparent and proactive response, step-bystep strengthening of foreign entry procedures, and voluntary participation by citizens to self-quarantine and self-isolate, there were only 30 confirmed cases of covid-19 by february 18. the situation seemed to gradually be turning to a stable phase. (2) the rapid escalation of covid-19 by members of the "shincheonji church of jesus": as the number of confirmed cases surged due to the unexpected "shincheonji" emergency, the korean government raised the alert level to red (level 4) and put all available resources to tackle the crisis along with designating special management regions against infectious diseases. on february 19, the kcdc identified the 31st confirmed case who was a 61-year-old korean female, a member of shincheonji. just after that the number of confirmed cases spiked and most of them came from the shincheonji cluster. the covid-19 situation in korea took on a completely new aspect of the noble crisis situation. consequently, the daegu city government acquired a list of the 9336 shincheonji members from the headquarters of the shincheonji and cross referenced the list with the kcdc, then asked all members to be tested for symptoms and to self-isolate. the korean government subsequently scaled up the alert level to red (level 4) and took extreme proactive actions in order to avoid a nation-wide transmission. as a follow up activity, central disaster and safety countermeasures headquarters (cdschqs), headed by the prime minister, were installed [16] . the hqs focused on isolating and treating potential cases in the specially managed regions of daegu city and cheongdo-gun in gyeongbuk province, and in other regions conducted epidemiological investigation and environmental disinfection to prevent a sporadic community epidemic as well as to identify shincheonji-related cases. on february 26, the total number of confirmed patients was 1261, and the rapid increase raised the sense of a crisis across the country. among them, the confirmed cases in daegu and gyeongbuk were 75% of the cases with 945 confirmed patients. instead of blockading the daegu and gyeongbuk regions, the korean government conducted a thorough survey of the members of the shincheonji cluster, who triggered the community spread in daegu and gyeongbuk; feasibly across the country, and conducted around 10,000 diagnostic tests per day to quickly identify confirmed cases. at the same time, measures were implemented to secure the necessary beds for the cases with the highest severity, and to solve the shortage of medical staff. in cases where life was threatened, patients were hospitalized and placed in negative pressure rooms or moved to infectious disease designated hospitals. non-threatening cases were provided with medical support at a designated 'life treatment center' within each region. moreover, doctors and nurses from other regions voluntarily and swiftly ran to daegu and gyeongbuk to relieve the shortage of medical personnel. the korean government also expedited the hiring of 724 public health doctors earlier than originally planned and deployed them to each region. on march 4, the kcdc developed and implemented standard operating guidelines for drive-through testing centers as an effective and rapid diagnostic test processing destination versus hospitals; multitudes quickly opened soon after. additionally, 254 hospitals were designated as 'for public use;' a hospital the public could visit without fear of infection. the korean government continued its vocal call and support for citizenry participation in personal hygiene practices and social distancing. the mois, by this time, had developed and released a safety protection application for self-isolated people to self-diagnosis their health status, to be informed of self-isolation life rules, and to automatically send alerts to a dedicated official when the person leaves the self-isolation site without approval. also by this time, as sales and usage of face masks spiked, temporary mask shortages began to be felt by everyone. to mitigate potential problems, the ministry of food and drug safety (mfdg) implemented a fiveday rationing system for selling and purchasing facemasks. on march 13, the government prepared guidelines for stronger preventative measures towards the usage of public spaces, call centers, and facilities that could accommodate many people. religious groups cooperated with the government measures and calls by holding weekly worships online and postponing or canceling large-scale religious events. with the government's proactive actions and citizens' participation, the number of confirmed cases decreased to 75 on march 15 and gradually began to show a stabilizing trend. (4) preventing overseas re-inflow and strengthening physical distancing: the korean government applied special entry procedures to block the influx of covid-19 from foreign countries, and shifted physical distancing policy from a voluntary participation to a strong administrative recommendation. with the declaration of the corona pandemic by the who and the rapid expansion in the number of confirmed cases in europe and the united states, concerns about a re-influx of covid-19 hosts from overseas to korea began to increase. on march 15, the korean government expanded the scrutiny of special entry procedures to those entering from five european countries: france, germany, spain, the uk and the netherlands; on march 19, travelers from all countries received special scrutiny. in addition, the government strengthened countermeasures to block the re-introduction of foreign risk factors into korea; including a 14-day self-isolation for all travelers from europe and a special travel advisory for koreans, urging the cancellation or the postponing of all overseas trips until mid-april at the very earliest. moreover, the korean government started to support the return of korean citizens residing abroad; starting with those in iran. upon arriving at incheon airport, returnees were tested, and if found to be negative of the virus, they agreed to self-quarantine at home. if found to be positive, returnees were taken directly to a hospital for treatment. the two policies of postponing the start of schools' spring semesters and forcing social distancing had been stronger measures that the korean government took to tackle the covid-19 spread. it was on march 18 that the special decision was taken to delay the start of the spring semester for daycare centers, kindergartens, elementary schools, junior high schools, high schools, and special schools nationwide by april 6. on march 21 and 22, the government strongly recommended to facilities with a high risk of collective contagion, such as religious facilities, indoor sports facilities, and entertainment venues, to close their doors to the public for two weeks, and asked all citizens to refrain from gathering at multi-use facilities and indoor sport arenas, or doing outdoor activities collectively for the same period. different countries have different styles of governance. this section summarizes some of the key lessons on governance at different level. strong government control: china showed a very strong government control from the third week of january when the covid-19 case was officially confirmed. apart from the lockdown in wuhan, hubei province, and gradually to all over the country, there was strict measures not to promote fake news and panic from the initial stage. supreme court advisory was issued on the fake news at an early stage. also, different provincial governments helped the most affected province and city (hubei and wuhan) with different types of supplies and resources. transparency and democracy: south korea proved to be successful in responding to covid-19 through disclosing accurate information transparently and holding to the democracy of the whole society [17] . since january 20, 2020, when the first covid-19 case was confirmed, the korean government, centered around the kcdc, shared relevant information among the who, chinese authorities and other related agencies, and transparently disclosed the government's responses; leading to voluntary participation of citizens without protest. the national and local governments of korea quickly identified the movement path of the confirmed cases through big data analysis; data obtained through credit card usage history, cctv analysis, etc., and disclosed them transparently through the cell broadcasting system's (cbs) mobile service and government's website [18] . the citizens who received the information were able to determine whether or not they had contact with the confirmed case. if so, most citizens voluntarily reported to a public health center. if they showed any signs of having the virus, a diagnostic test was requested. due to the fact that the korean government is well prepared for testing and conducting diagnostic analyses, all potentially infected citizens were able to be promptly analyzed, resulting in preventing the spread of infectious diseases. clear roles & responsibilities and unified efforts: an effective response against a novel infectious disease like covid-19 requires a very specialized knowledge and expertise, thus it is essential to develop and implement a holistic response plan by an expert group. from the beginning of the covid-19 response, the korean government set up a decision-making process centered around the quarantine countermeasure headquarters operated by the kcdc. on top of that, as the government-wide response became more vital due to the rapid increase in the number of confirmed cases, mois took charge of the monitoring and management of people self-isolating, finding and surveying those who had visited the wuhan region and may be contagious, locating and securing temporary living facilities and lifetime treatment centers through countermeasures support headquarters (cshqs). this delineation of roles and responsibilities between the responsible agency (kcdc) and the coordination agency (mois) made it possible for the kcdc and the ministry of health and welfare (mohw) to focus on epidemiological investigations and responses to the infectious disease. this effective response system was developed based on the double-loop learning process during the mers experience in 2015, the novel swineorigin influenza a(h1n1) in 2009, and severe acute respiratory syndrome (sars) in 2003. consequently, the successful covid-19 response can be directly attributed to the leadership of the president to accurately understand the fluctuating situation and emerging risk factors, and make accurate decisions based on the advice of expert groups, and the dedication of the prime minister who stayed in the daegu and gyeongbuk regions for three weeks to concentrate the capabilities of all ministries to cope with the crisis situation. expert based advices: japan took a different cautious approach not to call for a national emergency and lockdown. the legislation in japan does not permit a forced lockdown, but a request/advisory for the lockdown. japan's decision was based on close interaction with the expert group, which comprised of a diverse experts from the medical side, as well as economic, political and social side. based on the expert advices, regular government briefings and press meet by the prime minister, minister or senior officials were arranged. japan's governance approach was to flatten the growth curve, so that the health response mechanism has enough time and resources to respond to the situation, and that would possibly provide enough time to develop the vaccine and preventive measures. proactive prevention activities: the seoul and gyeonggi-do governments; with the highest populations in korea, took proactive measures from the initial outbreak. the seoul city government promptly produced and distributed guidelines on special entry procedures detailing the diagnosis and preventive tips for a corona virus, and temporarily restricted the use of large public squares. in addition, after a mass infection occurred at the guro call center, the seoul city government urgently conducted a survey of 417 private call centers and feasibly prevented a spread of covid-19 by improving the environment for telecommuters [19] . the government of gyeonggi-do, where the headquarters of the sincheonji church of jesus is located, conducted a thorough investigation of all sincheonji churches in the region and ordered the temporary closure. also, it ordered the members of the shincheonji to report to local public health centers and to self-isolate. in daegu city and gyeongbuk province, where the largest number of confirmed cases were identified, the governments established a system for investigating all members of the shincheonji and monitoring them exclusively by public officials. in addition, when hospital capacities became overwhelmed by the influx of patients, the government ordered the use of negative-pressure beds for the treatment of cases of highest severity only, and moved the cases with less severity out of the hospitals and into life treatment centers equipped with makeshift facilities where people could recover. business sectors, religious group and other regional governments assisted daegu and gyeongbuk during the crisis. for example, companies such as samsung and lg, and the religious community provided their training centers and facilities as life treatment centers. other local authorities including gwangju metropolitan city persuaded its citizens to open its hospitals and facilities for patients from daegu and gyeongbuk so that the regions could recover more rapidly. in case of china, hubei province showed a strong leadership in implementing stricter measures within the province. in japan, hokkaido announced an emergency in early march, and restricted gathering in public spaces. also, several other prefectures in japan (like osaka, hyogo) advised not to travel between the prefectures. tokyo metropolitan government also communicated with neighboring prefectures to advise travel limitations. prompt dissemination of the movement path of the confirmed cases: local governments, in cooperation with the kcdc, quickly identified the movement path of the confirmed cases and informed the residents of the areas in real-time via mobile text message using the cbs. in addition, they promoted safety rules through 24-h broadcasts, and posted on the governmental homepages covid-19 prevention tips and the movements of confirmed cases so that any citizen could find the information at any time. community-based activism, such as aggressively finding suspected cases and supporting vulnerable groups, was another advantage of korea to overcome the crisis. for example, in chungcheongbuk-do, a safety group organized from community units; such as a grassroots women's group and safety guards, actively participated in finding the people suspected of carrying the virus, and in sympathetically and humanly reported them to the community service center. in chungju city and boryeong city, local autonomous disaster prevention groups and women's associations voluntarily disinfected multi-use facilities and vulnerable facilities. furthermore, as the phenomenon of mask shortages across the country became serious, members of non-profit organizations such as the jeju women's association of seogwipo city and the cheonan city happiness support group started to produce face masks for those incapable of easily securing supplies far from home such as the elderly and the disabled. china also showed strong community governance with people making their community watch to strictly maintain the entry or exit from the community. this was not only implemented in the urban areas but also in the rural areas. several innovative technologies were used in different countries to identify affected people, to check their mobility, to reduce the risk of contamination, as well as to develop proactive recovery strategies and actions. artificial intelligence (ai), big data, 5g technologies were used in combination with other emerging technologies like drones, automated vehicles, robotics etc. in case of china, on 14th of february, the ministry of transport of people's republic of china [20] issued a circular to use new technologies for addressing covid-19 risk as well as to develop recovery strategy. highlights of china's use of technologies are described as follow: ai: fudan university and shanghai city government, along with the cdc (center for disease control) develop a unique ai based medical screening and check-up for respiratory blockage, which enhanced the speed of decision making of the scan system. the system was used with more than 93% of shanghai residents to make quick scan of the respiratory system [21] . big data: baidu big data was used to identify clusters of infected people. people's mobility data was used to identify movement of people from one place to another during an early stage of spread of the disease, which helped to take critical decisions on lockdown certain high-risk areas. this was also used in the recovery process, when the shops or factories are reopened to identify potential future risk areas as well [22, 23] . 5g: 5g data was used extensively in combination with different other technologies. primarily, it was used in transport system to identify the mobility of vehicles and related information (like number plates, driver etc.). combination of drones and 5g was used in the transport system to identify violation of laws in the emergency time. thermal camera was used with helmet of police and other public officials for quick thermal screening of people in guangdong, and the date was sent using 5g. combination of robotics and 5g was used for city sanitization in the peak period in wuhan when public services were also at risk. similarly, combination of automated vehicle and 5g was used for goods delivery in certain highly contaminated areas. 5g was also used for telemedical care and advices in the newly built hospital in wuhan. [21, 24] . health barcode: a unique health barcode system was developed to identify the affected people, as described in hua and shaw [7] . hangzhou city was first to use this system on 11th of february 2020, which gradually used in 200 other cities in china [25] for developing the health barcode, user sign up for the "close contact detector" app by registering their phone number, name and id, and then scanning a qr code on their smartphones [26] . the app will tell them whether they have been in proximity to someone who has been infected. the barcode system has three color coding: green (good health), yellow (caution required), and red (infected people), which enable or disable them to entering from different public buildings as well as public transport. with the health barcode, online mapping of affected people could be done, and people could avoid the clusters where affected people are concentrated. if a user is found to have in close contact with the affected person, the app recommends self-quarantine and also send an alert to health officials. career's big data was used in combination with baidu's r. shaw et al. progress in disaster science 6 (2020) 100090 location (gps) data to develop the health barcode. this was also used in wuhan on 18th february onward, and eventually to all hubei province from 10th march onward. on 21st march, the government announced to develop health information platform for the whole country using the same system. chen [26] argued positive and negative consequence of the system on the ground that tools like surveillance and epidemic maps need to be combined with a view of how people react under pressure. rapid diagnostic test kit and an innovative test method: in korea, the development of a kit for rapidly diagnosing the potentially infected and innovative test methods such as drive-through screening centers, enabled thousands of people to be tested every day. this large-scale diagnosis for covid-19 was able to detect and confirm cases in their early stages, thus lowering the fatality rate and preventing the wide spread of the infectious disease. the new diagnostic kit using real-time reverse transcription polymerase chain reaction (rt-pcr) reduced test time from 24 h to 6 h. this kit was able to be used thanks to the efforts of a small business company that has been working on development irrespective of deficits and the rapid approval by the kcdc and mfdg. the kcdc and the mfdg reduced the administrative process, which normally takes one year from development to approval, to one month, so that it could be applied quickly in the field [27] . in addition, the drive-through screening method made it possible for suspected cases to receive the result of the covid-19 diagnostic test from their vehicle within 10 min, reducing the risk of cross-infection. while the general screening center took 2 samples per hour or 20 possible cases per day, the drive-through method was able survey 6 people per hour and 60 possible cases per day [28] . the united states and germany already adopted this driving-thru method as a way to reduce the possibility of cross-infection and increase the efficiency. in korea, the 'walk-thru test booth' and 'open walk-thru booth' evolved from the drive-through screening method. for this method, a potential patient enters a booth, and then a medical staff securely outside the booth checks their condition verbally via an intercom and take on-the-spot samples from patients outside the booth by using a stethoscope. this method takes only 6-7 min per person and results in a much smaller chance of contagion thanks to a complete separation between patient and doctor. on march 16, the yangji hospital, located in seoul, started to implement this method for the first time; on march 25 the korean government installed the open walk-through booth at incheon airport in order to deal with the thousands of travelers from overseas countries. enhancing self-responsibility and improving administrative efficiency using ict: the kcdc developed a self-diagnosis mobile application to strengthen monitoring by allowing domestic and foreign travelers entering korea to self-diagnose fever and health conditions related to covid-19, and report it to their local health center or the kcdc. as users typed quarantine-related information such as passport information, nationality, and names in the app, the kcdc was able to monitor their status during their stay in korea [13, 29] . in addition, the mois developed a self-quarantine safety protection mobile application to reduce the enormous administrative costs used to monitor self-isolators by public officials for local governments. in general, public officials check the status of self-isolators by daily phone or irregular visit, but they cannot prevent people from leaving home without approval. this app helped to overcome previous shortcomings by including a gps function, so if a self-isolating person left their home without approval, a warning message is automatically sent and a dedicated official is notified and sent to the scene to prevent the patient from violating the selfisolation if necessary. this app allows self-isolating people to complete self-isolation under their own responsibility, and frees-up vital officials by allowing many administrative personnel not to have to visit the selfisolators' home or check their status by phone regularly [30] . compliance with citizens' voluntary codes of conduct and refrain from large-scale gatherings of religious groups: a group outbreak occurred in daegu and gyeongbuk after the 31st confirmed case was announced; a shincheonji believer in daegu, but the national government did not take any mandatory blockade measures in this regions, instead provided all financial and administrative support so that daegu and gyeongbuk could overcome difficulties. the citizens in daegu and gyeongbuk also voluntarily participated in refraining from leaving their homes, self-reported 1339 cases of suspicion, and complied with stricter hygiene rules. the phenomenon of stockpiling daily necessities did not appear. citizens from other regions faithfully fulfilled the government's request to refrain from visiting daegu and gyeongbuk. all over the country, citizens made washing their hands a daily life habit. in business offices, public facilities, and facilities where large numbers of people come and go, hand sanitizers had been prepared so that people could use them freely and frequently. citizens wore face masks when going out in order to prevent the spread of the infection. for example, the third confirmed person in incheon on february 25, 2020, voluntarily stopped working and began self-isolating at home as soon as a suspected symptom occurred. he even wore a face mask inside the house and refrained from going out. thanks to his efforts, all the 23 people who were in contact with him; including his mother whom he lived together with, proved to be negative. most religious groups also refrained from large-scale gatherings by conducting online worship services and delaying buddha's day celebrations, and actively participated in the "social distancing" campaign. nation-wide volunteer and donation: by the end of february 2020, the number of confirmed patients had rapidly increased in daegu and gyeongbuk, making medical examination and treatment of all confirmed and suspected cases in the regions impossible. upon hearing their desperate circumstances, medical doctors, nurses, and clinical pathologists from all over the country moved in to provide medical treatment, assistances, and relief. according to the cdschqs, from february 24 to february 27, a total of 853 people (58 doctors, 257 nurses, 201 nursing assistants, and 110 clinical clinicians) participated in volunteer services [13] . in particular, more than 3000 people applied to volunteer as a nurse, and korea was able to find hidden heroes such as nurse kim who gave up her immigration to the united states in the process of applying for this volunteer service, or nurse oh who sent a sincere letter saying, "if i am not selected as a volunteer, i would suffer the fact that i can't help others in trouble. [31] ". they stayed in daegu and gyeongbuk for more than a month, devoting themselves to the treatment and prevention of the infection. additionally, the president of a hotel in changwon city provided hotel rooms free-of-charge for the volunteering medical doctors and nurses who had a hard time finding adequate accommodations. efforts were also made to overcome covid-19 on the basis of community consciousness, such as donations from all around the country. good landlord movement: with the prolongation of covid-19, consumption contracted significantly and the domestic economy was starting to stagnate. as the economic crisis for small business owners or self-employed people with a large rent burden increased, the "good landlord movement" that temporarily lowers rent spreads across the country. for example, more than 5000 stores in dongdaemun market, gwangjang market, and tongin market in seoul city participated in the 'good landlord' campaign and cut the rent by 20-30%. in addition, a variety of "good landlord movements", such as the exemption of franchise commissions from the food brand chaeseondang, and a subsidy of 1 million korean won for affiliates of mega coffees, gave hope to the small-business owners facing difficulties. community support and solidarity: chinese people showed a strong level of community solidarity for the affected people in wuhan. not only they provided resources, including financial, human resources, they also helped in boosting morals of the frontline health workers, and shared different positive stories and experiences through the social media. while the world is still struggling with the pandemic, the number of confirmed cases and casualty is growing higher, the east asian examples and analysis draw a few important lessons as follow: pandemic is global, but its response is local: in the growing interconnected world, our movement is quite high and fast, and that possibly enhanced the spread of the virus globally very quickly, making it a global pandemic. however, different country showed differences in approaches in responses. thus, although the medical treatment is universal, we need to keep in mind that the healthy emergency response measures are not universal. it is a combination of country's regulation, governance mechanism, link to science-based decision making, local governance as well as community behavior. thus, learning from each other's experience is very important. use of technology: in the advanced stage of technological intervention, a pandemic response is not just a medical response anymore. it needs to link different types of technologies in an appropriate way. covid-19 response in east asia showed extensive use of emerging technologies (like big data, ai, drone, 5g, robotics, automated vehicle, block chain etc.) linked to medical technologies. risk assessment: djlante et al. [32] in a quick analysis has pointed out the need of converging the health response, emergency response and disaster risk reduction in the viewpoint of the sendai framework. they analyzed and concluded that current mechanisms and strategies for disaster resilience, as outlined in the sfdrr, can enhance responses to epidemics or global pandemics such as covid-19. some of the recommendations are as follow: recommendations concern knowledge and science provision in understanding disaster and health-related emergency risks, the extension of disaster risk governance to manage both disaster risks and potential health-emergencies, particularly for humanitarian coordination aspects; and the strengthening of community-level preparedness and response. a proper risk assessment is required taking into consideration of health risk, exposures, behaviors and policy framework. use of social media and sensitization on fake news: in different countries, with different level of social media penetration, the importance of distinction of proper news and fake news becomes more relevant. importance of negative consequences of fake news is well understood in longer run, not only to fight this pandemic, but also for the longer-term recovery process. economic implications: the global economic impacts of the pandemic are yet to be understood, but there is a unanimous agreement of a global recession due to the pandemic. however, in different countries, sectorial impacts are already prominent, especially in tourism and hospitality sectors. msmes (micro, small and medium enterprises) are possibly the hardest hit in all the countries need special economic revitalization package. socio-psychological impacts and lifestyle changes: country wide or partial local down in cities have initiated a different work culture in east asian countries, as well as in most of the other countries. tele-work is becoming popular, online meetings, online classes in the universities are getting common, online education 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process. key: cord-327096-m87tapjp authors: peng, liangrong; yang, wuyue; zhang, dongyan; zhuge, changjing; hong, liu title: epidemic analysis of covid-19 in china by dynamical modeling date: 2020-02-18 journal: nan doi: 10.1101/2020.02.16.20023465 sha: doc_id: 327096 cord_uid: m87tapjp the outbreak of the novel coronavirus (2019-ncov) epidemic has attracted worldwide attention. herein, we propose a mathematical model to analyzes this epidemic, based on a dynamic mechanism that incorporating the intrinsic impact of hidden latent and infectious cases on the entire process of transmission. meanwhile, this model is validated by data correlation analysis, predicting the recent public data, and backtracking, as well as sensitivity analysis. the dynamical model reveals the impact of various measures on the key parameters of the epidemic. according to the public data of nhcs from 01/20 to 02/09, we predict the epidemic peak and possible end time for 5 different regions. the epidemic in beijing and shanghai, mainland/hubei and hubei/wuhan, are expected to end before the end of february, and before midmarch respectively. the model indicates that, the outbreak in wuhan is predicted to be ended in the early april. as a result, more effective policies and more efforts on clinical research are demanded. moreover, through the backtracking simulation, we infer that the outbreak of the epidemic in mainland/hubei, hubei/wuhan, and wuhan can be dated back to the end of december 2019 or the beginning of january 2020. a novel coronavirus, formerly called 2019-ncov, or sars-cov-2 by ictv (severe acute respiratory syndrome coronavirus 2, by the international committee on taxonomy of viruses) caused an outbreak of atypical pneumonia, now officially called covid-19 by who (coronavirus disease 2019, by world health organization) first in wuhan, hubei province in dec., 2019 and then rapidly spread out in the whole china 1 . as of 24:00 feb. 13th, 2020 (beijing time), there are over 60, 000 reported cases (including more than 1, 000 death report) in china, among which, over 80% are from hubei province and over 50% from wuhan city, the capital of hubei province 2,3 . the central government of china as well as all local governments, including hubei, has tightened preventive measures to curb the spreading of covid-19 since jan. 2020. many cities in hubei province have been locked down and many measures, such as tracing close contacts, quarantining infected cases, promoting social consensus on self-protection like wearing face mask in public area, etc. however, until the finishing of this manuscript, the epidemic is still ongoing and the daily confirmed cases maintain at a high level. during this anti-epidemic battle, besides medical and biological research, theoretical studies based on either statistics or mathematical modeling may also play a non-negligible role in understanding the epidemic characteristics of the outbreak, in forecasting the inflection point and ending time, and in deciding the measures to curb the spreading. for this purpose, in the early stage many efforts have been devoted to estimate key epidemic parameters, such as the basic reproduction number, doubling time and serial interval, in which the statistics models are mainly used [4] [5] [6] [7] [8] [9] . due to the limitation of detection methods and restricted diagnostic criteria, asymptomatic or mild patients are possibly excluded from the confirmed cases. to this end, some methods have been proposed to estimate untraced contacts 10 , undetected international cases 11 , or the actual infected cases in wuhan and hubei province based on statistics models 12 , or the epidemic outside hubei province and overseas 6, [13] [14] [15] . with the improvement of clinic treatment of patients as well as more strict methods stepped up for containing the spread, many researchers investigate the effect of such changes by statistical reasoning 16, 17 and stochastic simulation 18, 19 . compared with statistics methods 20,21 , mathematical modeling based on dynamical equations 15,22-24 receive relatively less attention, though they can provide more detailed 2 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint mechanism for the epidemic dynamics. among them, the classical susceptible exposed infectious recovered model (seir) is the most widely adopted one for characterizing the epidemic of covid-19 outbreak in both china and other countries 25 . based on seir model, one can also assess the effectiveness of various measures since the outbreak 23, 24, [26] [27] [28] , which seems to be a difficult task for general statistics methods. seir model was also utilized to compare the effects of lock-down of hubei province on the transmission dynamics in wuhan and beijing 29 . as the dynamical model can reach interpretable conclusions on the outbreak, a cascade of seir models are developed to simulate the processes of transmission from infection source, hosts, reservoir to human 30 . there are also notable generalizations of seir model for evaluation of the transmission risk and prediction of patient number, in which model, each group is divided into two subpopulations, the quarantined and unquarantined 23, 24 . the extension of classical seir model with delays 31,32 is another routine to simulate the incubation period and the period before recovery. however, due to the lack of official data and the change of diagnostic caliber in the early stage of the outbreak, most early published models were either too complicated to avoid the overfitting problem, or the parameters were estimated based on limited and less accurate data, resulting in questionable predictions. in this work, we carefully collect the epidemic data from the authoritative sources: the such a design aims to minimize the influence of hubei province and wuhan city on the data set due to their extremely large infected populations compared to other regions. without further specific mention, these conventions will be adopted thorough the whole paper. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint in progress. a. generalized seir model {s(t), p (t), e(t), i(t), q(t), r(t), d(t)} denoting at time t the respective number of the susceptible cases, insusceptible cases, exposed cases (infected but not yet be infectious, in a latent period), infectious cases (with infectious capacity and not yet be quarantined), quarantined cases (confirmed and infected), recovered cases and closed cases (or death). the adding of a new quarantined sate is driven by data, which together with the recovery state takes replace of the original r state in the classical seir model. their relations are given in fig. 1 and characterized by a group of ordinary differential equations (or difference equations if we consider discrete time, see si). constant n = s + p + e + i + q + r + d is the total population in a certain region. the coefficients {α, β, γ −1 , δ −1 , λ(t), κ(t)} represent the protection rate, infection rate, average latent time, average quarantine time, cure rate, and mortality rate, separately. especially, to take the improvement of public health into account, such as promoting wearing face masks, more effective contact tracing and more strict locking-down 4 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint of communities, we assume that the susceptible population is stably decreasing and thus introduce a positive protection rate α into the model. in this case, the basic reproduction it is noted that here we assume the cure rate λ and the mortality rate κ are both time dependent. as confirmed in fig. 2a -d, the cure rate λ(t) is gradually increasing with the time, while the mortality rate κ(t) quickly decreases to less than 1% and becomes stabilized after jan. 30th. this phenomenon is likely raised by the assistance of other emergency medical teams, the application of new drugs, etc. furthermore, the average contact number of an infectious person is calculated in fig. 2e-f and could provide some clue on the infection rate. it is clearly seen that the average contact number is basically stable over time, but shows a remarkable difference among various regions, which could be attributed to different quarantine policies and implements inside and outside hubei (or wuhan), since a less severe region is more likely to inquiry the close contacts of a confirmed case. a similar regional difference is observed for the severe condition rate too. in fig. 2g -h, hubei and wuhan overall show a much higher severe condition rate than shanghai. although it is generally expected that the patients need a period of time to become infectious, to be quarantined, or to be recovered from illness, but we do not find a strong evidence for the necessity of including time delay (see si for more details). as a result, the time-delayed equations are not considered in the current work for simplicity. according to the daily official reports of nhc of china, the cumulative numbers of quarantined cases, recovered cases and closed cases are available in public. however, since the latter two are directly related to the first one through the time dependent recovery rate and mortality rate, the numbers of quarantined cases q(t) plays a key role in our modeling. a similar argument applies to the number of insusceptible cases too. furthermore, as the accurate numbers of exposed cases and infectious cases are very hard to determine, they will be treated as hidden variables during the study. leaving alone the time dependent parameters λ(t) and κ(t), there are four unknown coefficients {α, β, γ −1 , δ −1 } and two initial conditions {e 0 , i 0 } about the hidden variables (other initial conditions are known from the data) have to be extracted from the time series 5 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16 data {q(t)}. such an optimization problem could be solved automatically by using the simulating annealing algorithm (see si for details). a major difficulty is how to overcome the overfitting problem. to this end, we firstly prefix the latent time γ −1 , which is generally estimated within several days 5, 33, 34 . and then for each fixed γ −1 , we explore its influence on other parameters (β = 1 nearly unchanged), initial values, as well as the population dynamics of quarantined cases and infected cases during best fitting. from fig. 3a -b, to produce the same outcome, the protection rate α and the reciprocal of the quarantine time δ −1 are both decreasing with the latent time γ −1 , which is consistent with the fact that longer latent time requires longer quarantine time. meanwhile, the initial values of exposed cases and infectious cases are increasing with the latent time. since e 0 and i 0 include asymptomatic patients, they both should be larger than the number of quarantined cases. furthermore, as the time period between the starting date of our simulation (jan. 20th) and the initial outbreak of covid-19 (generally believed to be earlier than jan. 1st) is much longer than the latent time (3-6 days), e 0 and i 0 have to be close to each other, which makes only their sum e 0 +i 0 6 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint matters during the fitting. an additional important finding is that in all cases β is always very close to 1, which agrees with the observation that covid-19 has an extremely strong infectious ability. nearly every unprotected person will be infected after a direct contact with the covid-19 patients 5,33,34 . as a summary, we conclude that once the latent time γ −1 is fixed, the fitting accuracy on the time series data {q(t)} basically depends on the values of α, δ −1 and e 0 + i 0 . and based on a reasonable estimation on the total number of infected cases (see fig. 3c-d) , the latent time is finally determined as 2 days. in order to further evaluate the influence of other fitting parameters on the long-term forecast, we perform sensitivity analysis on the data of wuhan (results for other regions are similar and not shown) by systematically varying the values of unknown coefficients 35, 36 . as shown in fig. 3e-f , the predicted total infected cases at the end of epidemic, as well as the the inflection point, at which the basic reproduction number is less than 1 6 , both show a positive correlation with the infection rate β and the quarantined time δ −1 and a negative correlation with the protection rate α. these facts agree with the common sense and highlight the necessity of self-protection (increase α and decrease β), timely disinfection (increase α and decrease β), early quarantine (decrease δ −1 ), etc. an exception is found for the initial total infected cases. although a larger value of e 0 + i 0 could substantially increase the final total infected cases, it shows no impact on the inflection point, which could be learnt from the formula of basic reproduction number. we apply our pre-described generalized seir model to interpret the public data on the cumulative numbers of quarantined cases, recovered cases and closed cases from jan. 20th to feb. 9th, which are published daily by nhc of china since jan. 20th. our preliminary study includes five different regions, i.e. the mainland * , hubei * , wuhan, beijing and shanghai. through extensive simulations, the optimal values for unknown model parameters and 7 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16 initial conditions, which best explain the observed cumulative numbers of quarantined cases, recovered cases and closed cases (see fig. 4 ), are determined and summarized in table 1 . there are several remarkable facts could be immediately learnt from table 1 . firstly, the protection rate of wuhan is significantly lower than other regions, showing many infected cases may not yet be well quarantined until feb. 9th (the smaller α for wuhan does not necessarily mean people in wuhan pay less attention to self-protection, but more likely due to the higher mixing ratio of susceptible cases with infectious cases). similarly, although the average protection rate for hubei * is higher than that of wuhan, it is still significantly lower than other regions. secondly, the quarantine time for beijing and shanghai are the 8 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint shortest, that for mainland * is in between. again, the quarantine time for wuhan and hubei * are the longest. finally, the estimated number of total infected cases on jan. 20th in five regions are all significantly larger than one, suggesting the covid-19 has already spread out nationwide at that moment. we will come back to this point in the next part. the initial values for exposed cases and infectious cases separately. the time-dependent cure rate λ(t) and mortality rate κ(t) can be read out from fig. 2 and are given in si. most importantly, with the model and parameters in hand, we can carry out simulations for a longer time and forecast the potential tendency of the covid-19 epidemic. in fig. 4 and fig. 5a -b, the predicted cumulative number of quarantined cases and the current number of exposed cases plus infectious cases are plotted for next 30 days as well as for a shorter period of next 13 days. official published data by nhc of china from feb. 10th to 15th are marked in red spots and taken as a direct validation. overall, except wuhan, the validation data show a well agreement with our forecast and all fall into the 95% confidence interval (shaded area). and we are delighted to see most of them are lower than our predictions, showing the nationwide anti-epidemic measures in china come into play. while for wuhan city (and also hubei province), due to the inclusion of suspected cases with clinical diagnosis into confirmed cases (12364 cases for wuhan and 968 cases for hubei * on feb. 12th) announced by nhc of china since feb. 12th during the preparation of our manuscript, there is a sudden jump in the quarantined cases. although it to some 9 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint extent offsets our original overestimates, it also reveals the current severe situation in wuhan city, which requires much closer attention in the future. towards the epidemic of covid-19, our basic predictions are summarized as follows: 1. based on optimistic estimation, the epidemic of covid-19 in beijing and shanghai would soon be ended within two weeks (since feb. 15th). while for most parts of mainland, the success of anti-epidemic will be no later than the middle of march. the situation in wuhan is still very severe, at least based on public data until feb. 15th. we expect it will end up at the beginning of april. are not included into parameter estimation). by coincidence, on the same day, we witnessed a sudden jump in the number of confirmed cases due to a relaxed diagnosis caliber, meaning more suspected cases will receive better medical care and have much lower chances to spread virus. besides, wuhan local government announced the completion of community survey on all confirmed cases, suspected cases and close contacts in the whole city. besides the forecast, the early trajectory of the covid-19 outbreak is also critical for our understanding on its epidemic as well as future prevention. to this end, by adopting the shooting method, we carry out inverse inference to explore the early epidemic dynamics 10 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint of covid-19 since its onset in mainland * , hubei * , and wuhan (beijing and shanghai are not considered due to their too small numbers of infected cases on jan. 20th). with respect to the parameters and initial conditions listed in table 1 , we make an astonishing finding that, for all three cases, the outbreaks of covid-19 all point to 20-25 days before jan. 20th (the starting date for public data and our modeling). it means the epidemic of covid-19 in these regions is no later than jan. 1st (see fig. 5d ), in agreement with reports by li et al. 5, 33, 34 . and in this stage (from jan. 1st to jan. 20th), the number of total infected cases follows a nice exponential curve with the doubling time around 2 days. this in some way explains why statistics studies with either exponential functions or logistic models could work very well on early limited data points. furthermore, we notice the number of infected cases based on inverse inference is much larger than the reported confirmed cases in wuhan city before jan. 20th. in this study, we propose a generalized seir model to analyze the epidemic of covid-19, which was firstly reported in wuhan last december and then quickly spread out nationwide in china. our model properly incorporates the intrinsic impact of hidden exposed and infectious cases on the entire procedure of epidemic, which is difficult for traditional statistics analysis. a new quarantined state, together with the recovery state, takes replace of the original r state in the classical seir model and correctly accounts for the daily reported confirmed infected cases and recovered cases. based on detailed analysis of the public data of nhc of china from jan. 20th to feb. 9th, we estimate several key parameters for covid-19, like the latent time, the quarantine time and the basic reproduction number in a relatively reliable way, and predict the inflection point, possible ending time and final total infected cases for hubei, wuhan, beijing, shanghai, etc. overall, the epidemic situations for beijing and shanghai are optimistic, which are expected to end up within two weeks (from feb. 15th, 2020). meanwhile, for most parts of mainland including the majority of cities in hubei province, it will be no later than the middle of march. we should also point out that the situation in wuhan city is still very severe. more effective policies and more efforts on medical care and clinical research are eagerly needed. we expect the final success of anti-epidemic will be reached at the beginning 11 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint of this april. furthermore, by inverse inference, we find that the outbreak of this epidemic in mainland, hubei, and wuhan can all be dated back to 20-25 days ago with respect to jan. 20th, in other words the end of dec. 2019, which is consistent with public reports. although we lack the knowledge on the first infected case, our inverse inference may still be helpful for understanding the epidemic of covid-19 and preventing similar virus in the future. the authors declare no conflict of interest. epidemic doubling time of the 2019 novel coronavirus outbreak by province in mainland china. medrxiv epidemiological and clinical features of the 2019 novel coronavirus outbreak in china preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china the novel coronavirus, 2019-ncov, is highly contagious and more infectious than initially estimated. medrxiv serial interval of novel coronavirus (2019-ncov) infections. medrxiv assessing spread risk of wuhan novel coronavirus within and beyond china all rights reserved. no reuse allowed without permission author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the using predicted imports of 2019-ncov cases to determine locations that may not be identifying all imported cases. medrxiv epidemic size of novel coronavirusinfected pneumonia in the epicenter wuhan: using data of five-countries' evacuation action. medrxiv estimating the daily trend in the size of covid-19 infected population in wuhan. medrxiv estimation of the asymptomatic ratio of novel coronavirus (2019-ncov) infections among passengers on evacuation flights early dynamics of transmission and control of 2019-ncov: a mathematical modelling study. medrxiv the effect of travel restrictions on the spread of the 2019 novel coronavirus (2019-ncov) outbreak. medrxiv the impact of traffic isolation in wuhan on the spread of 2019-ncov. medrxiv feasibility of controlling 2019-ncov outbreaks by isolation of cases and contacts effectiveness of airport screening at detecting travellers infected with 2019-ncov. medrxiv predictions of 2019-ncov transmission ending via comprehensive methods all rights reserved. no reuse allowed without permission author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the a data driven time-dependent transmission rate for tracking an epidemic: a case study of 2019-ncov novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions. medrxiv estimation of the transmission risk of the 2019-ncov and its implication for public health interventions an updated estimation of the risk of transmission of the novel coronavirus (2019-ncov). infectious disease modelling transmission dynamics of 2019-ncov in malaysia. medrxiv lockdown may partially halt the spread of 2019 novel coronavirus in hubei province interventions targeting air travellers early in the pandemic may delay local outbreaks of sars-cov-2. medrxiv simulating the infected population and spread trend of 2019-ncov under different policy by eir model. medrxiv the lockdown of hubei province causing different transmission dynamics of the novel coronavirus (2019-ncov) in wuhan and beijing. medrxiv jing-an cui, and ling yin. a mathematical model for simulating the transmission of wuhan novel coronavirus. biorxiv a time delay dynamical model for outbreak of 2019-ncov and the parameter identification modeling and prediction for the trend of outbreak of ncp based on a time-delay dynamic system all rights reserved. no reuse allowed without permission author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the partial equilibrium approximations in apoptosis. ii. the death-inducing signaling complex subsystem chiu fan lee, and ya jing huang. statistical mechanics and kinetics of amyloid fibrillation we acknowledged the financial supports from the national natural science foundation all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity.the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16 author/funder, who has granted medrxiv a license to display the preprint in perpetuity.the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16 17 all rights reserved. no reuse allowed without permission.author/funder, who has granted medrxiv a license to display the preprint in perpetuity.the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint 18 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity.the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02. 16.20023465 doi: medrxiv preprint key: cord-327716-ehm4fgos authors: zhou, can title: evaluating new evidence in the early dynamics of the novel coronavirus covid-19 outbreak in wuhan, china with real time domestic traffic and potential asymptomatic transmissions date: 2020-02-18 journal: nan doi: 10.1101/2020.02.15.20023440 sha: doc_id: 327716 cord_uid: ehm4fgos the novel coronavirus (covid-19), first detected in wuhan, china in december 2019, has spread to 28 countries/regions with over 43,000 confirmed cases. much about this outbreak is still unknown. at this early stage of the epidemic, it is important to investigate alternative sources of information to understand its dynamics and spread. with updated real time domestic traffic, this study aims to integrate recent evidence of international evacuees extracted from wuhan between jan. 29 and feb. 2, 2020 to infer the dynamics of the covd-19 outbreak in wuhan. in addition, a modified seir model was used to evaluate the empirical support for the presence of asymptomatic transmissions. based on the data examined, this study found little evidence for the presence of asymptomatic transmissions. however, it is still too early to rule out its presence conclusively due to sample size and other limitations. the updated basic reproductive number was found to be 2.12 on average with a 95% credible interval of [2.04, 2.18]. it is smaller than previous estimates probably because the new estimate factors in the social and non-pharmaceutical mitigation implemented in wuhan through the evacuee dataset. detailed predictions of infected individuals exported both domestically and internationally were produced. the estimated case confirmation rate has been low but has increased steadily to 23.37% on average. the findings of this study depend on the validity of the underlying assumptions, and continuing work is needed, especially in monitoring the current infection status of wuhan residents. the novel coronavirus , first detected in wuhan, china in december 2019, has spread to 28 countries/regions with over 43,000 confirmed cases. much about this outbreak is still unknown. at this early stage of the epidemic, it is important to investigate alternative sources of information to understand its dynamics and spread. with updated real time domestic traffic, this study aims to integrate recent evidence of international evacuees extracted from wuhan between jan. 29 and feb. 2, 2020 to infer the dynamics of the covd-19 outbreak in wuhan. in addition, a modified seir model was used to evaluate the empirical support for the presence of asymptomatic transmissions. based on the data examined, this study found little evidence for the presence of asymptomatic transmissions. however, it is still too early to rule out its presence conclusively due to sample size and other limitations. the updated basic reproductive number was found to be 2.12 on average with a 95% credible interval of [2.04, 2.18] . it is smaller than previous estimates probably because the new estimate factors in the social and non-pharmaceutical mitigation implemented in wuhan through the evacuee dataset. detailed predictions of infected individuals exported both domestically and internationally were produced. the estimated case confirmation rate has been low but has increased steadily to 23.37% on average. the findings of this study depend on the validity of the underlying assumptions, and continuing work is needed, especially in monitoring the current infection status of wuhan residents. the novel coronavirus was first detected in wuhan, china in december 2019, and three months later, 28 countries/regions have reported confirmed cases of covid-19 infections, with a total of 43,101 confirmed cases globally (22pm cst on feb. 10, 2020) . illness associated with covid-19 infection ranges from asymptomatic or mild respiratory illness to severe respiratory symptoms and death . at the time of this writing, there has been 1,018 confirmed deaths globally from the infection. much about this virus is still unknown at this stage (see figure 1 for a timeline of important events). the initial batch of confirmed cases has links with a live animal market in wuhan (huanan seafood market), suggesting a zoonotic origin (li et al., 2020) . it is suspected that the virus originated from bats, but the definite source and its reservoir host(s) are still unknown. infections among colleagues and family members, who do not have a recent travel history to wuhan, and also among health care workers confirm the human-to-human transmission (bastola et al., 2020; chan et al., 2020; li et al., 2020; phan et al., 2020; world health organization, 2020) . a recent concern is the potential presence of asymptomatic transmission. one confirmed case in germany suggests that the infection may have been transmitted during the incubation period of the index patient (rothe et al., 2020) . in the dynamics of an outbreak, the basic reproductive number r 0 is an important epidemiological parameter: it measures the number of cases an initial infectious individual can generate in a fully susceptible population. a larger than one r 0 indicates the epidemic is growing, while a smaller than one r 0 indicates the epidemic is declining. two separate studies used the susceptible-exposed-infected-resistant (seir) model to study the epidemiological dynamics of the outbreak in wuhan, and the estimated r 0 ranges from 2.68 to 3.8 (read, bridgen, cummings, ho, & jewell, 2020; wu, leung, & leung, 2020) . the estimate of r 0 shows much variation among different studies, and also within each study with different model assumptions. in addition, both studies used different traffic data to model the population flow: historical air travel was used in read et al. (2020) , and historical air, train and road travel was used in wu et al. (2020) . it is assumed that the real time traffic pattern in wuhan is not affected by the outbreak. however, this assumption needs to be verified with the real time population flow, because wuhan, as a major air and train traffic hub in the central china and with a 36% floating population, has the capacity to drive substantial day-to-day variation in traffic. it is important to investigate alternative sources of information to understand the disease dynamics due to the inherent issues associated with the time series of the confirmed cases in china. the daily confirmed cases will likely show an increasing trend purely due to the increase in sample processing throughput. since jan. 1, 2020, the chinese cdc has progressively adopted different versions of the case definition, simplified the procedural burden to confirm a case and subsequently increased the throughput of processing virus samples. one study used a hypothesized temporally increasing confirmation rate to estimate r 0 (zhao et al., 2020) . however, the actual confirmation rate is unknown and the estimated r 0 is highly variable. another source of uncertainty is the suspected low confirmation rate of this disease. it has been estimated that only 5.1% of infections in wuhan are identified (read et al., 2020) . with these concerns, wu et al. (2020) and nishiura, jung, et al. (2020) used an alternative data source, i.e., the number of internationally exported cases between dec. 31, 2019 and jan. 28, 2020, to infer the disease dynamics. another alternative source of information comes from the evacuated foreign nationals, which provide snapshot views of the status of the epidemic in the city of wuhan. between jan 29 and feb 2, 2020, there have been 2,666 foreign nationals evacuated out of wuhan, and their health has been closely monitored after arrival at their destination, 12 of them have been tested positive for covd-19 infection as of this writing (feb 11, 2020) . there has been at least 9 days between the latest date of evacuation included in this study and the last day of confirmation to avoid any bias in the infection rate. it should be emphasized that these evacuation flights took place after the city of wuhan was quarantined, and all the successfully evacuated individuals have passed at least two rounds of body temperature screenings at the airport. in this study, it is assumed that these evacuees provide a representative sample of the status of the general population in wuhan at the time of extraction. a subset of the evacuees data has been analyzed in nishiura, kobayashi, et al. (2020) with updated real time domestic traffic data, this study aims to update the current status of the covd-19 outbreak in the city of wuhan with the alternative information from the evacuees between the end of january and the start of february. in addition, the currently used prediction model for this outbreak, i.e., seir, does not allow for potential transmission of infection from latent individuals. in this study, the author modifies the seir model to evaluate the empirical support for the presence of asymptomatic transmissions based on current evidence. the original internationally exported cases used in wu et al. (2020) contain 63 cases, of which 4 cases do not have a recent travel history to wuhan and they were excluded from analysis. additionally, one confirmed case in germany infected through contacts with a patient from wuhan (rothe et al., 2020) , and it is also excluded here. a total of 58 confirmed cases from 14 countries/regions were used in this study. in this study, the author adopts the same case definition as in wu et al. (2020) : a case is an individual that show symptoms, which can be detected by temperature screenings, or severe enough to require hospitalization, plus a recent travel history to wuhan. in wu et al. (2020) , the symptom onset date was used as the date of exportation. however, the onset date does not always coincide with the date of travel from wuhan. in this study, the date of exportation is defined as the date the individual exits wuhan (local time, 49 cases), and when the exit date is not available, the symptom onset date was used (4 cases), and when both the exit date and the onset date were not available, the confirmation date was used instead (4 cases). the export dates fall between dec. 31, 2019 and jan. 29, 2019. of the 40 cases, on which both the date existing wuhan and the symptom onset date were available, 57.5% (23 cases) were asymptomatic when leaving wuhan, 25% (10 cases) developed symptoms before leaving wuhan, and 17.5% (7 cases) developed symptoms on the same date when leaving wuhan. the infection status of a total of 2,666 individuals that successfully evacuated from wuhan between jan. 29 and feb. 2, 2020 were used in this study. these individuals . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 have passed through body temperature screenings at the time exiting wuhan, and their samples have been analyzed for infection and their health monitored after arrival at their destination. as of feb. 10, 2020, 12 of these evacuees have been tested positive for covd-19 infection, and many of those initially tested negative for virus infection are still under quarantine. based on the case definition adopted in this study, all the infectious individuals are excluded from the evacuees, and it is further assumed that the false positive rate of the body temperature screening is the same across all the individuals. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 where s(t), e(t), i(t), r(t) were the number of susceptible, latent, infected and removed individuals in the population at time t, respectively, n(t) is the total number of individuals in the population, r 0 is the basic reproductive number, l ij (t) is the daily number of individuals migrating from i to j, for i, j ∈{w: wuhan, i: international, c: other cities of china}, and z(t) is the daily force of zoonotic infection. it is assumed that the dynamics start on dec. 1, 2019 (day 0) with a population of c. 14 million susceptible individuals, initiated with a constant zoonotic infection equivalent to 43x2 infectious individuals until jan. 1, 2020 (day 31) when the huanan seafood market was disinfected. in this study, we only model the disease dynamics in the city of wuhan, which has 9.08 million permanent (2020). in the baseline model, only one parameter was estimated, i.e., r 0 , and it was given a non-informative prior r 0~u niform(0, 10). to investigate whether the observed infection data support the presence of asymptomatic transmission, an open population seair model ( figure 3 ) was formulated, which has one additional stage a, the asymptomatic infectious stage, between the latent (e) and the infectious (i) stages of a seir model: . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.02.15.20023440 doi: medrxiv preprint 0 , , , where r 0 is the basic reproductive number of this model, γ has a non-informative prior ~uniform(0,1) author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.02.15.20023440 doi: medrxiv preprint the ordinary differential equations were solved using the lsoda algorithm (petzold & hindmarsh, 1997) with both the absolute and relative tolerance set to 10 -3 . multiple chains with a metropolis-hastings sequential sampler were used to draw samples from the posterior of the model parameters. python packages numpy and pymc3 were used to estimate model parameters, and all the data processing was conducted in python 3.7 (rossum, 1995) and statistical program r 3.6 (r development core team, 2016). all the datasets used in this study are hosted on a public repository and made available at https://github.com/hvoltbb/2019ncov. model performance was evaluated using the waic (widely applicable information criterion) (gelman, hwang, & vehtari, 2014) , calculated as . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . where θ is the posterior mean estimate, and p waic is the data based bias correction term. where m is the number of candidate models. models with larger weights have more support from the empirical data than models with smaller weights. these weights can be used to construct an ensemble estimator ĥ , where ˆm h is the estimator from candidate model m. the major advantage of using the ensemble estimator is its ability to account for model uncertainty and obtain better predictive performance than any single constituent candidate model. to assess the significance of the seair model with respect to the seir model, parametric bootstrap samples were generated to estimate the small sample distribution of the model weights when the data generating model is seir. the simulation procedure is . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.02.15.20023440 doi: medrxiv preprint as follows. first, a random sample was drawn from the posterior of the r 0 in model seir, the seir model was solved for each of these r 0 s, then the number of internationally exported cases simulated from the poisson distribution for all the dates when such data are available, and the number of latent individuals simulated from the binomial distribution for each sample of evacuated foreign nationals. next, for each simulated data set, posterior estimates were drawn from both the seir and seair models, and waic and weight w calculated for both models. the significance of the weight of the seair model is evaluated against the simulated empirical null distribution of the weight when the true model is seir. based on rescaled real time domestic migration data, the population outflow from the city of wuhan differed significantly from its historical pattern in 2019. the net outflow between the day the first covd-19 case was confirmed and when wuhan was quarantined shows an exponential increase pattern (figure 4) . during this period, the overall outflow was 15% more than the same period (according to lunar calendar) in 2019. at its peak (days before wuhan was quarantined), over millions of individuals were leaving wuhan on a daily basis. two days after wuhan was quarantined, the net outflow reserved signs and stays at a relatively low level. both the seir and seair models were fitted to the infection data, and seir model has better performance than the seair model based on waic (table 1) . however, the difference in waic between both candidate models is small, i.e., 3.12. based on the estimated null distribution of the δ waic from parametric bootstrap samples, the p-value for waic 3.12 δ = is c. 0.06, slightly larger than the 5% . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.02.15.20023440 doi: medrxiv preprint significance level. technically, the seair model is not statistically significant at the 5% level; however, due to the relatively small sample size of the infection data with respect to the number of residents in wuhan, it is inconclusive whether the disease dynamics show evidence for the seair model. in the following, parameter estimates from both the seir and seair models are presented. the seir model produced an r 0 with a mean of 2.12 and a 95% credible interval author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . estimated to be on average 37,115 individuals with a 95% credible interval of [31354, 43099] individuals. the cumulative number of infected individuals in wuhan on feb. 7, 2020 is estimated at 80,084 on average with a 95% credible interval of [63060, 98567] individuals. due to the elevated population outflow since jan. 1, 2020, the number of cumulative infected individuals in wuhan is approximately linear between day 31 and day 51, then appears to stabilize afterwards, and then increases exponentially after the date wuhan was quarantined (figure 9 ). the predicted pattern closely resembles the trend of the cumulative number of officially confirmed cases in wuhan with a time lag of approximately 3 days (figure 1) . assuming a constant time lag of 3 days, the confirmation rate of this disease has been low, i.e., less than 10%, in january 2019 but has steadily increased ever since ( figure 10 ). on feb. 10, 2020, the overall case confirmation rate is estimated at 23.37% on average with a 95% credible interval of [18.72%, 29.26%]. the time lag between the onset of symptoms and official confirmation of the case probably have decreased with time due to people's increased awareness of this disease and also the reduced procedural burden to confirm a case with newer versions of the case definition from the chinese cdc. to evaluate other time lags, the estimated case confirmation rate was calculated with lags between 1 and 5 days. these time lags produced similar results on the case confirmation rate on feb. 10, 2020 (table 2) . at this stage, our understanding of the dynamics of covd-19 is still limited due to the relatively low case confirmation, a lack of comprehensive monitoring programs . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . and other limitations. it is thus important to consider alternative information to update our understanding about the outbreak. this study integrates the recent infection data on the early dynamics of the covd-19 outbreak in wuhan, china with updated real time domestic traffic data. little empirical evidence was found supporting the presence of asymptomatic transmission. however, it is still too early to rule out its presence conclusively due to the relatively low sample size and the validity of the assumptions used in this study. the updated basic reproductive number was found to be 2.12 on average, which is significantly smaller than previous estimates (read et al., 2020; wu et al., 2020; zhao et al., 2020) , probably because the new estimate factors in the social and non-pharmaceutical mitigation implemented in wuhan through the evacuee dataset. the real time traffic is a crucial piece of information to understand the dynamics and the spread of the covd-19 outbreak in wuhan. as a major traffic hub in central china, wuhan's capacity to drive significant population flows is driving the accelerated spread of the disease domestically. real time traffic flow out of wuhan was found to differ significantly from its historical patterns. from jan. 1, 2020, when the huanan seafood market was disinfected, to jan. 23, 2020, when the city of wuhan was quarantined, the net traffic flow has always been outwards. during this period, the overall net outflow is estimated to be over 9 million individuals. on feb. 11, 2020, the disease has already spread to all provinces of china with 44,653 confirmed cases in china. in early january, the number of cases in wuhan is only growing linearly ( figure 9 ) and even appears to have stabilized days before jan. 23, due to the accelerated outflow. it is thus very dangerous to overinterpret the temporal pattern of the number of cases without taking into account real time traffic. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 a limitation of this study is that the international traffic still relies on its historical patterns in 2019. due to the elevated domestic outflow, it is reasonable to expect a similar elevated outflow in the international traffic. the internationally exported cases inform the disease dynamics through the proportion of infected outbound international travelers from wuhan. increasing the outward flow effectively reduces the proportion infected and subsequently the basic reproductive number. generally, international traffic by air is less variable than domestic traffic by road, and the potential surge in outbound international traffic would be less than 15% (the surge in outbound domestic traffic). with a 15% increase in the international outbound flow, sensitivity analysis shows a c. 2% decrease in the estimated basic reproductive number. thus, the major conclusions of this study would not be affected by a potential surge. on the other hand, it is still important to update the model and verify the underlying assumptions when the real time international air traffic data become available. because of the inherent bias in the daily traffic data, this study refrains from predicting the disease dynamics in other cities of china using meta-population modeling, even though daily real time traffic data among cities are available. the transportation pattern in china is unique in that primary modes of travel is by road and train, which were expected to account for 96% of the holiday traffic in 2020 (xinhua news agency, 2020). many of those trips would take multiple days. for example, a trip from wuhan to beijing would span days if the traveler chooses to travel by road. but the real time traffic data would erroneously indicate flow from wuhan into some traffic hubs in between wuhan and the final destination, because of the daily accounting unit used in the calculation of the flow pattern. thus, a meta-population model with such traffic data . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https: //doi.org/10.1101 //doi.org/10. /2020 would substantially over-estimate the imported cases into major traffic hubs around wuhan, and subsequently under-estimate the imported cases to more distant, but popular destination cities, such as wenzhou. air travel on the other hand is less affected by this issue. to solve this problem, the original user usage data collected by tencent or baidu need to be reprocessed to reveal those direct long-distance trips. it is suggested that the first confirmed case in germany is the result of an asymptomatic transmission, although the index patient at that time did experience some minor non-specific symptoms (rothe et al., 2020) . from december, 2019 to early january, 2020, the estimated mean incubation period is 6.1 days (li et al., 2020) ; however, a more recent study put the median incubation period at 3 days . the heightened awareness of the disease from both the general public and healthcare workers may play a role in discovering early symptoms of this disease. in this study, the estimated most probable asymptomatic infectious period is close to zero and offers little evidence for the presence of asymptomatic transmission in the disease dynamics. the findings of this study depend on the validity of the underlying assumptions, all of which may render the model inference invalid, and continuing work is needed, especially in monitoring the current status of residents in wuhan. as shown previously, the assumptions on the start date and the infectious force of the zoonotic infection influences the inference on the basic reproductive number (read et al., 2020; wu et al., 2020) . reducing the zoonotic infection force or shortening its duration has the effect of increasing the estimate of the basic reproductive number, and vice versa. in addition, all the infection data used in this study are with foreign nationals, with the assumption that . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https: //doi.org/10.1101 //doi.org/10. /2020 they have a similar virus transmissibility with the chinese residents. however, it is known that the basic reproductive number vary with human social behavior and organization (delamater, street, leslie, yang, & jacobsen, 2019) . therefore, it is important to verify this assumption with local monitoring data. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 tables and figures . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 dec. 1, 2019 (feb. 23, 2020 corresponds to the day when the city of wuhan was quarantined. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 the first 2019 novel coronavirus case in nepal. the lancet infectious diseases a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster complexity of the basic reproduction number (r0) understanding predictive information criteria for bayesian models clinical characteristics of 2019 novel coronavirus infection in china. medrxiv early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the extent of transmission of novel coronavirus in wuhan, china the rate of underascertainment of novel coronavirus (2019-ncov) infection: estimation using japanese passengers data on evacuation flights lsoda (livermore solver of ordinary differential equations importation and human-to-human transmission of a novel coronavirus in vietnam r: a language and environment for statistical computing novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions python reference manual transmission of 2019-ncov infection from an asymptomatic contact in germany the author is thankful to dr. x.g. for providing insights into and firsthand key: cord-343767-nnx8adtl authors: liu, ziyuan; li, zhi; chen, weiming; zhao, yunpu; yue, hanxun; wu, zhenzhen title: path optimization of medical waste transport routes in the emergent public health event of covid-19: a hybrid optimization algorithm based on the immune–ant colony algorithm date: 2020-08-12 journal: int j environ res public health doi: 10.3390/ijerph17165831 sha: doc_id: 343767 cord_uid: nnx8adtl in response to the emergent public health event of covid-19, the efficiency of transport of medical waste from hospitals to disposal stations is a worthwhile issue to study. in this paper, based on the actual situation of covid-19 and environmental impact assessment guidelines, an immune algorithm is used to establish a location model of urban medical waste storage sites. in view of the selection of temporary storage stations and realistic transportation demand, an efficiency-of-transport model of medical waste between hospitals and temporary storage stations is established by using an ant colony–tabu hybrid algorithm. in order to specify such status, wuhan city in hubei province, china—considered the first city to suffer from covid-19—was chosen as an example of verification; the two-level model and the immune algorithm–ant colony optimization–tabu search (ia–aco–ts) algorithm were used for simulation and testing, which achieved good verification. to a certain extent, the model and the algorithm are proposed to solve the problem of medical waste disposal, based on transit temporary storage stations, which we are convinced will have far-reaching significance for china and other countries to dispatch medical waste in response to such public health emergencies. medical waste refers to wastes produced by medical and health institutions in the course of medical treatments, preventions, health care, and other related activities, which are directly or indirectly infectious, toxic, and have other hazardous characteristics. for large and medium-sized cities, how to set up an effective medical waste transport system has long been the focus of the world. the academic community has also put forward many ideas and solutions. for example, gerasimos mantzaras [1] developed an optimization model to minimize the cost of a collection, haul, transport, treatment and disposal system for infectious medical waste (imw). qiu cheng [2] believed that a bot (build-operate-transport) model could be used to solve the problem of medical waste treatment, and selected kunming city as an example for the research. liu xiaoli [3] analyzed the current situation of medical waste transport in primary hospitals with wuhan as an along with a novel decoding method to solve cvrp [30] ; mauro dell'amico proposed a new iterated local search metaheuristic method for cvrp that also includes a vital mechanism from the adaptive large neighborhood search combined with further intensification through local search [31] ; r. baldacci described a new integer programming formulation for cvrp based on a two-commodity network flow approach [32] ; fernando afonso santos introduced a branch-and-cut-and-price algorithm for two-echelon cvrp [33] ; jiafu tang developed a beam-mmax algorithm that combines a max-min ant system with beam search to solve cvrp [34] ; jacek mańdziuk proposed a solution to cvrp with traffic jams, which relies on application of the upper confidence bounds applied to the trees method [35] ; juan rivera presented a mixed integer linear program and a multistart iterated local search, calling a variable neighborhood descent to solve multitrip cumulative cvrp [36] ; vincent f. yu presented a symbiotic organism search heuristic method for solving cvrp [37] ; ehsan teymourian presented an enhanced intelligent water drop and cuckoo search algorithm for solving cvrp [38] . most of the research mentioned above only focused on the improvements of the cvrp solution and some preliminary applications of the theoretical model without considering practical applications such as the transport of medical waste. considering the particularity of the transport problem of medical waste, it is of paramount importance to establish a targeted model. in terms of the algorithm, the specific model discussed in this paper not only simplifies cvrp, but also involves location and its allocation; the algorithm above has its limitations, and we need to put forward a specific algorithm to solve this model. moreover, due to the emergency, urgency, and criticality of the pandemic, the establishment of an efficient transport system model of medical waste has become a priority in response to the emergent public health crash. in this paper, the immune algorithm, the q-value method, and the improved ant colony algorithm are applied to the model to solve the path planning problem of the transport of medical waste. finally, the strategy under the simulation parameters is given in the simulation experiment. the model could provide a valuable reference for emergency vehicle scheduling and transport of medical waste before and after such unprecedented public health events. the rest of this paper is organized as follows: in section 2, a complete mathematical description of the model is proposed. in section 3, the theory of the immune algorithm and the ant colony algorithm, which are used to lead to our improved algorithm, is explained, in addition to the initialization of some key parameters. in section 4, wuhan is taken as an example to verify the algorithm and to solve the model in the actual background. additionally, section 5 gives a review and conclusion of the whole work. the studies of this paper are to establish a number of transport stations and an efficient medical waste transport model between hospitals and transport stations and, eventually, optimize the transportation paths. this problem is a nonconvex and nonsmooth nonlinear programming problem with complex constraints. it is an np-hard problem, and it is difficult to solve in a traditional way. the problem can be divided into the following two subproblems: the first subproblem is to establish several waste transport stations for numerous existing hospitals. when establishing the model of the transport stations, factors including the environment and traffic need to be considered. the second subproblem is based on the first subproblem. after establishing the transport stations, we need to optimize the transportation paths between each of the hospitals and the corresponding transport stations. in path optimization, factors such as the load capacity of the transport vehicle and the amount of generated waste are taken into account. the second subproblem is similar to cvrp. in addition to the two problems above, considering the practical background of this problem, to reasonably initialize the amount of medical waste and the number of transport vehicles is also required. however, these problems are not major. as a result, their solutions are not presented as separate subproblems. to solve the problem of finding suitable transport stations, we have established the following mathematical description: explanation of the variables used in the model: n = 1, 2, . . . n is the serial number set of all hospitals; s is the upper limit of the distance between the transport station and the hospital we set; m i is the set of candidate transport stations, with a distance to hospital i less than s; ω i represents the amount of medical waste generated by hospital i every day; d ij represents the distance from hospital i to the nearest transport station j; z ij is a boolean variable, indicating whether there is a transshipment relationship between hospital i and transport station j. when z ij is 1, it means that the waste of hospital i will be transported to the transport station j; h j is a boolean variable. when h j is 1, it indicates that location j is selected as the relay station. p is the number of transport stations we set, which is a constant. explanation of the formula in the model: formula (1) is the goal of this model, which ensures a minimum transportation cost from the hospital to the transport station; formula (2) ensures that the waste of each hospital will only be transported to the only transport station corresponding to this hospital, which is convenient for management; formula (3) ensures that hospital waste can only be transported to the location set as a transport station; formula (4) ensures that the number of points selected as a transport station is p; formula (5) indicates that z and h are boolean variables; formula (6) indicates that all transport stations should be within the transportation range of the hospital. in addition to the establishment of these transport stations, we also need to consider their impact on ecological and human-activity areas. therefore, on the basis of the mathematical model, we also used the buffer analysis technology of arcgis software to exclude the areas where the environmental assessment indicators are unqualified. this exclusion belongs to the application of the model. thus, this exclusion is mentioned in section 3.4.1, later in the article. in the first problem, we established several transport stations, and each transport station is responsible for a certain number of hospitals. the waste of these hospitals only needs to be transported to their corresponding transport stations. hence, in path optimization, considering the transportation between each transport station and the corresponding hospital, as well as the transportation between the hospitals responsible for the same transport station, are needed. nothing else needs to be considered. for example, suppose there are two transport stations, a and b. a is responsible for two hospitals, c and d. then, we merely need to consider the transportation between a, c, and d, not the transportation between a and b, nor the transportation between b, c, and d. therefore, the problem has been simplified to a scheduling problem between one transport station and its corresponding hospitals. after understanding this simplification, we improved cvrp to make it suitable for our problem. then, we could get the following mathematical model: explanation of the variables used in the model: for one transport station, m is the number of transport vehicles we assign to it; d i is the amount of daily waste generated by hospital i; c ij is the distance of the transport vehicle from hospital i to hospital j; b k is the capacity of transport vehicle k; x k ij is a boolean variable used to indicate the vehicle's path. when x k ij is 1, it means that vehicle k visits hospital j immediately after visiting hospital i. explanation of the formula in the model: formula (7) is the goal of the model, which ensures that the transportation path between each transport station and its corresponding hospitals is the shortest; formula (8) indicates that the transport vehicles depart from the transport station and return to the transport station after completing the transportation task. each car's path forms a hamilton tour; formulas (9) and (10) indicate that the vehicle must serve all hospitals and they can only be served once; formula (11) indicates that when each vehicle serves the hospitals, its own load cannot be lower than the total amount of medical waste of the hospitals it passes through. evolutionary algorithms have strong robustness to solve complex optimization problems [39] . the immune algorithm (ia) is a new intelligent algorithm inspired by biological immune systems. it applies the diversity of the immune system to generate and maintain the diversity of the population, which overcomes the "premature" problems that are difficult to deal with in the general optimization process, especially in the multimodal function, and finally obtains the global optimal solution [40] . the ant colony optimization (aco) algorithm, as one of the modern heuristic algorithms, has received wide attention since it was proposed. it has the advantages of positive feedback, parallelism, and robustness, which show good performance in solving task allocation and path optimization. however, at the same time, the ant colony algorithm also has some defects, such as when solving large-scale problems, as problems such as long operation time, slow convergence speed, and ease of getting into the local optimal solution frequently happened. the tabu search (ts) algorithm constructs a tabu table to avoid getting into the global optimal solution and improves the optimization ability of the algorithm. in this paper, a hybrid intelligent algorithm of ia-aco-ts is proposed to solve the problem of the model in a realistic background. as an extension of the emerging intelligent algorithm and the genetic algorithm, the immune algorithm has good robustness and global search ability for the location of the transport station, the coordinates of the distribution of hospitals, and the transport station are selected. for the path optimization problem between the transport station and the hospitals, we used the ant colony optimization algorithm and the tabu search algorithm to solve it, which is a vehicle routing problem with load constraints (cvrp). considering that the ant colony algorithm can easily fall into local optimum and its stability is not good enough, we optimized the pheromone updating mechanism using the basic idea of the tabu search algorithm and set the tabu table and aspiration criterion in order to improve the effectiveness of the algorithm to solve the problem. the specific process of the immune algorithm is shown in the flowchart in figure 1 . we can find more specific information in [41] . if the memory library is not empty, then the antibody population is generated from the memory library. otherwise, the initial population would be generated in the feasible solution space randomly. simple coding is used here. each selection of the location can produce an antibody of length ( if the memory library is not empty, then the antibody population is generated from the memory library. otherwise, the initial population would be generated in the feasible solution space randomly. simple coding is used here. each selection of the location can produce an antibody of length p (p for the number of transport stations), while each antibody represents the sequence selected for the hospital to which the transport station belongs. for example, consider the problem containing 10 hospitals, with 1 to 10 being the sequence of hospitals. suppose you pick three of them, and antibody 1, 2, 3 represent a feasible solution, which means 1, 2, 3 have been chosen for the transport stations. (1) affinity between antibody and antigen antibody-antigen affinity indicates the recognition degree of antigen to antibody. according to this model, we set up affinity function a: the first term of the denominator is the objective function of the model, and the second term gives a penalty function to the solution violating the distance constraints. c is a large, positive number. we use the affinity between the antibody and antigen as a fitness function. (2) affinity between antibodies the antibody-antibody affinity reacts to the degree of similarity between antibodies. in this paper, we use the r-continuous bit matching rule proposed by forrest in 1994 to calculate the affinity. where k v,s is the number of the same bits between antibody v and s. l is the length of the antibody. ( the concentration of the antibody is the percentage of the antibody's population to the whole population. (4) expected reproductive probability in a population, the expected reproductive of each individual is determined in part by antibody-antigen affinity a and antibody concentration. 3.1.4. immune operation (1) selection. we used the roulette selection mechanism for select operation. the individual selection probability is expected to be the more reproductive probability. (2) the algorithm uses a single-point crossover for crossover operation. (3) mutation random selection of mutation bits is used for mutation operation. ant colony optimization (aco) is an optimization algorithm that simulates the foraging behaviors of ants. it was first proposed by italian scholar dorigo, m. and others in 1991 and used in solving tsp (the traveling salesman problem) for the first time. aco uses the concept of pheromones to simulate the communication mechanism between individuals, which endows the artificial ant with certain memory abilities, so the path chosen would be optimized gradually with the increase of the number of drops. the pheromone update formula for each path is presented as follows: the formula represents the updating of pheromone on path (i, j) at time (t + n); τ ij (t) represents the pheromone on path (i, j) at time t; ρ represents the information volatilization factor. when the ant colony algorithm is used to solve cvrp, ants produce pheromones on each path. the pheromones indicate the attraction degree of the next customer j to the vehicle k. when the vehicle's load meets the needs of customers, the vehicle will select customers according to the transport rules we set. after all the selected customers form loops, the pheromone of each path is updated, and then an iteration is operated. when the iteration reaches the maximum number of times, a pareto solution can be obtained. compared with other heuristic algorithms, aco has higher performance. when ant k is at node i, solve for the probability density function to the next node according to the following rules: in the expression, τ ij represents the concentration of pheromone on edge (i, j), η ij is the attraction of transporting from one node to another, and we could let η ij = 1 d ij , where d ij is the distance between the nodes. n k i (t) is the set of optional nodes. when the transport probability is worked out, a random number table is generated to determine the next transport station. according to the above description, aco is applied to solve the vehicle routing problem in a specific region. the steps of the algorithm are as follows: (1) parameters initialization. set the maximum number of iteration n c , the current optimal shortest path length shortest len , the customer demand load[j], and the current optimal path tabu table tabu min . calculate the pheromone's initial value τ 0 , transport attractiveness η ij (i, j = 1, 2, . . . .tabu and the optimal path is updated globally. the specific process of the whole algorithm is shown in the flowchart in figure 2 . replace with [ ]. and the optimal path is updated globally. the specific process of the whole algorithm is shown in the flowchart in figure 2 . according to "technical principles for environmental impact assessment of construction projects of hazardous waste and medical waste disposal facilities (for trial implementation)", the location of hazardous waste and medical waste disposal facilities must strictly abide by the relevant provisions of national laws, regulations, and standards. additionally, the site selection should be based on a comprehensive analysis of the social environment, natural environment, site environment, engineering geology, hydrogeology, climate, emergency rescue, and other factors. according to the assessment guidelines of the actual situation in wuhan, this paper summarizes the exclusion criteria that are not suitable for the construction of medical waste disposal facilities in the analysis process using arcgis, as shown in table 1 . under such epidemics, the distribution of limited carrying capacity is a common resource allocation problem, which is a typical case of the application of mathematics in the political field. the goal is to be as fair and reasonable as possible when a large group allocates certain resources to a small group. since carrier forces are quantized, the key to solving the problem is to propose a fairness measure that satisfies the following five principals: 1. an increase in population on one side would not result in the loss of a place on the other; 2. on an average basis throughout the period, each side will receive its own share; 3. increases in the total number of places would not result in a decrease in the number of places for one side; 4. neither side's places will deviate from its proportional places; 5. the absence of a place transport from one side to the other will bring both sides closed to their share. since there is no absolute fair distribution, people have devoted themselves to the study of relative fairness. the famous q − value method was developed in 1982 by d.n. burghes and i. huntley, which is a simple method that can overcome some contradictions of other methods, so it has been widely used in the problem of fair allocation of resources. for the specific problem in this paper, we have the following model: suppose that there are m vehicles participating in n distributable transport stations, where the resources of i are p i . the total resource of m is p = m i=1 p i , and the vehicles for i are n i . how do we find a set of integers n 1 n m that make m i=1 n i = n as fair as possible? the ideal fair distribution scheme is the distribution according to the proportion of resources; that is, the number that the i should distribute is n i = p i p n, which often is not an integer, and a "round-off" leads to unfairness, so the classical q − value method was put forward. the q − value method is used to derive a standard quantity q i for the allocation of seats, m) . according to it, we determine which side should be allocated the next seat, as follows: first, each side is assigned a seat based on the calculated value of qi. the larger side has priority to get the next seat. then, calculate the value again, and so on, until all seats are allocated. we applied the q − value method to solve the problems of assigning buses to each transport station in wuhan. in this paper, the total quantity of waste in each transport station is taken as the parameter p in the method, and it is known that wuhan has 50 vehicles that can transport waste at present. the p-value is substituted into the formula, and the total number of vehicles assigned to each transport station is solved circularly. the q − value method is used to allocate the vehicles, and the carrying capacity is reasonably distributed in each area of wuhan so that the existing manpower and material resources can be used more evenly and efficiently. based on the data we have, we initialize the amount of medical waste generated by hospitals of all levels. the result is shown in table 2 . for the amount of medical waste, the number is initialized by statistics. hospitals are divided into three levels according to the objective hospital grade, with the lowest level being 1 and the remaining two levels being 1.25 and 1.54, respectively. in this model, we consider the temporary shelter hospitals established during the special period of the pandemic. considering that the shelter hospitals only accept patients with coronavirus and their scale is limited, taking into account the fact that this part of the patients' household waste would be classified as medical waste, all the shelter hospitals in the second class are clarified. since the outbreak of covid-19 in wuhan in december 2019, the epidemic has escalated rapidly, with more than 400,000 confirmed cases worldwide and a total of 35 countries declaring a state of emergency. as another significant field of epidemic prevention and control, the treatment of highly infectious medical waste has also been attached with great importance by the chinese government. with the reference of the latest data from the ministry of ecology and environment of the people's republic of china, the average daily output of medical waste in wuhan before the outbreak was 400,000 tons, while after the epidemic developed at an unprecedented level, the topmost output of medical waste was 2.4 million tons, whose rate was much faster than its incineration at medical waste disposal centers. during the period of epidemic prevention and control, medical waste generated from the medical treatment of confirmed and suspected patients and their close associations, as well as people isolated at home, was highly contagious, and therefore territorial medical waste was completely cleaned every day, which burdened the medical waste disposal units heavily. since the disposal centers did not have excess disposal capacity, many designated treatment hospitals also needed to concentrate on sanitizing the excessive medical waste immediately. although wuhan's medical waste treatment capacity has greatly improved, it is still in a "tight balance", with a daily medical waste loading rate of 93.2 percent, as the director of the emergency response office of the chinese ministry of ecology and environment said at a press conference. he mentioned that we are now faced with many problems, such as the relative lag of the linkage efficiency of various positions, the inability to transport medical waste in a punctual way, and the high pressure on communities and medical institutions (including 48 designated hospitals and 16 shelter hospitals). the question of how to solve these problems of the existing medical waste management system in public health emergencies is considerable, for further reducing the risk of secondary transmission of the virus, reducing the transportation time cost of medical waste, and promoting the progress of epidemic prevention and control. based on the major public health event in wuhan, the transport efficiency of medical waste is not enough; this paper takes wuhan during the epidemic period as an example to verify our model. the data of wuhan is used for data visualization (dataset information, hospital/shelter hospital coordinates and relay station coordinate scatter points, ia-aco-ts parameter setting, result visualization) to verify the applicability and validity of the model. the research also provides the perspective of medical waste transport for the world to fight against the epidemic. the first step in setting up medical waste disposal sites is using the criteria of table 2 to exclude inappropriate areas based on gis software. as shown in figure 3 , the yellow areas are unsuitable and the pink areas are suitable for the construction of medical waste disposal facilities. given that most of the clinical waste is generated in urban areas, in order to minimize transportation costs, we needed to select a location that is closer to the city center, acting as the final disposal point, the coordinates of which are 30.491111, 114.182922. using the immune algorithm to optimize our calculation, we obtained the geographical coordinates of each relay station and then screened the stations according to the environmental evaluation criteria. the result is shown in figure 4 and table 3 . as shown in figure 5 , with the increase in the number of iterations, the results gradually converged and we obtained a relatively stable optimal solution. the first step in setting up medical waste disposal sites is using the criteria of table 2 to exclude inappropriate areas based on gis software. as shown in figure 3 , the yellow areas are unsuitable and the pink areas are suitable for the construction of medical waste disposal facilities. given that most of the clinical waste is generated in urban areas, in order to minimize transportation costs, we needed to select a location that is closer to the city center, acting as the final disposal point, the coordinates of which are 30.491111, 114.182922. using the immune algorithm to optimize our calculation, we obtained the geographical coordinates of each relay station and then screened the stations according to the environmental evaluation criteria. the result is shown in figure 4 and table 3 . the − value method is used to assign the corresponding vehicles to each transport station. the error function is defined as ℎ is the staging area, is the number of vehicles allocated, and is the proportion of waste to the total. after calculation, the vehicle allocation and the resulting error are shown in table 4 . the cumulative error is = 0.02897. this result is in line with the actual demand, which means the distribution effect is good. to demonstrate the effectiveness of our algorithm, we applied real data from wuhan, including its current capacity and the distribution of hospitals, as well as the shelter hospitals, to the model. the final road map is shown in figure 6 . the q − value method is used to assign the corresponding vehicles to each transport station. the error function is defined as where i is the staging area, n is the number of vehicles allocated, and p is the proportion of waste to the total. after calculation, the vehicle allocation and the resulting error are shown in table 4 . the cumulative error is ε = 0.02897. this result is in line with the actual demand, which means the distribution effect is good. to demonstrate the effectiveness of our algorithm, we applied real data from wuhan, including its current capacity and the distribution of hospitals, as well as the shelter hospitals, to the model. the final road map is shown in figure 6 . as it can be seen, there are eight relay stations in total in the diagram, which are color-coded. each transport station has its corresponding hospital. the green line is the result of path optimization by utilizing the ant colony-tabu hybrid algorithm. this result ensures the efficiency of medical waste dispatch in the area controlled by each transport station effectively. as it can be seen, there are eight relay stations in total in the diagram, which are color-coded. each transport station has its corresponding hospital. the green line is the result of path optimization by utilizing the ant colony-tabu hybrid algorithm. this result ensures the efficiency of medical waste dispatch in the area controlled by each transport station effectively. focusing on each of the transport stations, we get the information shown in figure 7 . with the increase in the number of iterations, the convergence of the algorithm is shown in figure 8 . as can be seen in figure 8 , with the increase of the number of iterations, the results gradually converge and obtain a relatively stable optimal solution. in view of this, we are certain that the model of this paper has a good fit and dispatching effect even for wuhan, which is a very complicated city. therefore, by giving different parameters to different cities, it is quite convenient to apply our strategy, which would provide an effective scheme to optimize the scheduling of the whole urban transport system of medical waste. in past studies, balvinder singh gill et al. studied the transmission of covid-19 in malaysia [42] , and carol i. blvd et al. made algorithmic scheduling for the delivery of medical forces [43] . compared to their approach, our approach is more comprehensive, practical, and provides a better picture of what delivery scheduling actually looks like when covid-19 outbreaks occur in cities. in figures 6 and 7 , the center point of each small area is the medical center of the area, and the green line segment indicates that if two points belong to the same subdivision area, they are connected by a line segment. the distribution of cars is obviously different at disparate transport stations. in the areas where the hospitals are more concentrated, the routes are more complex. with the increase in the number of iterations, the convergence of the algorithm is shown in figure 8 . the outbreak of covid-19 in wuhan has exposed the inefficiency of transporting medical waste and urges us to solve this impending problem. therefore, in this paper, several temporary storage points were discussed above, according to the environmental impacts and assessment criteria, utilizing the − value method to allocate medical waste transport vehicles, and applying the immune-based ant colony algorithm, together with the tabu search algorithm, to arrange the correct pathways of waste transportation. eventually, a complete "build-match-transport" system model for medical waste is established during these procedures. the application of this model to the epidemic situation of wuhan has achieved excellent results, which has practical significance and enlightenment to the emergency response and dispatch of wuhan and other major cities. as can be seen in figure 8 , with the increase of the number of iterations, the results gradually converge and obtain a relatively stable optimal solution. in view of this, we are certain that the model of this paper has a good fit and dispatching effect even for wuhan, which is a very complicated city. therefore, by giving different parameters to different cities, it is quite convenient to apply our strategy, which would provide an effective scheme to optimize the scheduling of the whole urban transport system of medical waste. in past studies, balvinder singh gill et al. studied the transmission of covid-19 in malaysia [42] , and carol i. blvd et al. made algorithmic scheduling for the delivery of medical forces [43] . compared to their approach, our approach is more comprehensive, practical, and provides a better picture of what delivery scheduling actually looks like when covid-19 outbreaks occur in cities. the outbreak of covid-19 in wuhan has exposed the inefficiency of transporting medical waste and urges us to solve this impending problem. therefore, in this paper, several temporary storage points were discussed above, according to the environmental impacts and assessment criteria, utilizing the q − value method to allocate medical waste transport vehicles, and applying the immune-based ant colony algorithm, together with the tabu search algorithm, to arrange the correct pathways of waste transportation. eventually, a complete "build-match-transport" system model for medical waste is established during these procedures. the application of this model to the epidemic situation of wuhan has achieved excellent results, which has practical significance and enlightenment to the emergency response and dispatch of wuhan and other major cities. an optimization model for collection, haul, transfer, treatment and disposal of infectious medical waste: application to a greek region. waste manag analysis on medical waste management and disposal in kunming city an optimization model for collection, haul, transfer, treatment and disposal of infectious medical waste: application to a greek region analysis on medical waste management and disposal in kunming city current situation and countermeasures of medical waste management in primary medical institutions of wuhan. chin medical waste management in jordan: a study at the king hussein medical center safe transportation of biomedical waste in a health care institution public opinion polarization by individual revenue from the social preference theory 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new efficient approach for solving the capacitated vehicle routing problem using the gravitational emulation local search algorithm an improved hybrid firefly algorithm for capacitated vehicle routing problem analytic centre stabilization of column generation algorithm for the capacitated vehicle routing problem bilayer local search enhanced particle swarm optimization for the capacitated vehicle routing problem an adaptive iterated local search for the mixed capacitated general routing problem an exact algorithm for the capacitated vehicle routing problem based on a two-commodity network flow formulation a branch-and-cut-and-price algorithm for the two-echelon capacitated vehicle routing problem beam search combined with max-min ant systems and benchmarking data tests for weighted vehicle routing problem uct in capacitated vehicle routing problem with traffic jams a multistart iterated local search for the multitrip cumulative capacitated vehicle routing problem symbiotic organisms search and two solution representations for solving the capacitated vehicle routing problem enhanced intelligent water drops and cuckoo search algorithms for solving the capacitated vehicle routing problem evolutionary algorithm based offline/online path planner for uav navigation artificial immune systems: theory and applications artificial immune system assessment of covid-19 waste flows during the emergency state in romania and related public health and environmental concerns modelling the effectiveness of epidemic control measures in preventing the transmission of covid-19 in malaysia the authors declare no conflict of interest. key: cord-136515-e0j2iruo authors: xue, ling; jing, shuanglin; miller, joel c.; sun, wei; li, huafeng; estrada-franco, jose guillermo; hyman, james m; zhu, huaiping title: a data-driven network model for the emerging covid-19 epidemics in wuhan, toronto and italy date: 2020-05-28 journal: nan doi: nan sha: doc_id: 136515 cord_uid: e0j2iruo the ongoing coronavirus disease 2019 (covid-19) pandemic threatens the health of humans and causes great economic losses. predictive modelling and forecasting the epidemic trends are essential for developing countermeasures to mitigate this pandemic. we develop a network model, where each node represents an individual and the edges represent contacts between individuals where the infection can spread. the individuals are classified based on the number of contacts they have each day (their node degrees) and their infection status. the transmission network model was respectively fitted to the reported data for the covid-19 epidemic in wuhan (china), toronto (canada), and the italian republic using a markov chain monte carlo (mcmc) optimization algorithm. our model fits all three regions well with narrow confidence intervals and could be adapted to simulate other megacities or regions. the model projections on the role of containment strategies can help inform public health authorities to plan control measures. the development of international trade and tourism has accelerated the spatial spread of infectious diseases. the limited data available on emerging epidemics adds to the challenge of mitigating the spread of emerging infections [1] . the unprecedented coronavirus disease 2019 outbreak began at the end of 2019. the number of reported cases keeps rising worldwide and thousands of lives have been claimed. this pandemic is having an enormous impact on world health, disturbing the stability of the societies, and triggers great economic losses. predicting the future of the pandemic, assessing the impacts of current interventions, and evaluating the effectiveness of alternate mitigation strategies are of utmost importance for saving lives. mathematical models can be used to understand the dynamics of epidemics and help inform control strategies. a numerous number of models are being used to project the current covid-19 pandemic. ziff and ziff analyzed the number of reported cases for wuhan (china) and showed that the growth of the daily number of confirmed new cases indicates an underlying fractal or small-world network of connections between susceptible and infected individuals [2] . wang et al. developed an seir model to estimate the epidemic trends in wuhan, assuming the prevention and control measures were either sufficient or insufficient to control the epidemic [3] . kucharski et al. combined a stochastic transmission model with data on cases of covid-19 in wuhan and international cases to estimate how the transmission had varied over time between january and february in 2020 [4] . kraemer et al. analyzed the impact of interventions on the spread of covid-19 in china using transportation data [5] . chinazzi et al. used a global meta-population disease transmission model to project the impact of travel limitations on the national and international spread of the epidemic. they showed that the travel restriction of wuhan, china had a more marked effect on the international scale than that on mainland china [6] . ferguson et al. found that optimal mitigation policies (combining home isolation of suspected cases, home quarantine of those living in the same household as suspected cases, and social distancing of the elderly and others at most risk of severe disease) might reduce peak healthcare demand by 2/3 and deaths by half [7] . likewise, hellewell et al. developed a stochastic transmission model and found that highly effective contact tracing and case isolation is enough to control a new outbreak of covid-19 within three months in most scenarios [8] . zhang et al. fitted the reported serial interval (mean and standard deviation) with a gamma distribution to estimate the basic reproduction number at the early stage of a covid-19 outbreak, indicating the potential of second outbreaks [9] . maier et al. developed a compartmental model dividing individuals into susceptible, exposed, removed, and quarantined symptomatically infected and showed that the distinctive subexponential increase of confirmed cases in mainland china could be explained as a direct consequence of containment policies that effectively deplete the susceptible population [10] . most of these models are based on assuming the population is homogeneously mixing, that is, the contacts between people are random and uniformly distributed throughout the population. however, different individuals may have varying numbers of acquaintances and contacts in the real world. the important role that heterogenous contact networks play in the transmission dynamics of infectious diseases is often overlooked [11] . models that take into account contact heterogeneity better represent the actual transmission network through a population and are more likely to capture the true epidemic dynamics. disease propagation is closely linked with the structure of social contact networks [12] . the ubiquitous diversity in contact patterns and heterogeneity among individuals depends on differences in social structures, spatial distances, and behavior [13] . the heterogeneity exists at a wide range of scales and leads to highly variable transmission dynamics of infectious diseases [14, 15] . many real-world social networks can be characterized by a random watts-strogatz (ws) small-world network [16, 17] . in a small-world network, most nodes can be reached from every other node by a small number of hops or steps, even if they are not immediate neighbours. this type of network model allows us to adapt changes to some realistic network structures and examine the effects of control and intervention countermeasures such as social distancing, self-isolation, and personal protection. the framework and analysis can be applied to study the transmission dynamics in different regions and many other infectious diseases. the covid-19 epidemic in wuhan ended in april, while the epidemics in the greater toronto area (gta, canada) and the italian republic are continuing to grow. we fit the parameters of our network model to the confirmed cases in each of these regions. although wuhan, toronto, and italy differ in some ways, the way that sars-cov-2 is transmitted from one person to another is quite similar. individuals may acquire infection from other infectious individuals, even if they do not contact each other directly. the watts-strogatz model supplies an ideal tool to study the spread of epidemics among individuals even if their locations are not considered. we used the watts-strogatz model to generate random networks with the small world properties appropriate for infectious disease transmission in these cities [16, 17] . the epidemic curves are all fitted very well using the small-world network structure models, indicating that the typical small-world property is able to capture the contact patterns during covid-19 epidemics. the differences in these fitted parameters and starting times reflect the differences in the underlying transmission mechanisms and potential spread in the regions. the model then projected the trends of covid-19 spread by simulating epidemics in the wuhan, toronto, and italy networks. our findings can guide public health authorities to implement effective mitigation strategies and be prepared for potential future outbreaks. we develop a network-based model by extending the network sir model [18] by incorporating the characteristics of covid-19 transmission to assess the spread of the disease in heterogeneous populations. we derive the explicit expression of the epidemic threshold and discuss the final epidemic size for the network model. we classify individuals by their average number of contacts in a typical day (time unit for the modeling) represented on the network by their degree k (k = 1, 2, · · · , n). individuals with degree k are divided into susceptible (s k ), exposed (e k ), asymptomatically infected (a k ), symptomatically infected (i k ), hospitalized (h k ), recovered (r k ), and dead (d k ) states. our model is formulated as follows and d k = d k /n k represent the fractions of susceptible, exposed, asymptomatically infected, symptomatically infected, hospitalized, recovered, and dead individuals with degree k, respectively. here, n k is the total number of individuals with degree k, and n k = s k +e k +a k + i k +h k + r k +d k , and s k +e k +a k + i k +h k + r k +d k = 1. p (k ′ |k) represents the probability that an edge from a node with degree k connects to a node with degree k ′ . for uncorrelated networks, p (k ′ |k) = k ′ p (k ′ )/ k [19] . since the node with degree k ′ shares an edge with the node degree k, and only has (k ′ − 1) free edges, a fraction k ′ −1 k ′ of nodes may acquire the infection. we assume that the transmission rates of symptomatically infected individuals and asymptomatically infected individuals are β and σβ, respectively. the factor σ accounts for the different transmission rates between asymptomatically infected individuals and symptomatically infected individuals. βks k k ′ k ′ −1 k ′ p (k ′ |k)i k ′ represents the fraction of nodes with degree k infected by symptomatically infected nodes, and σβks k k ′ k ′ p (k ′ |k)σa k ′ represents the fraction of nodes with degree k infected by asymptomatically infected nodes. here, k ′ −1 k ′ p (k ′ |k)i k ′ represents the probability that an edge from a degree k node connects to a symptomatically infected node with degree k ′ , and k ′ −1 k ′ p (k ′ |k)σa k ′ represents the probability that an edge from a degree k node connects to an asymptomatically infected node with degree k ′ . in model (2.1), the term (1 − k ′ −1 k ′ p (k ′ |k)i k ′ ) represents the probability of not being infected by a symptomatically infected node with degree k ′ , and (1 − k ′ −1 k ′ p (k ′ |k)σa k ′ ) represents the probability of not being infected by an asymptomatically infected node with degree k ′ . thus, is the probability that a node will neither be infected by a symptomatically infected nor be infected by an asymptomatically infected neighbor with degree k ′ , and is the probability of being infected by a symptomatically infected or an asymptomatically infected neighbor with degree k ′ . therefore, the susceptible individuals are infected at rate and enter the exposed state. after incubation period with a mean time of 1/ǫ days, exposed individuals become symptomatically infected and asymptomatically infected with probabilities δ and 1−δ, respectively. symptomatically infected individuals are hospitalized at rate ξ, and die at rate µ. asymptomatically infected individuals, symptomatically infected individuals, and hospitalized individuals recover at rates γ a , γ, and γ h , respectively. both the hospitalized individuals and symptomatically infected individuals die at rate µ. we derive the epidemic threshold to predict whether the epidemic will spread or die out and derive final epidemic size to quantify the total number of infected individuals. to estimate the transmission potential of the epidemic, we derive the important epidemic threshold, r 0 , defined as the average number of secondary cases produced by an infected individual in a completely susceptible population [20] . there exists a disease-free equilibrium, (s 1 , · · · , s n , e 1 , · · · , e n , a 1 , · · · , a n , i 1 , · · · , i n , h 1 , · · · , h n , r 1 , · · · , r n , d 1 , · · · , d n ) t = (1, · · · , 1, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0) t =: e 0 . we compute r 0 following the next generation matrix approach presented by van den driessche and watmough [21] . for simplicity, we only consider the compartments related to infection, namely, e k , a k and i k , and rewrite the equations as the difference between vectors f k and v k following the notations in [21] [ here, f ik represents the rate at which new infections are produced and v ik represents the rate at which individuals transfer between compartments, i = 1, 2, 3 and k = 1, · · · , n for model (2.1). the jacobian matrix f is where z = (z j ) = (e 1 , · · · , e n , a 1 , · · · , a n , i 1 , · · · , i n ) and the matrices v and v −1 are where i n is the n × n identity matrix, and the next generation matrix is since the rank of matrix f ′ is 1, the spectral radius of f ′ is its trace, i.e., it follows from (2.2) that the basic reproduction number r 0 becomes where β 1−δ γa σ and β δ γ+µ+ξ represent the average numbers of secondary cases produced by an asymptomatically infected individual and a symptomatically infected individual in a homogeneously mixed population, respectively. the hence, model (2.1) can be simplified as for a homogeneous network where all nodes have identical degree k, model (2.3) can be reduced to the following model by model (2.4) and a direct calculation, we have (2.5) by the first equation in model (2.4), we further have where s(+∞) = lim t→∞ s(t). to determine the final size of susceptible individuals, s(+∞), we set where y 0 = s 0 + e 0 . by (2.5), (2.6) and the definition of f (x), we have it is clear that f (x) is a positive, increasing, strictly convex function, and f (s 0 ) < s 0 . thus, f has a unique fixed point s + in the interval (0, s 0 ), which can be calculated numerically by using the iteration method and where f m denotes composition of f for m times. then, the final size of susceptible individuals for a homogeneous network, s(+∞), can be determined by s + . we now derive the final size for heterogeneous networks. integrating the first equation in model (2.3) from 0 to t, we have by summing and integrating the equations in model (2.3), where y k (t) = s k (t) + e k (t). we set by equations (2.7),(2.8) and (2.9), we have where g k (0) ≥ 0, ∀k. therefore, for all k = 1, ..., n, the final size of susceptible individuals satisfies we define a map g : to analyze the properties of g(x), we shall introduce some notations. for the above definition defines a partial order in r n . for later use, we could extend this partial order to n × n matrices as follows. for any n × n matrices a, b, we have . . , w n (0)] t , by the definition of g(x) and partial order defined in (2.10), we have where g m is the composition function of g for m times. by the monotone criterion, we obtain due to the continuity of g, g(s) = s and g(s) = s. therefore, we have the following property [23] . due to the continuous differentiability of g, for any x ∈ r n and 1 ≤ i, j ≤ n. moreover, we shall simply write (2.11) in terms of the matrix form by . by the monotony of g, dg is also monotonous, i.e., dg(x) ≤ dg(y) for any 0 ≤ x ≤ y ≤ s(0). by utilizing the properties of w(x) and g(x), we can obtain the following theorem. (2) when w(0) > 0, g has a unique fixed point s ++ satisfying 0 ≪ s ++ < s(0). the proof of theorem 2.1 directly follows the proof in [23] . hence, the final size of susceptible individuals for a heterogeneous network, s(+∞), can be determined by s ++ to quantify the number of susceptible individuals left theoretically. we parameterized the model with reported data on covid-19 cases and presented forecasts of the epidemic trends for the three areas. we simulated the spread of covid-19 in wuhan, toronto, and italy on the watts-strogatz network with degree k min = 1 and k max = 10. the study period for wuhan starts from january 11, 2020, after the confirmed cases were reported, the public becomes aware of the infection and most people are trying to avoid gathering. the study period starts from january 26 for toronto and from january 31 for italy. in toronto and italy, usually people do not gather, especially after lockdown on wuhan city, the awareness of avoiding exposure to the virus is increasing. most people stay home during the study period, and the family sizes in wuhan, toronto, and italy on average are all around 3. therefore, the range of the node degrees is assumed to be between 1 and 10. the watts-strogatz model starts with a ring of n vertices in which each vertex is connected to its 2m nearest neighbors (m vertices clockwise and m counterclockwise). each edge is connected to a clockwise neighbor with probability p and preserved with probability 1 − p [19] , where the degree distribution is when p → 1, the expression reduces to a poisson distribution as follows in the simulations, we used this degree distribution. the total number of nodes for wuhan, toronto, and italy are 11081000, 5928000, and 59430000 as shown in table 1 , table 3 , and the rate at which the fraction of the cumulative number of cases changes is dc k /dt = ξi k , where c k (t) represents the fraction of the cumulative number of infected individuals with degree k. the number of newly infected can be expressed as where p k represents the number of new cases with degree k, and n k represents the total number of individuals with degree k. we run the mcmc simulation for 20000 iterations to fit the value of p k . zhou et al. showed that the median time from illness onset (i.e., before admission) to discharge was 22 days (iqr 18-25), whereas the median time to death was 18.5 days with iqr between 15 and 22 days [27] . we assume an exponential distribution for the time to recovery for asymptomatically infected individuals, symptomatically infected individuals, and hospitalized individuals. this results in the recovery rates γ a = γ = γ h = 1/22 per day, and the mortality rate, µ is 1/18.5 per day. the incubation period of covid-19 is around 7 days [4] , resulting in the progression rate ǫ = 1/7. qiu et al. reported that around 30% − 60% of people infected with covid-19 are asymptomatic or only have mild symptoms, and their transmissibility is lower, but still significant [28] . thus, we assume that the probability that an infected individual is asymptomatic is 1 − δ = 0.6, and σ = 1 for simulations. we divided the wuhan epidemic into four phases according to the reported data [3] . the first phase is before lockdown on jan 23, 2020. the second phase is between jan 24, 2020 and feb 1, 2020 when the hospitals were short of beds. the third phase is between feb 2, 2020 and feb 6, 2020 when the thunder god mountain hospital (tgmh) and fire god mountain hospital (fgmh) were put into use. the fourth phase began when doorto-door screening was implemented on feb 7, 2020 and tgmh, fgmh, and mobile cabin hospitals (mch) were put into use. the study period for toronto (canada) was decomposed into two phases, namely, the period before mar 18 and the period after mar 18 when the city announced the emergence and schools and universities in toronto were closed on mar 18. the study period for italy was divided into two phases. the early epidemic phase was between jan 31, 2020 and mar 8, 2020 when the infection was spreading through the northern provinces. the second period begins on mar 9, 2020 when the national lockdown started. the parameters and initial conditions of simulations for wuhan on the ws network are shown in table 1 . the probability of transmission through adequate contact is estimated by mcmc. the 5000 realizations of the basic reproduction numbers derived for wuhan using the parameter values listed in table 1 are shown in table 2 . from jan 11 to mar 31, we estimate that the mean reproduction number on the ws network decreases from 3.41 in the first phase to 5.34 × 10 −3 in the fourth phase. the epidemic on the ws network is shown in figure 1 . up to jan 23, 2020 when wuhan lockdown started, the estimated epidemic size is 3.96 × 10 6 . during the second stage, after the lockdown of wuhan and before the tgmh and fgmh were put into use, the predicted final size is 2.17 × 10 6 . thus, the lockdown of wuhan reduced the expected final size by 45.22%. during the third stage, after tgmh and fmgh were put into use, the final size is 1.02 × 10 5 . hence, the city lockdown and the usage of tgmh and fgmh reduced the final size by 97.42%. during the fourth stage, after mch was put into use, the predicted final size is 51269, and the expected final size of infection is reduced by 98.70% due to the increase of healthcare capacity. the variability of the numbers of confirmed new cases is consistent with the variability of the reproduction numbers listed in table 2 . in the first two phases, the epidemic spread rapidly with larger reproduction numbers that are larger than 1, and the numbers of infected cases increase. in the last two phases, the spread of disease is controlled, and the reproduction numbers are smaller than 1. in the third phase, because a large number of cases are confirmed by door-to-door screening and expanded healthcare capacity, the cumulative number of confirmed cases increased. on the other hand, the epidemic will die out because the reproduction number is less than one. in the fourth phase, the spread of the disease has been under control with the reproduction number being less than one. hence, the number of new cases decreases. the parameters and initial conditions of simulations for the gta are shown in table 3 . the 5000 realizations of the basic reproduction numbers derived for toronto using the parameter values listed in table 3 are shown in table 2 . the reproduction numbers are much smaller due to social distancing policy, school closure, as well as behavior changes. the summary of the simulations is shown in table 4 and table 5 . simulation results are shown in figure 2 . the peak size is 60.19 (95%ci: 47.42-72.97), the peak time is apr 2 (95%ci: mar 29-apr 7), and the final size is 2712 (95%ci: 1603-3820). the parameters and initial condition of simulations for italy is shown in table 6 . the 5000 realizations of the basic reproduction numbers derived for italy using the parameter values listed in table 6 are shown in table 2 . the reproduction numbers in the second phase are much smaller than that in the first phase due to the awareness of the severity of the epidemic. the summary of the simulation results is shown in table 7 and table 8 . figure 3 shows that the peak number of new cases is 5492 (95%ci: 5277-5708) on mar 26 (95%ci: mar 24-mar 27), and the final size is 2.59 × 10 5 (95%ci: 2.10 × 10 5 − 3.08 × 10 5 ). the close contacts identified by contact tracing will be quarantined due to exposure to covid-19 to see if they become sick. to evaluate the impact of mitigation strategies on the spread of covid-19, model (2.1) is rewritten as follows where sq k = sq k /n k represents the fraction of quarantined individuals with degree k. the parameter q represents the rate at which susceptible individuals are quarantined, and λ represents the rate at which the quarantined and uninfected close contacts transfer to the susceptible compartment again. in the simulations, we let λ = 1/14 to approximate a mean time of 14 days in the exposed state. for wuhan, the cumulative number of infected individuals after lockdown and tgmh, fgmh, as well as mch were put into use are shown in figure 4 . the results show that the lockdown and the increase in healthcare capacity are effective in controlling the numbers of confirmed cases. for toronto, the number of newly infected individuals and the cumulative number of infected individuals produced on the ws network after implementing additional containment strategies besides school closure are shown in figure 5 . we simulated the scenarios of implementing various containment strategies for toronto. simulation results showed that personal protection, reducing the node degrees of symptomatically infected individuals, and quarantine of close contacts are effective in reducing the peak epidemic size and final epidemic size. reducing the transmission rate β, by x% also reduces r 0 by x%. when β is reduced by 20% by personal protection or social distancing, the peak occurs one day earlier, and the final epidemic size is reduced by around 18%. when β is reduced by 40%, the peak occurs two days earlier, and the final epidemic size is reduced by around 33.3%. when q = 1/8, the peak occurs four days earlier, and the final epidemic size is reduced by 45.21%. when q = 1/4, the peak appears five days earlier, and the final epidemic size is reduced by 58.22%. when the node degrees of symptomatically infected individuals are reduced by 1, 2, and 3, the number of new cases produced per day at the peak is reduced by 13.74%, 26.93%, and 39.18%. the final epidemic size is reduced by 15.15%, 29.65%, and 43.55% when the node degrees of symptomatically infected individuals are reduced by 1, 2, and 3, respectively. for italy, the number of newly infected individuals and the cumulative number of infected individuals simulated on the ws network after implementing hypothetical containment strategies are shown in figure 6 . various scenarios of implementing mitigation strategies showed that the peak epidemic size and final epidemic size in italy are greatly reduced by personal protection, social distancing, behavior change of symptomatically infected individuals, and quarantine. the simulations show that the peak would have arrived earlier if the containment had been intensified. when the probability of contact transmission coefficient β, is reduced by 20% by personal protection or social distancing, the peak occurs one day earlier, and the final epidemic size is reduced by 21.56%. when β is reduced by 41.44%, the peak occurs one day earlier, and the final epidemic size is reduced by around 40%. when q = 1/8, the peak occurs six days earlier, and the final epidemic size is reduced by 52.87%. yet, when q = 1/4, the peak occurs eight days earlier, and the final epidemic size is reduced by 67.12%. when the node degree of symptomatically infected individuals is reduced by 1, 2, and 3, the number of new cases produced per day at the peak is reduced by 16.50%, 32.93%, and 49.11%, respectively. the final epidemic size is reduced by 17.90%, 34.70%, and 50.51% when the node degrees of symptomatically infected individuals are reduced by 1, 2, and 3, respectively. modelling the dynamics of covid-19 epidemics and assessment of mitigation strategies could be instrumental to public health agencies for surveillance and healthcare planning. for the models to be reliable, the simulated epidemic must account for the stochastic and heterogeneous contact among individuals. hence, we developed a network model that captured the contact heterogeneity among individuals. we applied the model to analyze the transmission potential, and mitigation strategies for curbing the spread of covid-19 epidemics in the cities of wuhan, china and toronto, canada, and in the italian republic. the epidemic threshold derived from our network model can be used to predict the risks of spreading scenarios. we also provided an explicit expression of the final epidemic size, which facilitates estimating the scale of an outbreak for any region of interest. our results provide insights in defining a mathematical framework for the analysis and containment of epidemic transmission in the real world. the flexible network model framework can simulate a wide range of mitigation strategies can be examined by the flexible model framework. it can be extended to quantify the effectiveness of personal protection, social distancing, reducing the node degree of infected individuals, and quarantine on the dynamics of epidemics in different regions. when the mitigation strategy is intensified, the model predicts that the number of new cases peaks earlier and the final epidemic size is greatly reduced. the social contact network structure and parameter values determine the transmission and epidemic course of such an emerging infectious disease. we choose the watts-strogatz to approximate real social networks, when the exact contact tracing data is unavailable. we assumed that the range of the node degree is between one and ten for each network in the absence of real contact tracing data, that is, on average each day an infected person would have between one and ten contacts where they could transmit the infection to another person. in the real world, the range of the degree will depend on the distribution of the household sizes of the region and time being studied. moreover, the network structure can be altered by behavior change of individuals during epidemics. when this happens, the network structure can be adapted in our model to predict the impact of these changes on the epidemic threshold, epidemic peak value, peak time, stopping time, and final size of infected population. the epidemics for the three places under study were fitted very well by our model with a small confidence interval. hence, the forecasts by the model can be reliable. we did not provide the stopping time since too many uncertainties may affect the duration of the epidemics. as shown in the simulations, the transmission dynamics for four phases in wuhan are quite different due to the variability on the intensity of interventions, the availability of healthcare facilities, as well as the utilization of personal protective equipment (ppe). the dynamics in the first phase is quite different from that in the second phase for toronto. the same phenomenon is observed in italy. at the early stage, almost no interventions were implemented, and the public was not aware of or did not pay much attention to the severity of the highly contagious disease. with the increase of the number of reported confirmed cases and with the aid of social media, the public becomes aware of the severe consequence and has increased the level of personal protection and have avoided gathering, so that the reproduction number decreases and the estimated epidemic size declines by reducing the node degree of the network. similarly, after applying the mitigation measures in italy on march 8 and closing all schools in toronto on march 18, the epidemics tend to be under control. hence, social distancing, self-isolation, quarantine, the utilization of ppe, and other measures of avoiding exposure to the virus can greatly reduce the size of infection during the covid-19 outbreak. therefore, it is essential to raise the awareness of these countermeasures to avoid contact between individuals. the possibility of recurrent outbreaks of the disease cannot be overstated. even if the number of new cases is declining, it is still necessary to continue taking protective measures to prevent the occurrence of future outbreaks. the social media should warn the public not to relax their vigilance against the contagion of such a highly infectious disease. infectious diseases of humans: dynamics and control fractal kinetics of covid-19 pandemic phase-adjusted estimation of the number of coronavirus disease early dynamics of transmission and control of covid-19: a mathematical modelling study the effect of human mobility and control measures on the covid-19 epidemic in china the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak impact of non-pharmaceutical interventions (npis) to reduce covid-19 mortality and healthcare demand feasibility of controlling covid-19 outbreaks by isolation of cases and contacts estimation of the reproductive number of novel coronavirus (covid-19) and the probable outbreak size on the diamond princess cruise ship: a data-driven analysis effective containment explains subexponential growth in recent confirmed covid-19 cases in china statistical inference to advance network models in epidemiology epidemics and percolation in small-world networks when individual behaviour matters: homogeneous and network models in epidemiology non-linear transmission rates and the dynamics of infectious disease a generalized stochastic model for the analysis of infectious disease final size data collective dynamics of small-world networks complex networks: structure and dynamics statistical mechanics of complex networks, of lecture notes in physics, chapter epidemic spreading in complex networks with degree correlations dynamical processes on complex networks on the definition and the computation of the basic reproduction ratio r 0 in models for infectious diseases in heterogeneous populations further notes on the basic reproduction number revisiting nodebased sir models in complex networks with degree correlations further dynamic analysis for a network sexually transmitted disease model with birth and death dram: efficient adaptive mcmc clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study covert coronavirus infections could be seeding new outbreaks we declare that there is no conflict of interest associated with this work. key: cord-261079-rarud78k authors: meng, mei; zhang, sheng; zhai, chun-juan; chen, de-chang title: rapidly organize redeployed medical staff in coronavirus disease 2019 pandemic: what we should do date: 2020-09-20 journal: chin med j (engl) doi: 10.1097/cm9.0000000000001033 sha: doc_id: 261079 cord_uid: rarud78k nan based on the strong coordination of the chinese medical system, an outstanding response was taken to combat this public health emergency. this involved a massive redeployment of healthcare professionals throughout the country to support the fight against covid-19 in wuhan. by march 4, 2020 , approximately 43,000 medical staff from different regions across the country were assigned to different hospitals in hubei province, working in the frontline of the outbreak and treating patients with covid-19. [5] the mobilization and transfer of medical staff is entirely led by the government. the chinese government has set up a general anti-epidemic headquarters in wuhan. due to the increased number of patients during the outbreak period, the general anti-epidemic headquarters decided the numbers of medical workers to be mobilized, the amount of medical equipment to be carried with, as well as the types of hospitals to be arranged. medical staff from other provinces took over the management of patients in local hospitals of wuhan city and hubei province. for example, on the new year's eve, the first batch of shanghai experts who rushed to wuhan jinyintan hospital for support, set out within 4 h after receiving the assignment of the hospital. they arrived in wuhan at midnight and received the training of prevention and control of hospital infection the next day. on the third day, a new intensive care unit ward was set up for covid-19 patients. almost every interim medical team with more than 100 members was rapidly organized within 1 or 2 days, including determining the personnel list, preparing medical materials, and gathering medical staff to leave for wuhan. this kind of organization with high efficiency significantly saves time and is suitable for gathering a large number of medical staff to participate in the treatment of patients during the peak period of the outbreak. healthcare workers have been shown to be at personal risk of infection during highly virulent outbreaks. governments and hospitals took responsibility for supplying ppe for medical staff teams, which assured that all teams participating in managing covid-19 patients were well protected from virus contracting and spreading. the governments and hospitals attached great importance to preventing infection of medical staff in the frontline fighting the epidemic. the aim of hospital infection prevention and control is "zero infection." to achieve this goal, several measurements have been taken. first, strengthen the training of medical staff. because the medical staff participating in the rescue come from different professional departments, mainly from the infectious disease department, respiratory department and critical care medicine department, most of whom had no experience in the prevention and control of infectious diseases. therefore, pre-job training is very important. [6] after arriving in wuhan, we organized special training on how to put on and take off protective clothing. second, ensure the frontline medical supplies such as ppe. in the stage of the outbreak, the shortage of medical protection supplies is a serious problem that every country and region will face, as it was in wuhan. [7] the governments and hospitals tried their best to cover the demand of the medical staff in the frontline. third, keep continuous supervision of the prevention of hospital infection. during the work, hospital prevention and control personnel supervised the medical process, and medical personnel supervised and reminded each other in the process of putting on and taking off ppe. with such efforts, all the medical staff supporting wuhan have been evacuated safely in april. the nucleic acid and antibody tests proved that the goal of "zero infection" has been achieved. each redeployed medical team contained approximately 130 to 140 members to independently manage a single department in wuhan hospitals. the chinese authorities assigned for each medical team an administrative leader who was responsible for the supplies, daily life, and the safety of team members. in the meantime, senior physicians were responsible for overseeing medical care. in addition, hospital infection experts were responsible for supervising the personal protection of all team members. almost all medical teams were temporarily established. the medical staff of each medical team came from different hospitals and departments, and most of them were complete strangers to each other. how to work as a team with tacit understanding in a short period of time required the excellent leadership and coordination ability of the team leaders. leaders of medical teams redeployed to wuhan all have rich management experience to soon understand the expertise of their team members and assign them to the right job. there were also exchanges and mutual help between different medical teams, such as mutual support of protective materials, case discussion, and exchange of treatment experience. [8] fourth, communication is a key element for optimizing the effectiveness of the medical team frontline medical staff in wuhan had numerous difficulties, including missing their family, worrying about becoming infected, and potential shortages of protective equipment. psychological experts have provided counseling to those requiring additional support during this highly stressful time. we have done a survey of 450 medical staff (unpublished). the results showed that more than 90% of medical staff were willing to participate in the support of wuhan to fight against the epidemic. however, at the same time, more than 80% of them were worried mainly about being infected, and 30% had sleep disorders. the medical team regularly held meetings, and psychological experts were responsible for the psychological consultation of the medical staff. they have printed special books and performed psychological service hotline to help relieve the pressure of the medical staff. [9] fifth, shift length must be minimized as much as possible wearing ppe for an extended period of time can lead to excessive fatigue. as such, each nurse's shift was limited to 4 to 6 h (with 4 h encouraged). special logistics teams were enabled to assist with day to day needs of the medical staff. during caring for patients with covid-19, medical staff wearing ppe sweated a lot, which makes them easy to be fatigued. therefore, it is necessary to shorten the continuous working time of medical staff, which can help to protect the health of medical staff, ensure the work efficiency, and improve the quality of medical work at the same time. [10] sixth, fully affirm and acknowledge the efforts of the medical staff working in the frontline of the epidemic media reported a lot about the hard work of the medical staff in the frontline, and expressed appreciation and admiration to them. the behavior of the medical staff also let more and more people realize that chinese doctors and nurses were brave and mentally strong. local governments and hospitals also cared about the frontline medical workers by paying bonuses and taking care of their families. after the medical staff finished their support work in wuhan, they all had vacation time to have a rest. due to the coordinated response of the chinese medical system to this unprecedented public health emergency, we wined the fight against covid-19. scientific deployment of medical staff should be an important part for coping with the pandemic. there is an urgent need for researches regarding how to resolve the shortage and properly redeployment of medical staff during the pandemic in the future. clinical characteristics of coronavirus disease 2019 in china a novel coronavirus from patients with pneumonia in china priorities for the us health community responding to covid-19 intubation and ventilation amid the covid-19 outbreak: wuhan's experience the novel coronavirus (sars-cov-2) infections in china: prevention, control and challenges healthcare simulation in china: current status and perspectives early transmission dynamics in wuhan, china, of novel coronavirusinfected pneumonia covid-19 in china: ten critical issues for intensive care medicine an examination of the effect of loneliness on the innovative behavior of health science faculty students special attention to nurses' protection during the covid-19 epidemic rapidly organize redeployed medical staff in coronavirus disease 2019 pandemic: what we should do the authors would like to express their appreciation to craig m. coopersmith, md (director of emory critical center, emory university school of medicine, atlanta, ga) who edited for this manuscript. none. key: cord-355528-y4a1g6km authors: balla, mamtha; merugu, ganesh prasad; patel, mitra; koduri, narayana murty; gayam, vijay; adapa, sreedhar; naramala, srikanth; konala, venu madhav title: covid-19, modern pandemic: a systematic review from front-line health care providers’ perspective date: 2020-03-30 journal: j clin med res doi: 10.14740/jocmr4142 sha: doc_id: 355528 cord_uid: y4a1g6km coronavirus disease 2019 (covid-19) caused infection in 168,000 cases worldwide in about 148 countries and killed more than 6,610 people around the world as of march 16, 2020, as per the world health organization (who). compared to severe acute respiratory syndrome and middle east respiratory syndrome, there is the rapid transmission, long incubation period, and disease containment is becoming extremely difficult. the main aim of this systematic review is to provide a comprehensive clinical summary of all the available data from high-quality research articles relevant to the epidemiology, demographics, trends in hospitalization and outcomes, clinical signs and symptoms, diagnostic methods and treatment methods of covid-19, thus increasing awareness in health care providers. we also discussed various preventive measures to combat covid-19 effectively. a systematic and protocol-driven approach is needed to contain this disease, which was declared as a global pandemic on march 11, 2020, by the who. coronavirus disease 2019 (covid19) infection, which is a global pandemic declared on march 11, 2020, by world health organization (who), was reported to have infected 168,000 cases worldwide in about 148 countries and territories and killed more than 6,610 people around the world as of march 16, 2020 [1]. there is a rapid transmission, long incubation period, and the containment of the disease is extremely difficult compared to prior epidemics of severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) [2] . there is a paucity of literature on this pandemic as it is novel. we aimed to provide a concise clinical summary of all the quality data relevant to the epidemiology, trends in hospitalization and outcomes, clinical signs and symptoms, diagnostic and treatment methods of covid-19, thus increasing awareness in health care providers at the front-line. we also discussed various preventive measures to combat and contain covid-19 effectively. we conducted a systematic search of published articles from pubmed, google scholar databases and in-press literature from google search engine through snowballing. there were two independent reviewers, each focusing on covid-19, novel coronavirus (ncov), sars and mers, and third independent reviewer to resolve any conflicting article of interest. we used the keywords as mentioned above and after stringent exclusion criteria, a total of 58 articles, including reports from the trusted newspapers and websites. most of the articles were single case reports, multiple case studies and systematic reviews (11 retrospective studies, one meta-analysis, three systematic reviews, six case series, five case reports, five newspapers, 24 science research articles, and rest 3 reference's from official websites). slcovzc45 and bat-sl-covzxc21, 79% identity with the sars coronavirus and 50% identity with mers coronavirus [4, 5] . according to chan et al, sars-cov-2 is thought to be transmitted via contaminated hands, surfaces and aerosolized droplets, and extensive human-to-human transmission is evident [6] . according to li et al, the average incubation period is 5 days but is highly variable and can last up to 2 weeks [7] . sars-cov-2 is thought to have originated from bats and transmitted to humans from an intermediate host, civets and dromedary camels, respectively. still, no source or intermediate host has been confirmed yet via genome sequencing and phylogenetic analysis [2] . this hypothesis was made because previous coronavirus strains have originated from the rhinolophus affinis bat [8] . however, xiao et al reported the isolation and characterization of a 2019-ncov-like coronavirus from pangolins (manis javanica) [9] . similarly, in october 2019, a viral metagenomic study of pangolins identified severe acute respiratory syndrome-coronavirus (sars-cov)-related sequences [10, 11] . according to the study by xu et al, 60% of people diagnosed with covid-19 had traveled to wuhan or nearby regions (60%), 36% had close contact with novel coronavirus pneumonia (ncp) patients and 4% had no definite exposure [12] . according to the study by tian et al, 40 .5% of people diagnosed with covid-19 had traveled to wuhan or nearby regions [13] . beijing is the fourth mostaffected city in china [13] . according to xu et al, their patients with mild, common and severe covid-19 were of mean ages of 44 years, 55 years and 66 years, respectively [12] . the age distribution of cov-id-19 diagnosed patients in the study by tian et al included ages < 1 (1%), 1 -12 (3%), 13 -44 (43%), 45 -64 (35%) and > 65 (18%) [13] . liu et al described covid-19 in children. they analyzed a total of 366 hospitalized patients, and 6% (six patients) of them were positive for covid-19. according to huang et al and chen et al, sars-cov-2 seems to have a predilection for the elderly male population and patients with comorbidities [14, 15] . according to the study published in osong public health and research perspectives, 7% of the population were greater than 60 years of age, and 93% were less than 60 years of age [16] . these findings are summarized in figure 1 . males are experiencing a higher rate of incidence and case fatality compared to females [17] . in a study reported from south korea, 46% were females and 54% were males [16] . these results for multiple studies are summarized in figure 2 . xu et al analyzed 50 patients with covid-19 confirmed cases and symptoms included fever (42%), cough (20%), expectoration (14%), fatigue (16%), headache (10%), gastrointestinal discomfort (2%), shortness of breath (sob) (8%) and muscle ache (16%) [12] . fever is the most common symptom [12] . in china and symptoms included fever (82%), cough (46%), fatigue (26%), sob (7%) and headache (6%) [13] . in severe cases, sob was present in 32.6% of the patients. tian et al reported that the median time of incubation was approximately 7 days [13] . the median time from onset of illness to a hospital visit and hospital visit to the defined confirmed case were 4.5 and 2.1 days, respectively [13] . yang et al analyzed 149 cases of rt-pcr confirmed covid-19 in china and symptoms included fever (76%), cough (58%), expectoration (32%) and sob (1%) [18] . however, a significant number of patients do present with atypical symptoms [19] , including nausea, vomiting (1-3%) and diarrhea (2-10%) [3, 15] . chen et al analyzed 99 patients in a retrospective single-center study in wuhan, and patients presented with fever (83%), cough (82%), sob (31%), muscle aches (11%), confusion (9%), headache (8%), sore throat (5%), rhinorrhea (4%), chest pain 2%, diarrhea (3%), nausea and vomiting (1%) [15] . according to wang et al, even though fever is the most common symptom of covid-19, the absence of fever in covid-19 cases is more frequent than in sars-cov and mers-cov infection [20] . lillie et al presented a case where symptom onset started with fever, which then progressed to sore throat and dry cough followed by diffuse myalgia [21] . according to the study published in osong public health and research perspectives, they analyzed the first 28 cases reported in south korea. out of 28 patients, 32% reported fever and sore throat, 18% cough with or without sputum, 18% chills, 14% muscle aches, 11% generalized weakness and 11% headache at the time of presentation. moreover, 64% developed pneumonia. the incubation period was 4.6 days [16] . luo et al analyzed 83 patients confirmed with covid-19 infection in anqing, china; of these, eight patients were asymptomatic at confirmation, one of whom did not develop any signs or symptoms during the entire 17-day hospitalization. this patient was a 50-year-old female with no comorbidities. despite her negative labs and radiological tests, her throat swabs and anal swabs were positive of virus nucleic acid for at least 17 days, indicating that healthy carriers are very likely a possibility [22] . hu et al [23] described clinical characteristics in 24 asymptomatic patients after screening among close contacts in nanjing, china. out of 24 patients, seven patients did have a normal computed tomography (ct) and had no symptoms during their entire hospitalization. the median age of these seven patients was 14 years younger than the rest of the patients. the median communicable period is defined as the first day of a positive nucleic acid test to the first day of the negative nucleic acid test. it can be up to 21 days in asymptomatic patients [23] . a case report describing the first case of canada showed that the patient had symptoms of hemoptysis on days 2 through 6 along with fever and non-productive cough on presentation [24] . lillie et al presented a case where symptom onset started with fever, which then progressed to sore throat and dry cough followed by diffuse myalgia. this seems to be the most consistent pathway of symptom onset [21] . the most common symptoms include fever (83%), cough (82%) and breathlessness (31%) [3] . according to the chinese centers for disease control and prevention (cdc), 81% of infections were considered mild and only 1.2% asymptomatic [3] . according to huang et al, the current published data indicate a long mild incubation period followed by rapid progression of the disease with 8 days being the median time from initial symptoms to the onset of breathlessness, 9 days to acute respiratory distress syndrome (ards) and 10 days to admission to the intensive care [14] . the clinical signs and symptoms from different studies covid-19 is diagnosed via rt-pcr [12, 13, 25] . multiple sources found that a normal to slightly reduced leukocyte count occurred in patients with covid-19 (98%) [12, 25] . xu et al reported a decreased lymphocyte count in 28% of their patients [12] , while yang et al reported leukopenia and lymphopenia in 24% and 35% of their patient population respectively [18] . an elevated c-reactive protein (crp) was reported in 52-55% of the patients [12, 18] . thrombocytopenia was seen in 13% of patients. acute kidney injury was present likely due to dehydration, not from the virus directly [21] . according to the meta-analysis done by lippi et al, elevated procalcitonin levels were associated with almost five-fold increased risk of severe covid-19 infection (odds ratio (or): 4.76; 95% confidence interval (ci): 2.74 -8.29). they advised that serial measurements of procalcitonin may play a pivotal role in analyzing the worsening of the disease to more severe form [26] . according to the case report by ruan et al, they found a patient with a negative nucleic acid test, tested twice 8 days apart. as the patient was showing typical ct imaging patterns suspicious for covid-19 and deterioration of symptoms, repeat testing on day 11 was positive. as exact biological characteristics of covid-19 are still not defined well, multiple sampling from multi-sites for the highly suspected population can be useful for covid-19 detection at a much earlier stage [27] . specimens should be tested for routine bacterial and viral infections, as well as using both upper and lower respiratory tract samples to test for sars-cov-2 [3] . serological tests are in development, and they can be used if rt-pcr is not available [3] . as per the case reported by chen et al, the oropharyngeal swab test of covid-19 rna turned positive even during the convalescence period in a confirmed case; it emphasizes the significance of active surveillance of covid-19 rna for inactivity assessment [28] . the laboratory results from different studies are summa-rized in figure 5 . according to zhang et al, in a month, out of 1,467 suspected patients suspected of coronavirus pneumonia, 152 patients (10%) had typical imaging findings or positive nucleic acid tests [29] . chest ct is an important tool for diagnostic for lung diseases. combining imaging with clinical and laboratory findings could facilitate early diagnosis of covid-19 pneumonia. because the time of onset of symptoms to ards can be as short as 9 days, early recognition of the disease is therefore essential for management. in a retrospective study done in wuhan on 81 patients from december 20, 2019 to january 23, 2020, they were able to describe the characteristics of the chest ct at specified time points during the disease course. they have divided the patients into four different groups, as shown in table 1 [30] . based on the review, covid-19 pneumonia is described radiographically as bilateral, subpleural ground-glass opacities with air bronchograms, ill-defined margins and slight predominance on the right lower lobe. it was also noted that the radiological evolution of covid-19 pneumonia is consistent with the clinical course of the disease. therefore, serial ct could help monitor disease progression. the study also pointed out that patients with old age, male and with underlying comorbidities as well as progressive radiographic deterioration on follow-up are the risks for poor prognosis [30] . according to chen et al, the majority (75%) of patients had bilateral pneumonic changes on ct imaging [15] . guan et al reported 230 out of 1,099 (20%) cases [31] , and chung et al reported three out of 21 (14%) have normal ct scans for patients diagnosed with symptoms along with confirmation of infection with rt-pcr [32] . according to a single-center study done by chen et al in 99 patients, 75% of patients showed bilateral pneumonia, ards developed in 17% and 11% of them died with multi-organ failure [15] . as per the review of literature, the ct scans of the chest showed lesions or abnormalities more commonly found in bilateral lower lobes with the right middle lobe least affected. multilobar involvement was seen in 96-98% of the patients [12, 25, 33] . the lesions are mostly located in the peripheral area under the pleura with possible extension into the pulmonary hilum (36% in the periphery and 2% in the center of the lung) [12, 18, 25] . these lesions sometimes were accompanied by air bronchograms but rarely pleural effusions [12, 33] . regarding lobar involvement, right lower lobe is most commonly involved in approximately 95% of cases followed by left lower lobe (88%), left upper lobe (80%) and right upper lobe (73%) [12] . pneumothorax, as well as bilateral pleural effusions, was identified only in 1% of the patients [25, 33] . approximately 11% of the patient had normal ct findings. ct findings based on the stage of the disease are as follows [12] : 1) mild novel coronavirus pneumonia patients have no abnormalities seen on a ct scan. 2) the early-stage infection which is more common has ground-glass opacities identified in the periphery and about 75% of the patients, mixed groundglass opacity along with consolidation in approximately 53% of the patients, nonuniform density with air bronchograms in about 53% and thickened interlobular/intralobular septa in 75% of the patients. 3) patients who are severe or critically ill have multiple patches of ground-glass opacities as well as consolidation in approximately 69% of the patients and mixed findings in about 77% of the patients in bilateral lungs. almost all patients have thickened interlobular septa. the patients generally have multilobar involvement bilaterally more commonly in lower and upper lobes. approximately 4 -10 days after infection, most lesions were absorbed with a reduced extent and decreased density with the formation of fibrotic stripes. lesions can also become worse starting with ground-glass opacities and areas of consolidation in the center of opacities on day 2 progressing to multiple lungs on day 6 with thickened interlobular septa by day 9. the lesions can get worse before getting better. ct scan of the chest shows the greatest severity approximately 9 -10 days after the onset of initial symptoms [25] . the bilateral patchy shadows or ground-glass opacities from various studies are summarized in figure 5 . patients infected with covid-19 and had multiple medical comorbidities were reported to have higher morbidity and mortality. as per the analysis by wang et al involving 138 cases of covid-19, approximately 46% of them have comorbidities, and more importantly, patients admitted to the intensive care unit had a higher number of comorbidities (72%) compared to who did not (37%) [34] . as per the meta-analysis of yang et al involving 46,248 covid-19 infected patients, the most prevalent comorbidity was hypertension with a range of 10-24%, diabetes mellitus with a range of 2-14%, cardiovascular diseases with a range of 129% and respiratory diseases around 2%. as per the final analysis, underlying hypertension, cardiovascular disease and respiratory system disease might be risk factors in patients with severe infection compared to patients with known severe infection [35] . other studies discussing about comorbidities are summarized in table 2 . in a case study with 99 patients performed by chen et al, 17% of diagnosed patients developed ards, 13% required non-invasive respiratory support, 4% needed invasive ventilation and 3% needed extracorporeal membrane oxygenation (ecmo) [15] . in a review by tian et al, approximately 1% of patients died from covid-19 out of 262 patients, all of whom had respiratory failure and were above the age of 50 [13] . yang et al described that 2.6% of 54,406 in the hubei province in china died from coronavirus vs. 0% of 499 patients diagnosed in wenzhou city up until february 15, 2020 [18] . these numbers show that there is a regional difference in mortality of covid-19 as the wenzhou province has more resources than the former. yang et al estimated the overall adjusted case fatality rate (cfr) among confirmed patients to be 3% with a sample size of 8,866 [36] . the course of hospitalization, morbidity and mortality are summarized in figure 6 . tients who are elderly with several comorbidities. mulbsta score is an early warning model for predicting morbidity in viral pneumonia in 90 days as summarized in table 3 . it has a sensitivity of 77.6% and specificity of 77.8%. it has better predictive ability than curb-65 (confusion, blood urea nitrogen, respiratory rate, blood pressure and age greater than 65 years) [37] . xu et al performed high-resolution ct scan on 50 patients admitted with sars-cov-2. it was classified into four types, as summarized in an outbreak of a novel coronavirus (covid-19 or 2019-cov) infection causes significant morbidity and mortality. coronavirus-specific treatments and antiviral treatments were very useful for the treatment of sars and mers and should be considered as potential treatments for covid-19 [17] . there is an emergent need for other treatment options and a review of the literature for alternate treatment to control the disease mentioned below. multiple vitamin supplements and antioxidants can be considered to reduce the risk of infection. vitamins a, b, thymosin alpha-1, thymopentin can be promising options for the adjunctive treatment of coronavirus and the prevention of lung infection [17] . vitamin c supplementation might decrease the susceptibility to respiratory infections, as three human controlled clinical trials showed a lower incidence of pneumonia in supplemented groups [17] . decreased vitamin d and e in calves had been reported to cause the infection of bovine coronavirus [17] . it could be another therapeutic option for this virus. selenium with ginseng stem-leaf saponins could induce an immune response to a live bivalent infectious bronchitis coronavirus vaccine in chickens. selenium supplementation could be a possible choice for the treatment [17] . zinc and pyrithione combination at low concentrations can inhibit the replication of sars coronavirus (sars-cov) [17] . type i ifns, including ifn-b, could inhibit the replication of sars-cov and can be potent inhibitors of mers-cov replication in vitro. still, no in vivo experiments have been performed [17] . ifn treatment was used in 96% of patients [18] . ifn-α vapor inhalation was administered at a dose of 5 million units for adults, two times/day for no longer 10 days [38] . glycyrrhizin, baicalin and ginseng are all chinese medicinal treatments that can help enhance host immunity against cov-id-19 infection. they have been found to inhibit sars-cov in vitro [17] . covid s-protein uses ace-2 as a sole receptor for entry into human cells. monoclonal antibody neutralizes sars-cov and inhibits syncytia formation between cells expressing the s-protein and ace-2 receptor [17] . chloroquine is a potent sars-cov inhibitor through interfacing with ace-2 [17] . chloroquine is a potent sars-cov inhibitor through interfacing with ace-2 [17] . gao et al described chloroquine as a cheap and safe drug available for more than 70 years, which has been shown to have apparent efficacy and decent safety against pneumonia associated with covid-19 in multicenter trials performed in china. as per the review of results from 10 hospitals and more than 100 patients, they showed that chloroquine phosphate is superior to control in decreasing the exacerbation of covid-19 pneumonia. the anti-inflammatory and antiviral property of chloroquine may be responsible for its potent efficacy against covid-19 pneumonia [39] . chloroquine phosphate is orally administered at a dose of 500 mg for adults, two times/day. chloroquine was found to block sars-cov-2 infection at low micromolar concentration, with a half-maximal effective concentration (ec50) of 1.13 µm and a half-cytotoxic concentration (cc50) greater than 100 µm [40] . emodin or promazine blocks interaction between s-protein and ace-2, therefore, it could abolish sars-cov infection by being a competitive inhibitor [17] . nation has shown to synergistically inhibit the replication of sars-cov in animal and human cell lines [41] . kim et al have reported a case of mers-cov successfully treated with triple combination therapy with lopinavir/ritonavir, ribavirin and ifn-alpha2a therapy in south korea [42] . remdesivir has been reported to inhibit human and zoonotic coronavirus in vitro and restrains sars-cov in vivo [17] . remdesivir + ifn-b was found to be superior to lopinavir/ritonavir + ifn-b therapy against mers-cov in vitro and in vivo. yamamoto et al have found that nelfinavir could strongly inhibit the replication of sars-cov [43] . akerstrom et al have reported that organic nitric oxide could significantly inhibit the replication cycle of sars-cov in a concentration-dependent manner and could be taken via inhalation [44] . favipiravir is a drug currently undergoing testing to combat covid-19. it was approved for the treatment of novel influenza in china. favipiravir is an rna-dependent rna polymerase (rdrp) inhibitor. it inhibits the replication of rna viruses like noro, arena, flavi, alpha, bunya, filo groups. therefore, favipiravir may have potential antiviral action on sars-cov-2, which is an rna virus. a clinical trial involving 80 patients has shown that favipiravir had more potent antiviral action than that of lopinavir/ritonavir. it had significantly fewer adverse events than the lopinavir/ritonavir group [38] . remdesivir is a drug currently undergoing testing to combat covid-19. remdesivir is a nucleoside analog and a broad-spectrum antiviral [3, 38] . animal experiments indicated that remdesivir could effectively reduce the viral load in lung tissue of mice infected with mers-cov, improve lung function and alleviate pathological damage to lung tissue [38] . wang et al found that remdesivir potently blocks sars-cov-2 infection at low-micromolar concentrations and has a high selectivity index (ec50: 0.77 µm; cc50 > 100 µm; si > 129.87) and had in vitro activity against sars-cov-225 [45] . holshue et al reported that remdesivir yielded promising results in the treatment of a patient with covid-19 in the united states. a recent randomized controlled trial (rct) is being performed [46] . it may also be possible to enhance the protective host immune response to infection [2] . darunavir is a second-generation hiv-1 protease inhibitor. on february 4, 2020, researchers in china announced that darunavir inhibited sars-cov-2 infection in vitro [38] . sars-cov-2 uses the cellular protease tmprss2 receptor, sars-cov receptor and ace-2 for entry into target cells as mentioned by hoffmann et al. a tmprss2 inhibitor would block entry and thus constitute a treatment option [47] . imatinib has anti-coronal activity primarily because it inhibits the fusion of virions with the endosomal membrane [38] . arbidol is orally administered at a dose of 200 mg three times a day in adults and able to inhibit sars-cov-2 infection in vitro in a clinical study. lopinavir/ritonavir is administered 400 mg/100 mg for adults, two times a day for no longer than 10 days. stockman et al reported to inhibit sars-cov reproduction in vitro [3, 48] . ribavirin is administered intravenously at a dose of 500 mg for adults, 2 to 3 times daily, in combination with ifn-α or lopinavir/ritonavir. chu et al suggested that patients treated with the combined therapy had a lower risk of ards and death in patients with sars [49] . steroids increase viral shedding in patients with mers-cov, so who advised against their use in covid-19 other than patients with ards [50] . according to current who guidelines, they do not recommend corticosteroid use as it did not reduce mortality and potentially delayed viral clearance [3] . patients who have respiratory tract infections can have coexisting gut dysfunction. with more severe infections, there is a lung-gut cross-connection. this mechanism might also happen with covid-19 infection, hence identifying and targeting gastrointestinal microbes can be a new treatment option or at least adjuvant treatment choice [19] . it has profound antiviral activity, and there have been previous reports on its inhibitory effect on both sars-cov and previous strains of coronaviruses. it can inhibit 2019-ncovr at a low concentration. compared to regular infections without drug treatment, the viral rna yields were significantly lower in vitro when using cep; thus, our data suggest that cep can potently inhibit coronavirus infection at viral entry and postentry phases [51] . cep has low toxicity in animals and has no significant side effects in humans [51] . mefloquine is an antimalarial drug found to have antiviral activity against both mers-cov and sars-cov in vitro [51] . no in vivo trials have been performed. selamectin is a topical broad-spectrum anti-parasitic in cats and dogs to control fleas, heartworms, hookworms, roundworms, etc. the antiviral mechanism is unknown, but selamectin could be a 2019-ncovr specific inhibitor [51] . no in vivo trials have been performed. mechanism of action of cep, mefloquine and selamectin is unknown. all possible therapeutic options are summarized in table 5 . the primary mode of transmission is via respiratory droplets with the most significant risks of transmission within 3 feet but up to 6 feet [33] . portable radiography should be used to limit covid-19, modern pandemic j clin med res. 2020;12(4):215-229 patient transportation [33] . hospital care workers are recommended to wear full isolation gown with n95 mask or higher, disposable gloves, eye protection with goggles, with a face mask in front of goggles when caring for patients [33] . surfaces of ct, mri machines, ultrasound probes, blood pressure cuffs and mouse/keyboards of radiologic equipment should be disinfected with soap or alcoholic-based disinfectant [33] . zhang et al stated that viral nucleic acid was found in stool samples from the patients who are suffering from covid-19 pneumonia. so fecal-oral transmission is also possible. hence, more consideration is given to hand hygiene, disinfection of contaminated surfaces as well as patient's stools and vomitus [52] . close contact tracing and longitudinal surveillance through serial nucleic acid tests are essential in combating disease as asymptomatic carriers play a significant role in spreading the disease [23] . effective management and treatment play a very crucial role, starting from identifying appropriate treatment and curing patients. covid-19 imposes a significant public health concern as it became "once in a century pandemic" [53] due to its severe contagious transmission. effectively identifying and treating one patient can help in preventing the development of several patients in the community. an action plan needs to be implemented in every organization to combat the disease at an early stage. patients should be offered to wear a nasal mask irrespective of symptoms when they visit the hospital. it is essential to take travel history for every individual regardless of whether they are having symptoms suspicious for covid-19 either to a different state or a different country. the second question is if they have any symptoms of cough either dry or with expectoration, increasing shortness of breath, congestion, fever, chest pain, headaches, generalized body aches and pains. the third question is contact with a patient with a confirmed coronavirus infection. drills and emergency preparedness about covid-19 should be performed in all health care facilities involving providers who will be in touch with covid-19 suspected patients. as escalating infection control in a health care setting can effectively prevent health care providers in contracting virus. according to cheng et al, 2020, a bundled approach involving active and enhanced laboratory surveillance, early airborne isolation, contact tracing with unprotected exposure, rapid testing completely prevented nosocomial transmission of covid-19 [53] . if the patient responds yes to the above questions, health care personal entering the room should be appropriately wearing personal protective equipment to encounter a patient suspected covid-19. it is crucial as the disease spread among healthcare providers will result in the rapid spread of the virus, thus increasing the morbidity and mortality. once the patient is identified as a suspect of covid-19 with presenting symptoms of fever, cough, congestion, chest pain, nausea and generalized body aches, they should be placed in a negative pressure isolation unit. the emergency room physician should order basic labs, including complete blood count (cbc), including a differential (cbc), complete metabolic panel (cmp), respiratory viral panel and a portable chest x-ray to rule out other etiologies. if other etiologies are ruled out and the patient is suspected of having covid-19, the local health department should be notified, and pcr testing is recommended. the patient should be transported to a negative pressure isolation room in the hospital. all isolation rooms should have negative air pressure and specially filtered air, containing and eliminating the circulation of the virus in the air. all staff should be well educated on the use of cleaning supplies and appropriate cleaning methods. all team members involved in patient care should receive regular education on the use of personal protective equipment. we should continuously monitor the united states centers for disease control and prevention (cdc) guidelines and adopt best practices as sooner they become available if possible health care professionals should be able to use a robotic mode of delivering medication and checking vitals to prevent the spread of the disease. this method helped in containing the disease in patients treated at china, in washington dc. an emergency covid-19 response team should be prepared in every hospital comprising of a hospitalist, infectious disease specialist and pulmonary/critical care physician to help with managing patients daily. all the essential up-to-date changes in treatment and management should be delivered to all the health care professionals daily in that hospital and to the community to help in treating other patients. the mode of transmission is when a patient with covid-19 coughs or exhales, they release droplets of fluid, which is infected, and most of these droplets fall nearby objects such as telephones tables and desks as well as other equipment. the public can catch the disease by touching these contaminated objects, and later touching the nose eyes or mouth. notably, this is called transmission through fomites [54] . patients can catch it by breathing in droplets if they are standing within 1 m of covid-19 patients. they should be visited restrictions at all facilities encouraging people to visit patients by a telephone or electronically. we should also encourage people coming to the health care facilities for testing/treatment to limit the number of people who accompanied them. since the virus causes significant mortality in older adults with significant comorbidities, they should be more restrictions placed on nursing homes such as no visitor policies in a high-risk environment. we should encourage social distancing, which means avoiding crowds and staying 6 feet away from other people as much as possible. we should also cancel or postpone all nonessential community events. all travel should be avoided unless absolutely necessary particularly to highly endemic zones of covid-19. according to wang et al, those having had close contacts with infections are currently being asked to receive medical observation and quarantine for 14 days [20] . influenza and covid-19 differ by multiple means. the first, only 1% of reported cases are asymptomatic and most patients develop symptoms within 2 days from covid-19. with influenza, people who are infected might not get sick be due to herd immunity developed over the years [55] . the second difference is that covid-19 causes more severe illness than influenza as it is a new virus and community have not developed any immunity, which makes more people susceptible to severe infection [5] . globally, covid-19 mortality is 3.4% compared to influenza with mortality of less than 1% [5] . third, no vaccines are there for covid-19 at present, unlike seasonal flu which has a vaccine. currently, more than 20 vaccines are in the clinical trial stage. fourth, contact tracing and containment will possibly help for covid-19 compared to influenza [55] . these are the reasons why who recommends "everything we can do to contain the virus" suggests a comprehensive approach to treat covid-19. screening should start in the outpatient setting with patients who should undergo infrared temperature detection before en[29] . contact tracing and testing all the suspected contacts at an early level and isolating them in isolation wards will help in halting disease at the early stages. identifying and treating the entire community plays a pivotal role than detecting and single patients in this epidemic. testing and identifying individuals even if they have an uncomplicated upper respiratory tract should be advised [50] . medical professionals treating these patients should take the following precautions including: 1) wearing disposable work caps; 2) wearing protective glasses or face masks (antifog type); 3) wearing medical protective masks (n95); 4) wearing protective clothing or isolation clothing; 5) wearing disposable latex gloves (double layered); 6) wearing disposable shoe covers; and 7) strictly implementing good hand hygiene. in everyday clinical practice, the most common phrase heard is covid-19, also called as novel coronavirus. as of march 16, 2020, a total of 168,019 confirmed cases in 148 countries were reported. among 87,002 more than 3,400 deaths of covid-19 have been reported to who outside of china, and it exceeded china's death rate [1]. while cases from china have been decreasing according to the recent available data, the reported cases from outside of china have been increasing at an alarming rate. the number of cases reported were nine times more in the rest of the world compared to china since january 22, 2020 [12] . reviewing the history of the disease, as of december 2019, a total of 41 cases of pneumonia of unknown origin have been confirmed in the city of wuhan. most of them visited local fish and wild animal market within 30 days of infection in wuhan, hubei province, china [5] . it was first identified and announced as a new coronavirus (2019 ncov) by a scientific team lead by dr. jianguo xu, an academician of the chinese academy of engineering [51] . in human coronaviruses, there is a spectrum of the viruses, which can cause infections ranging from the common cold to fatal diseases including, sars and mers, which are zoonotic. the unique pathogenesis of covid-19 compared to sars and mers is, it mainly affects the lower respiratory tract as well as the involvement of the gastrointestinal system causing diarrhea, compared to few patients with mers and sars having diarrhea [25] . it was estimated that covid-19 has a reproductive rate ranging from 2.24 (95% ci: 1.96 -2.55) to 3.58 (95% ci: 2.89 -4.39), which is correlated to eight-fold to two-fold rise in reporting rate [56] . imai et al provided the first estimation of the reproduction factor, using r 0 of 2.6 and based on the number of cases in china and those detected in other countries [57] . other authors estimated r 0 to be 3.813, 6.4714, 2.215 and 2.6816 [20] . according to wang et al, the model used to calculate r 0 was assumed of the model from wuhan, china, as summarized in table 6 . the model used to calculate r 0 assumed that there were no new transmissions from animals, no differences in individual immunity, the time-scale of the epidemic is much faster than specific times for demographic processes (natural birth and death), and there are no differences in natural births and deaths [20] . assuming the epidemic continues to develop with r 0 = 1.9, 2.6 and 3.19 from december 1, 2019, the number of infections will continue to rise. by the end of february 2020, covid-19 cases would be 11,044, 70,258 and 227,989 in wuhan, china with r 0 = 1.9, 2.6 and 3.1, respectively [20] . according to read's research, r 0 for covid-19 outbreak is much higher compared with other emergent coronaviruses [58] . we see a decreased trend in r t as discussed in table 6 with effective implementation of public health measures to control the spread of the disease. after reviewing cases from hubei province, severe cov-id-19 cases occur mostly in men, and many of them do have comorbid conditions, including cerebrovascular, cardiovascular and diabetes. several sequelae were seen including, coagulation activation, cellular immune deficiency, hepatic and kidney injury, secondary bacterial infection and myocardial injury. lymphopenia and sustained inflammation seen in patients with severe disease and death are most likely secondary to antibody-dependent enhancement (ade) of covid-19 due to previous exposure to other coronaviruses [30] . especially this kind of pattern is also seen in patients who had sars during an epidemic in 2003 [40] . covid-19 is a significant clinical threat to the general populaphase 1 an early phase of the epidemic when few prevention and control measures were implemented. r 0 was 3.1. phase 2 public transportation to and from wuhan, as well as public transportation within wuhan, were stopped. while gathering events inside wuhan was banned, quarantine and isolation were gradually established in wuhan. r t was 2.6. phase 3 new infectious disease hospitals and mobile cabin hospitals came into service, and many medical and public health teams from other provinces and cities in china arrived in wuhan. the quarantine and isolation at the community level were further enhanced. r t decreased to 1.9. phase 4 the peak of public health restrictions in wuhan, china. r t became 0.9. tion and health care workers worldwide. unfortunately, knowledge about the novel virus is limited, causing lots of concern and panic. to decrease morbidity and mortality associated with covid-19, public health and infection control measures are urgently required to limit the global spread of the virus. all efforts should be made to slow the spread of the illness in order to provide time for health care systems and the general public to prepare and to develop timely diagnostics, therapeutics and vaccines. finally, although the improvement of internet communication enhances information dissemination, it also has the potential to spread misinformation. hence, we need to educate the public to follow information from a reliable website such as the cdc in the us. there are several unanswered questions at present in the management of covid-19. even though several case studies, rcts and systemic reviews were done, there is no clarity regarding the exact pathogenesis of the disease, duration of shedding of virus and the possibility of other contaminant viral infections including influenza as well as secondary bacterial infections. the pandemics like covid-19 put stress on every part of society, posing significant treat to international health and the economy. several vaccines and promising treatments are being tested on clinical trials. however, the rising number of infected people, as well as mortality from it and the highly contagious nature of covid-19 with a prolonged incubation period and asymptomatic carriers shredding the virus, makes it challenging to contain the spread. at present, handwashing, isolating and quarantine patients who are exposed or infected with the virus, disinfecting the 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at shenzhen third people's hospital. fecalto-mouth transmission risk of new coronavirus escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease 2019 (covid-19) due to sars-cov-2 in hong kong who director-general's opening remarks at the media briefing on covid-19 -3 preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak report 3: transmissibility of 2019-ncov. reference source novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions i thank all the authors who contributed in carrying out research. none to declare. none to declare. mb, gpm, mp, vg and sa were involved in data collection, review and preparation of the manuscript. mb and mp created figures/bar graphs. mb, sn, nmk and vmk involved in the analysis of data and final review the manuscript, preparation of tables. all of the authors reviewed the manuscript and agreed with the findings and interpretation. pubmed, google scholar databases and in-press literature from google search. the authors declare that data supporting the findings of this study are available within the article. key: cord-259368-k8t8brjy authors: ren, xiang; li, yu; yang, xiaokun; li, zhili; cui, jinzhao; zhu, aiqin; zhao, hongting; yu, jianxing; nie, taoran; ren, minrui; dong, shuaibing; cheng, ying; chen, qiulan; chang, zhaorui; sun, junling; wang, liping; feng, luzhao; gao, george f.; feng, zijian; li, zhongjie title: evidence for pre‐symptomatic transmission of coronavirus disease 2019 (covid‐19) in china date: 2020-08-07 journal: influenza other respir viruses doi: 10.1111/irv.12787 sha: doc_id: 259368 cord_uid: k8t8brjy background: between mid‐january and early february, provinces of mainland china outside the epicentre in hubei province were on high alert for importations and transmission of covid‐19. many properties of covid‐19 infection and transmission were still not yet established. methods: we collated and analysed data on 449 of the earliest covid‐19 cases detected outside hubei province to make inferences about transmission dynamics and severity of infection. we analysed 64 clusters to make inferences on serial interval and potential role of pre‐symptomatic transmission. results: we estimated an epidemic doubling time of 5.3 days (95% confidence interval (ci): 4.3, 6.7) and a median incubation period of 4.6 days (95% ci: 4.0, 5.2). we estimated a serial interval distribution with mean 5.7 days (95% ci: 4.7, 6.8) and standard deviation 3.5 days, and effective reproductive number was 1.98 (95% ci: 1.68, 2.35). we estimated that 32/80 (40%) of transmission events were likely to have occurred prior to symptoms onset in primary cases. secondary cases in clusters had less severe illness on average than cluster primary cases. conclusions: the majority of transmissions are occurring around illness onset in an infected person, and pre‐symptomatic transmission does play a role. detection of milder infections among the secondary cases may be more reflective of true disease severity. a novel coronavirus named "severe acute respiratory syndrome coronavirus 2" (sars-cov-2) was first identified in january 2020 as the pathogen responsible for a cluster of cases of atypical pneumonia in wuhan, a large city located in hubei province in central china. 1, 2 genetic analysis of the virus indicates that it originated from a bat coronavirus. 2 sars-cov-2 is considered distinct from sars-cov or mers-cov, and coronavirus disease 2019 caused by it has rapidly become a global health concern. 3 incidence of infections slowly increased through january 2020 with a reproductive number estimated to be in the range 2.2-3.6. [4] [5] [6] [7] starting in mid-january 2020, covid-19 cases began to be identified in other cities in china and also in other countries. 8, 9 a number of studies suggested the probable phenomenon of covid-19 transmissions during incubation period, [10] [11] [12] these studies used cluster cases in limited number of families for analysis, and the relative frequency of pre-symptomatic transmission was not quantified. moreover, there was an analysis on publicly available data indicating the existence of negative serial intervals, also implying pre-symptomatic transmission. 13 here, we retrospectively analyse data on cases identified outside of hubei province through the chinese public health event surveillance system at the early stage of transmission in china, in order to provide insights on the transmission dynamics of covid-19. data were extracted from the epidemiological reports of the chinese public health event surveillance system, through which the first confirmed case or potential outbreaks leading to clusters of suspected cases for each county were required to be investigated and reported. the extracted variables included demographic data, possible exposure and travel history, and clinical data using a structured form. the events reported by 29 january 2020 were included for data extraction. for events by 23 january 2020, which was the date of "locking down" wuhan city, all events (168 cases) in the system were extracted, and we used these data to construct an epidemic curve and estimate the incubation period distribution. of the events (281 cases) reported between 24 january and 29 january 2020, we focused on those events which included probable human-to-human transmission or epidemiologically linked cases, so that we could capture a larger number of these clusters for analyses of serial intervals, transmission events and comparative severity between primary cases and secondary cases. all cases included in our analyses were laboratory-confirmed cases, and the case definitions followed we drew the epidemic curve by illness onset for cases who reported that they had been in wuhan in the 14 days of preceding onset, and a separate epidemic curve for the other cases. cases with onset dates closed to the end of epidemic curve may not be reported due to delays in seeking medical attention and consequent delays in laboratory testing. to allow for onset-to-reporting delays, we used the nowcasting approach described by van de kassteele et al 15 to jointly estimate the augmented case number on the most recent dates and the onset-to-reporting distribution. based on 1000 augmented epidemic curves, then we fitted exponential growth models to obtain estimates of the growth rate and doubling time. we examine the characteristics of confirmed cases and compared the demographics, onset symptoms and results of some clinical tests between confirmed sporadic and cluster primary cases and cluster secondary cases. we also obtained information on secondary cases that had not been to wuhan but had close contact with another case that had been to wuhan and were presumed to be infected by that particular case. in these pairs of primary and secondary cases, we fitted a normal distribution to the serial intervals between illness onset dates, allowing for negative and zero serial intervals, and correcting for growth rates in the early stage of an epidemic. specifically, the parameters of the fitted normal distribution were corrected to normal (µ′,σ) where µ′ = µ + σ 2 ρ for the epidemic growth rate r estimated below (personal communication, neil ferguson). because information was available on the periods during which each secondary case had been exposed to their presumptive infector, we were able to identify cases where exposure is likely to have occurred before or after illness onset in the primary case infector. when the exposure window overlapped the onset date, we used our fitted incubation period distribution to resample 1000 infection times at random, excluding any that fell outside the exposure window, and counted the proportion of resampled times that fell before symptom onset in the infector. we collected detailed information on 168 confirmed cases, including 145 and 23 reporting that they had or had not, respectively, been in wuhan in the past 14 days. the demographics of the 145 and 23 cases were very similar (data not shown). the median age was 48 f i g u r e 1 panel a: occurrence by date of illness onset of cases identified outside of hubei province in persons with a history of travel from wuhan in the 14 d prior to onset. panel b: occurrence by date of illness onset of cases identified outside of hubei province in persons without a history of travel from wuhan in the 14 d prior to onset. panel c: augmented occurrence (yellow bars) by date of illness onset of cases identified outside of hubei province in persons with a history of travel from wuhan in the 14 d prior to onset with back filled cases considering delays between illness onset and seeking care and being tested (range 10-81) and 91 (54%) were male. only three (2%) of the cases who had visited wuhan also reported visiting the huanan seafood wholesale market. figure 1 shows the epidemic curve by illness onset of the cases in persons that had been to wuhan compared to cases in other persons that were presumed to represent onwards transmission. we used data augmentation to correct for reporting delays in cases with recent onset ( figure 1c ) and estimated that the growth rate was 0.14 per day (95% ci: 0.11, 0.17), and the doubling time was 5.3 days (95% ci: 4.3, 6.7). in this analysis, the mean onset to reporting delay was estimated to be 5.7 days (95% ci: 5.3, 6.1). we obtained data on exposure windows for 98 cases in individuals that had been in wuhan, by assuming that they had been infected while they were in wuhan. we fitted a lognormal distribution to the data on exposure periods and onset dates, correcting for epidemic growth, and estimated that the incubation period had mean 5. (14%) occurred in those who had a meal together, 2 (3%) were colleagues working together, 2 (3%) were those who took the same vehicle, and 1 (1%) occurred among neighbours. the identified 80 observations of transmission events were used for estimation of the serial interval ( figure 2b ). we fitted a normal distribution to these data, with allowing 4 negative serial intervals and correcting for epidemic growth, and estimated that the serial interval distribution had mean 5.7 days (95% ci: 4.7, 6.8) and standard deviation 3.5 days ( figure 2b ). in detailed investigations of contact patterns, we obtained information on the period when the secondary infection could have occurred, and related this to the illness onset date of the infector. figure 3 shows that of 80 pairs identified, pre-symptomatic transmission occurred in 9 pairs, post-symptomatic transmission occurred in 16 pairs, and in the remaining 55 pairs, transmission could have occurred either before or after the corresponding infector's illness onset date. in these 55 pairs, we used monte carlo simulations based on the incubation period distribution described above to estimate that 23/55 of transmission events had greater than 50% chance to be pre-symptomatic transmissions. thus, in total we infer that 32/80 (40%) of the observed transmission events were likely or very likely to have occurred prior to the onset of symptoms in the infector. we examined demographic and clinical characteristics of all the confirmed sporadic and clusters cases ( table 1) . age distributions were similar between the two groups of patients, while less male cases were identified in cluster secondary cases (43% vs 60%). cluster primary and sporadic cases were generally more severe, with 26% and 7% in severe and critical conditions, respectively, compared with 12% and 1% in cluster secondary cases. nearly all the primary and sporadic cases (96%) had a radiologic indication of pneumonia, compared with 74% in the secondary cases. among 80 cluster secondary cases, 87% had been classified as mild cases, while 66% (110/166) of the cluster primary and sporadic cases were mild. the primary and sporadic cases showed largely similar onset symptoms as the secondary cases. fever is the most common symptom, followed by headache, fatigue, dry cough and myalgia. generally higher proportions of the cluster primary cases and sporadic cases reported an onset of the symptoms than cluster secondary cases (table 1 ). in addition to systemic and respiratory presentations, a small proportion of the cases also reported gastrointestinal symptoms, including vomiting and diarrhoea. in this study, we report estimates of the transmission dynamics of covid-19 based on cases identified outside of hubei province. importantly, we examine quantitative evidence for pre-symptomatic infectiousness, a feature which complicates control strategies. we transmission events used to infer the occurrence of pre-symptomatic transmission. dots indicate the dates of onset of primary and secondary cases, and the shaded area in each row indicates the period of exposure of the secondary case to the primary case during which the secondary infection is thought to have occurred. brackets indicate the exposure window when the primary case was thought to have been infected. data were resolved to the nearest day, and so transmission windows are plotted from the start of the first date to the end of the last date, onset dates are plotted in the middle of the corresponding day, and if the secondary onset date is the same as the primary onset date, then the former is offset slightly so that both can be seen note: for patients having clinical test results of both lymphocyte count and proportion, a normal lymphocyte count refers to both the lymphocyte count within the range of 1-4 × 10 9 /l and the lymphocyte proportion to be 20%-40%. patients with either lymphoycyte count or lymphocyte proportion lower or higher than the normal range will be classified as "decreased" or "increased," respectively. a category of lymphocyte count is determined by both the count and proportion of lymphocyte (the proportion is derived as lymphocyte count divided by white blood cell count) in the blood test. demonstrate that the phenomenon of pre-symptomatic transmission is not uncommon, having occurred in a minimum of 9/80 transmission events ( figure 3 ). using statistical inference based on our estimated incubation period distribution, we estimated that pre-symptomatic transmission was likely to have occurred in up to 40% of the 80 transmission events in our data set. this observation should be interpreted in the context of isolation of some cases after illness onset, reducing the amount of post-symptomatic transmission that might otherwise have occurred. this also implies that social distancing measures may be some of the most important strategies to reduce transmissibility, for example closing schools and encouraging, or facilitating working at home, in addition to control of onwards transmission by sequestering symptomatic persons at home or in isolation facilities. our finding was consistent with other reports that the serial interval distribution was similar to, or much lower than the incubation period distribution, 13,18-21 consistent with the occurrence of pre-symptomatic transmission in case reports. [22] [23] [24] [25] [26] pre-symptomatic infectiousness is generally not thought to occur for most respiratory viruses, but measles is a well-known example of a respiratory infection that can be spread before symptom onset, 27 and viral shedding during the incubation period has also been reported for influenza. 28 viral shedding has been reported during the incubation period for covid-19, 29 and there were also asymptomatic cases for covid-19 across all age groups, in varying proportions depending on the intensity of surveillance and testing. 30, 31 in conducting investigations of clusters of cases, it is often found that secondary cases have on average milder illnesses than primary cases; for example, this was noted for middle east respiratory syndrome coronavirus infections. 32 here, we found that secondary cases were more likely to have milder disease (table 1) , which would be consistent with the existence of some milder covid-19 infections, which were not laboratory confirmed. the cluster investigations that we report here are not likely to represent the full spectrum of mild infections, and better information would be provided by prospective studies of close contacts with repeated collection of respiratory swabs and sera. our estimates of the growth rate of infections in wuhan in early january 2020 of around 0.14 per day (95% ci: 0.11, 0.17) are very consistent with previous reports. 4, 6 our estimate of the effective reproductive number in wuhan is now slightly lower than the previous estimate of r 0 4 and some other estimates of r 0 5-7 but that is because of the shorter serial interval. we included a limited number of cases in other cities in china that were detected in persons that had not been to wuhan ( figure 1b ), but the sample size was insufficient at the time of analysis to determine whether there has been sustained transmission in any other cities. the incubation period averaged 4.6 days and up to 11.1 days in 95% of infections (figure 2a) , which is important for specifying quarantine periods and also for understanding transmission dynamics. the city of wuhan was put under lockdown on 23 january 2020, and other nearby cities were also locked down on the following days. this stopped exportation of infections to other chinese cities, and the effect of this intervention has become more apparent in early february, given the delays that occur between infection, illness onset, admission to hospital and then laboratory testing. we restricted the study participants to covid19 analysis were also subject to ascertainment of symptom onset date, which was self-reported by the patient and could be less reliable especially at the early stage of symptom presentation. in conclusion, our analysis showed evidence indicative of pre-symptomatic transmission of covid-19. quarantine of exposed persons having close contact with infected cases before symptom onset could reduce the risk of further transmission. we gratefully thank benjamin j. cowling, peng wu, jessica y. wong, yiu chung lau, tim k. tsang from school of public health, university of hong kong for their guidance and support on study design, data analysis and interpretation. we appreciate the staff members of the county-, city-and province-level centers for disease control and prevention of china for their fieldwork on case investigation, data collection and validation. clinical features of patients infected with 2019 novel coronavirus in wuhan a novel coronavirus from patients with pneumonia in china a novel coronavirus outbreak of global health concern early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia pattern of early human-to-human transmission of wuhan nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov in china, from 2019 to 2020: a data-driven 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cases on board the diamond princess cruise ship a well infant with coronavirus disease 2019 (covid-19) with high viral load middle east respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility evidence for pre-symptomatic transmission of coronavirus disease 2019 (covid-19) in china key: cord-321358-plxz5mkg authors: zheng, jun title: sars-cov-2: an emerging coronavirus that causes a global threat date: 2020-03-15 journal: int j biol sci doi: 10.7150/ijbs.45053 sha: doc_id: 321358 cord_uid: plxz5mkg an ongoing outbreak of pneumonia caused by a novel coronavirus, currently designated as the severe acute respiratory syndrome coronavirus-2 (sars-cov-2), was reported recently. however, as sars-cov-2 is an emerging virus, we know little about it. in this review, we summarize the key events occurred during the early stage of sars-cov-2 outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients as well as the possible transmission pathways of the virus. furthermore, we also review the current knowledge on the origin and evolution of the sars-cov-2. we highlight bats as the potential natural reservoir and pangolins as the possible intermediate host of the virus, but their roles are waiting for further investigation. finally, the advances in the development of chemotherapeutic options are also briefly summarized. on 23 feb 2020, the lock-down of wuhan, a central city in china, has alarmed people all over the world of an emerging novel coronavirus that is posing a major public health and governance challenges. the novel virus, previously called the 2019-novel coronavirus (2019-ncov), is currently designated as the severe acute respiratory syndrome coronavirus-2 (sars-cov-2). as of 27 feb, this emerging infection has been reported in 47 countries, causing over 82,294 infections with 2,804 deaths ( fig. 1 ) [1] . this novel virus is also becoming a mounting threat to chinese and global economies. coronaviruses (covs) are members of the family coronaviridae, the enveloped viruses that possess extraordinarily large single-stranded rna genomes ranging from 26 to 32 kilobases in length [2] . covs have been identified in both avian hosts and various mammals, including bat, camels, dogs and masked palm civets, and are previously regarded as pathogens that only cause mild diseases in the immunocompetent people until the emergence of the coronavirus causing severe acute respiratory syndrome (sars-cov) in late of 2002 [3] [4] [5] [6] . currently, at least seven coronavirus species are known to cause diseases in humans. the viruses of 229e, oc43, nl63 and hku1 only cause common cold symptoms, which are mild. severe illness can be caused by the remaining three viruses, namely sars-cov, which resulted in the outbreak of sars in 2002 and 2003 [3, 4] ; the coronaviruses that are responsible the middle east respiratory syndrome (mers-cov), which emerged in 2012 and remains in the circulation in camels [7] ; and sars-cov-2, the viruses emerged in december 2019 in wuhan of china and a great effort is being undertaken to contain its spreading [8] . in this review, we will briefly introduce the outbreak history of sars-cov-2, the signs and symptoms of the infected patients, its transmission dynamics, the advances in the understanding on its evolutional origin and the chemotherapeutic options being developed for the treatment of its infection. the key events of sars-cov-2 outbreak and the pathogen characteristics since december 2019, an increasing number of patients with pneumonia of unknown etiology in wuhan, a city with 11 million people, have alarmed the local hospital. on 29 december 4 cases were linked to huanan seafood wholesale market [9] , where non-aquatic live animals, including several kinds of wild animals, were also on the sales. the local center for disease control (cdc) then found additional patients linked to the same market after investigation, and reported to china cdc on 30 dec 2019 [9] . the second day, world health organization (who) was informed of the cases of pneumonia of unknown etiology by china cdc [10]. on 6 jan 2020, a level 2 emergency response was launched by china cdc [11] . the causal agent was not identified until 7 jan 2020; a new type of coronavirus was isolated by chinese authority [10] . the genome sequence of sars-cov-2 (wh-human_1) was first released and shared by china on 10 jan [12] . the isolation and identification of sars-cov-2 apparently facilitated the development of molecular diagnostic methods and the confirmation of the infected patients. as of 21 jan, there are 270 cases were confirmed from wuhan [13]. on 23 jan, wuhan city was locked down by local government. on 30 jan, who declared a "public health emergency of international concern" (fig. 1) . subsequently, the viruses were successfully isolated from several laboratories [8, 14, 15] . the virion of sars-cov-2 looks like a solar corona by transmission electron microscopy imaging: the virus particle is in a spherical shape with some pleomorphism; the diameter of the virus particles range from 60 to 140 nm with distinctive spikes about 8 to 12 nm in length [8] . the observed morphology of sars-cov-2 is consistent with the typical characteristics of the coronaviridae family. the genome sequence of sars-cov-2 from clinical samples has been obtained by several laboratories with deep sequencing [8, [14] [15] [16] [17] [18] . the viral genome of sars-cov-2 is around 29.8 kilobase, with a g+c content of 38%, in total consisting of six major open reading frames (orfs) common to coronaviruses and a number of other accessory genes [14, 16] . the sequences analysis showed that the genome sequences of viruses from different patients are very conserved [14, 15, 19] , implying that the human virus evolves recently. a typical characteristic of the sars-cov-2 infected patient is pneumonia, now termed as coronavirus disease 2019 , demonstrated by computer tomographic (ct) scan or chest x -ray [3, 8, 18] . in the early stages, the patients showed the acute respiratory infection symptoms, with some that quickly developed acute respiratory failure and other serious complications [20] . the first three patients reported by the china novel coronavirus investigating and research team all developed severe pneumonia and two of these three patients with available clinical profiles showed a common feature of fever and cough [8] . a subsequent investigation of a family of six patients in the university of hong kong-shenzhen hospital demonstrated that all of them had pulmonary infiltrates, with a variety of other symptoms [18] . the chest x-ray and ct imaging in a study showed that 75% of 99 patients demonstrated bilateral pneumonia and the remaining 25% unilateral pneumonia [21] . overall, 14% of the patients showed multiple mottling and ground-glass opacity [21] . the first cases of coronavirus infection in the united states also showed basilar streaky opacities in both lungs by chest radiography. however, the pneumonia for this patient was only detected on the day 10 of his illness [22] . it is also of note that one of patients among the family of six patients did not present any other symptoms and signs, but had ground-glass lung opacities identified by ct scan [18] . at least four comprehensive studies on the epidemiological and clinical characteristics of sars-cov-2 infected patients have been performed [21, [23] [24] [25] . the most common signs and symptoms of patients are fever and cough [21, [23] [24] [25] . fatigue was complained by 96% of patients (n=138) in one study [24] , but was less outstanding (18%, n=44) in another report [23] . a combinational analysis of the common recorded signs or symptoms of the reported cases found that fever was observed in around 90% of the sars-cov-2 infected patients; the number of patients with cough is relatively less (68%) compared to fever (table 1 ). in addition, shortness of breath or dyspnea, muscle ache, headache, chest pain, diarrhea, haemoptysis, sputum production, rhinorrhoea, nausea and vomiting, sore throat, confusion, and anorexia were also observed in a proportion of the patients [21, [23] [24] [25] (table 1) . a common feature of patients of sars, mers or covid-19 is the presence of severe acute respiratory syndrome; however, the estimated fatality rate of covid-19 (2.3%) is much lower than sars (~10%) and mers (~36%) [26, 27] . furthermore, the viruses responsible for above three diseases are evolutionary distinct (see below for details) [19] . it is clear now that sars-cov-2 can be transmitted by human-to-human despite the majority of the early cases had contact history with the huanan seafood market [11, 18, 28] . analysis of 425 patients with confirmed covid-19 showed that the incubation period is 3 to 7 days. the mean was 5.2 days (95% ci: 4.1 to 7.0), and the 95 th percentile of the distribution is 12.5 days (95% ci: 9.2 to 18) [11] . notably, it was reported that the incubation period could be as long as 24 days in a rare case [25] . the basic reproductive number (r 0 ) up to the period of 4 jan 2020 was estimated based on the study of 425 patients to be 2.2 (meaning that one patient has been spreading infection to 2.2 other people) [11] , slightly smaller than the value of 2.68 by a modelling in another [29] . the r 0 of sars-cov-2 from both of these two studies is smaller than that of sras, which are 3 before public health measures were implemented [30] . however, subsequent investigation based on the analysis of high-resolution real-time human travel and infection data estimated that the r 0 is much larger, ranging from 4.7 to 6.6 before the control measures [31] , implying that sars-cov-2 is highly contagious and more infectious than initially estimated. this conclusion is consistent with the wide spread of sars-cov-2 within a short period time and was also echoed by the finding that sars-cov-2 spike (s) protein had 10-to 20-fold higher affinity to human angiotensin-converting enzyme 2 (ace2) receptor than that of sars-cov based on the cryo-em structure analysis of s proteins [32] . similar to sars-cov, the entry of sars-cov-2 into host cells depends on the recognition and binding of s protein to ace2 receptor of the host cells [14, 33] . the high affinity of s protein to ace2 receptor likely contributes to the quick spreading of virus. the finding of ace2 as the receptor of sars-cov-2 also indicates that human organs with high ace2 expression level, such as lung alveolar epithelial cells and enterocytes of the small intestine, are potentially the target of sars-cov-2 [34] . as a new coronavirus, it is not known yet about how sars-cov-2 spreads. current knowledge for sars-cov-2 transmission is largely based on what is known from the similar coronaviruses, particularly sars-cov and mers-cov, in which human-tohuman transmission occurs through droplets, contact and fomites. sars-cov is predominantly transmitted through indirect or direct contact with mucous membranes in the mouth, eyes, or nose [35] . it has been shown that unprotected eyes and exposed mucous membranes are vulnerable to sars-cov transmission [36] . a member of the national expert panel on pneumonia was infected by sars-cov-2 after the inspection in wuhan [37] . as he wore a n95 mask but not any eye protector, and experienced eye redness before the onset of pneumonia, it was thus suspected that unprotected exposure of the eyes to sars-cov-2 might be another transmission pathway [37] . however, sars-cov-2 was not detected from the conjunctival swab sample in a confirmed covid-19 patent with conjunctivitis [38] , suggesting that more evidences are needed before concluding the conjunctival route as the transmission pathway of sars-cov-2. the mode of transmission by mers-cov is not well understood but is believed to spread largely via the respiratory close contact route [39, 40] . based on the transmission mode of sars-cov and mers-cov, a serial of preventive measures have been recommended, including avoiding close contact with people suffering from acute respiratory infections and frequent hand-washing [41] . the viruses of sars-cov-2 were also detected in the stool samples in some patients but not all [18, 22] , suggesting that a possible fecal-oral transmission occurs [42] . a systematic study showed that viruses could be detected in oral swabs, anal swabs and blood samples of the patients, and the anal swabs and blood could test positive when oral swab tested negative [43] . furthermore, a trend of shift from more oral positive in the collected samples during the early period of patient infection to more anal positive during later period of infection was also found [43] . therefore, a multiple shedding routes of sars-cov-2 might exist. one of the challenges for preventive control of sars-cov-2 spreading is that the viruses are likely transmitted by asymptomatic contact. a german businessman was found infected by sars-cov-2 after attending a conference together with a colleague, who had no signs or symptoms of infection but had become ill due to the sars-cov-2 infection later [44] . this observation suggests that infected patients likely start to shed viruses before the onset of any symptom, which undoubtedly will bring great challenge to the current practice of preventive control by measuring body temperature. despite the claim of the transmission by asymptomatic contact has been challenged [45] , other asymptomatic carriers were also observed to transmit the viruses of sars-cov-2 [46, 47] . consistently, a study found that an asymptomatic patient had a similar vial loads in the samples of nasal and throat swabs to that of the symptomatic patients [48] . it is critical to identify the origin, native host(s) and evolution pathway of the virus that causes an outbreak of a pandemic. this information can help understand the molecular mechanism of its cross-species spread and implement a proper control measure to prevent it from further spreading. the association of initially confirmed sars-cov-2 cases with huanan seafood market suggested that the marketplace has played a role in the early spreading [11, 23] , however, whether it is the origin of the outbreak and what is the native host(s) of sars-cov-2 remain uncertain. in fact, the firstly documented patient was not linked to huanan seafood market [23] . the analysis of sars-cov-2 origin was firstly performed based on the genome sequence of virus isolates from six patients [19] . when compared with sars-cov and mers-cov, the nucleotide sequences of sars-cov-2 showed a higher homology with that of sars-cov while was relatively poor with that of mers-cov [19] . despite some of the six major ofrs of sars-cov-2 genes share less than 80% identity in nucleotide acids to sars-cov, the seven conserved replicase domains in orf1ab has 94.6% sequence identity in amino acids between sars-cov-2 and sars-cov [14] , suggesting that these two viruses might belong to the same species. the origin of sars-cov has been extensively investigated. masked palm civets were initially considered to transmit sars-cov to humans as a close variant of sars-cov was detected from palm civets [49] . this conclusion was supported by the fact that three of the four patients had the record of contact with palm civets during the two small-scale of sars outbreaks occurred in late 2003 and early 2004 [50, 51] . however, a deep investigation based on the genome sequence of isolated viruses showed that sars-cov-like virus in civet had not been circulating for long [52] . subsequently, coronaviruses with high similarity to the human sars-cov or civet sars-cov-like virus were isolated from horseshoe bats, concluding the bats as the potential natural reservoir of sars-cov whereas masked palm civets are the intermediate host [53] [54] [55] [56] . it is thus reasonable to suspect that bat is the natural host of sars-cov-2 considering its similarity with sars-cov. the phylogenetic analysis of sars-cov-2 against a collection of coronavirus sequences from various sources found that sars-cov-2 belonged to the betacoronavirus genera and was closer to sars-like coronavirus in bat [19] . by analyzing genome sequence of sars-cov-2, it was found that sars-cov-2 felled within the subgenus sarbecovirus of the genus betacoronavirus and was closely related to two bat-derived sars-like coronaviruses, bat-sl-covzc45 and bat-sl-covzxc21, but were relatively distant from sars-cov [15, 18, [57] [58] [59] . meanwhile, zhou and colleagues showed that sars-cov-2 had 96.2% overall genome sequence identity throughout the genome to batcov ratg13, a bat coronavirus detected in rhinolophus affinis from yunnan province [14] . furthermore, the phylogenetic analysis of full-length genome, the receptor binding protein spike (s) gene, and rna-dependent rna polymerase (rdrp) gene respectively all demonstrated that ratg13 was the closest relative of the sars-cov-2 [14] . however, despite sars-cov-2 showed high similarity to coronavirus from bat, sars-cov-2 changed topological position within the subgenus sarbecovirus when different gene was used for phylogenetic analysis: sars-cov-2 was closer to bat-sl-covzc45 in the s gene phylogeny but felled in a basal position within the subgenus sarbecovirus in the orf1b tree [57] . this finding implies a possible recombination event in this group of viruses. of note, the receptor-binding domain of sars-cov-2 demonstrates a similar structure to that of sars-cov by homology modelling but a few variations in the key residues exist at amino acid level [15, 19] . despite current evidences are pointing to the evolutional origin of sars-cov-2 from bat virus [15, 57] , an intermediate host between bats and human might exist. lu et. al. raised four reasons for such speculation [15] : first, most bat species in wuhan are hibernating in late december; second, no bats in huanan seafood market were sold or found; third, the sequence identity between sars-cov-2 and bat-sl-covzc45 or bat-sl-covzxc21, the closest relatives in their analyses, is lower than 90%; fourth, there is an intermediate host for other humaninfecting coronaviruses that origin from bat. for example, masked palm civet and dromedary camels are the intermediate hosts for sars-cov [49] and mers-cov respectively [60] . a study of the relative synonymous codon usage (rscu) found that sars-cov-2, bat-sl-covzc45, and snakes had similar synonymous codon usage bias, and speculated that snake might be the intermediate host [61] . however, no sars-cov-2 has been isolated from snake yet. pangolin was later found to be a potential intermediate host for sars-cov-2. the analysis of samples from malytan pangolins obtained during anti-smuggling operations from guangdong and guangxi customs of china respectively found novel coronaviruses representing two sub-lineages related to sars-cov-2 [62] . the similarity of sars-cov-2 to these identified coronaviruses from pangolins is approximately 85.5% to 92.4% in genomes, lower than that to the bat coronavirus ratg13 (96.2%) [14, 62] . however, the receptor-binding domain of s protein from one sub-lineage of the pangolin coronaviruses shows 97.4% similarity in amino acid sequences to that of sars-cov-2, even higher than that to ratg13 (89.2%) [62] . interestingly, the pangolin coronavirus and sars-cov-2 share identical amino acids at the five critical residues of rbd of s protein, while ratg13 only possesses one [62] . the discovery of coronavirus close to sars-cov-2 from pangolin suggests that pangolin is a potential intermediate host. however, the roles of bat and pangolin as respective natural reservoir and intermediate host still need further investigation. as an emerging virus, there is no effective drug or vaccine approved for the treatment of sars-cov-2 infection yet. currently, supportive care is provided to the patients, including oxygen therapy, antibiotic treatment, and antifungal treatment, extra-corporeal membrane oxygenation (ecmo) etc. [21, 22] . to search for an antiviral drug effective in treating sars-cov-2 infection, wang and colleagues evaluated seven drugs, namely, ribavirin, penciclovir, nitazoxanide, nafamostat, chloroquine, remdesivir (gs-5734) and favipiravir (t-750) against the infection of sars-cov-2 on vero e6 cells in vitro [63] . among these seven drugs, chloroquine and remdesivir demonstrated the most powerful antiviral activities with low cytotoxicity. the effective concentration (ec 50 ) for chloroquine and remdesivir were 0.77âµm and 1.13âµm respectively. chloroquine functions at both viral entry and post-entry stages of the sars-cov-2 infection in vero e6 cells whereas remdesivir does at post-entry stage only. chloroquine is a drug used for an autoimmune disease and malarial infection with potential broad-spectrum antiviral activities [64, 65] . an ec90 (6.90 âµm) against the sars-cov-2 in vero e6 cells is clinically achievable in vivo according to a previous clinical trial [66] . remdesivir is a drug currently under the development for ebola virus infection and is effective to a broad range of viruses including sars-cov and mers-cov [67, 68] . functioning as an adenosine analogue targeting rdrp, remdesivir can result in premature termination during the virus transcription [69, 70] . the ec90 of remdesivir against sars-cov-2 in vero e6 cells is 1.76 âµm, which is achievable in vivo based on a trial in nonhuman primate experiment [63, 69] . encouragingly, in the first case of sars-cov-2 infection in the united states, treatment with remdesivir was provided intravenously to the patient on the day 7 without any adverse events observed. the patient's clinical condition was improved on day 8 and the previous bilateral lower-lobe rales disappeared, implying the remdesivir might be effective to the treatment of sars-cov-2 infection [22] . this result, however, should be interpreted with caution as this is only single case study and a proper trial control was lacking. in addition, baricitinib, a janus kinase inhibitor, was also predicted to reduce the ability of virus to infect lung cell by an analysis of benevolentai [71] . currently, chloroquine and remdesivir are under phase 3 clinical trial and open-label trial for treatment of sars-cov-2 infection respectively (table 2 ) [72] . preliminary results showed that chloroquine phosphate had apparent efficacy in treatment of covid-19 [73] . however, caution must be taken during clinical use of chloroquine as its overdose is highly fatal without known antidote [74] . despite the lack of documented in vitro data supporting the antiviral efficacy on sars-cov-2, several antiviral chemotherapeutic agents have been registered for the clinical trials for the treatment of covid-19 (table 2 ) [72] . sars-cov-2 is an emerging pathogen, without any effective drug available for treatment 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that no competing interest exists. key: cord-350822-m3t7l9zw authors: mo, yuanyuan; deng, lan; zhang, liyan; lang, qiuyan; liao, chunyan; wang, nannan; qin, mingqin; huang, huiqiao title: work stress among chinese nurses to support wuhan in fighting against covid‐19 epidemic date: 2020-05-20 journal: j nurs manag doi: 10.1111/jonm.13014 sha: doc_id: 350822 cord_uid: m3t7l9zw aims: to investigate the work stress among chinese nurses who are supporting wuhan in fighting against coronavirus disease 2019 (covid‐19) infection and to explore the relevant influencing factors. background: the covid‐19 epidemic has posed a major threat to public health. nurses have always played an important role in infection prevention, infection control, isolation, containment and public health. however, available data on the work stress among these nurses are limited. methods: a cross‐sectional survey. an online questionnaire was completed by 180 anti‐epidemic nurses from guangxi. data collection tools, including the chinese version of the stress overload scale (sos) and the self‐rating anxiety scale (sas), were used. descriptive single factor correlation and multiple regression analyses were used in exploring the related influencing factors. results: the sos (39.91 ± 12.92) and sas (32.19 ± 7.56) scores of this nurse group were positively correlated (r = 0.676, p < .05). multiple regression analysis showed that only children, working hours per week and anxiety were the main factors affecting nurse stress (p = .000, .048, .000, respectively). conclusions: nurses who fight against covid‐19 were generally under pressure. implications for nursing management: nurse leaders should pay attention to the work stress and the influencing factors of the nurses who are fighting against covid‐19 infection, and offer solutions to retain mental health among these nurses. in december 2019, patients with pneumonia of unknown cause were emerged in wuhan, china (catton, 2020; huang, wang, & li, 2020; li et al., 2020) . local works and those conducted by the experts from who confirmed that the pathogen causing this novel pneumonia is sars-cov-2, and this type of pneumonia is called the coronavirus disease 2019 . the covid-19 epidemic has posed a remarkable threat to public health (pan et al., 2020) . on 11 march 2020, who director-general dr. tedros adhanom ghebreyesus said that there was deep concern about the extent and severity of the covid-19 epidemic, which the world health organization (who) assessed to be characterized as a pandemic (e.g., social network or clinical setting; the novel coronavirus pneumonia outbreak has acquired pandemic characteristics, 2020). as of 23:59 on 19 march 2020, a total of 234,073 confirmed cases and 9,840 deaths have been reported globally. in europe, the cumulative number of cases reached 104,591, with 4,899 deaths. covid-19 has been reported in 176 countries and regions, and more than 150,000 cases have been confirmed outside china (e.g., social network or clinical setting; coronavirus disease 2019 (covid-19) situation report-60, 2020). as of this date, the number of confirmed and suspected cases outside china is increasing dramatically, as is the number of deaths. covid-19 presents a vast public health challenge, not only to china but also around the world. nurses have always played an important role in infection prevention, infection control, isolation, containment and public health (graeme, 2020) . as of 1 march, a total of 28,679 nurses had been sent to hubei province to fight against covid-19 infection (e.g., social network or clinical setting; the white coat went out to battle, 2020). nurses on the front line in this event are showing the commitment and compassion that nurses do everywhere, but the truth is they are putting their lives at risk in the course of their duties (catton et al., 2020) . one third of all fatalities during the 2003 sars outbreak in china were health care professionals (hung, 2003) . in the early days of the outbreak, more than 3,000 medical workers in hubei province were infected, 40% in hospitals and 60% in communities (e.g., social network or clinical setting; national support wuhan medical staff 'zero infection' novel coronavirus pneumonia, 2020). the unfolding emergency caused by the covid-19 in wuhan is putting nursing services under intense pressure. when nurses are exposed to working environments with high job demands and low resources, higher job stress and greater physical and psychological stress symptoms may adversely affect health and well-being (chou, li, & hu, 2014; khamisa, oldenburg, peltzer, & ilic, 2015; lin, liao, chen, & fan, 2014; malinauskiene, leisyte, romualdas, & kirtiklyte, 2011) . maintaining the mental health of nursing staff is essential to control infectious diseases (kang et al., 2019; xiang et al., 2020) . at present, studies on the epidemic situation of covid-2019 mostly focused on epidemiological investigation, prevention and control, diagnosis and treatment. fewer studies have investigated the mental health problems of clinical medical workers during the epidemic of covid-19. the purpose of the present study was to investigate the work stress load among chinese nurses who support wuhan in fighting against covid-19 infection and to explore the relevant influencing factors for the development of psychological interventions for chinese nurses in order that they can adjust to public health emergencies. a cross-sectional survey. by means of convenient sampling, nurses from guangxi supporting wuhan were selected to carry out the survey. the inclusion criteria were as follows: nurses from guangxi who are involved in fighting against covid-19, those who have entered the clinical front line to participate in the rescue work and those who volunteered to participate in this study. as of 21 february 2020, all the nurses (around 210) were invited to participate in this study. the response rate was 85.71%, which resulted in a sample of 180 nurses. according to literature review and expert consultation, self-made general information and demographic questionnaires, including gender, age, nursing age, education, professional qualifications, marital status, fertility status, whether the participants are the only child in their families, whether their family supports them, whether they have been trained in sars-cov-2 prevention and control knowledge, self-assessment of the mastery of covid-19 prevention and control knowledge, whether they participate in protective skills training, self-assessment of the mastery of the protection skills, experience in related departments (e.g., fever clinic, infection department, respiratory and critical medicine department, critical medicine department and emergency department), whether they volunteer to participate in the support work, whether they regret participating in the support work, whether they have completed the support work with confidence, the name of the hospital where they are working in, the time they participated in support and working hours per week, were completed. amirkhan (2012) developed a sos, and qian & leilei (2014) introduced it and conducted cultural commissioning. the chinese version of the sos has good reliability and validity. the cronbach's α value is 0.936, and the content validity is 0.860. the scale consists of two dimensions: event load (12 entries) and individual vulnerability (10 entries), with 22 entries using a 5-point scoring method, 'never before' scores 1 point and 'always there' scores 5 points, with the total score in the range of 22-110 points. the higher the score is, the greater the pressure load will be. cronbach's α value is 0.777, and the half-coefficient is 0.757, which has good reliability and validity (tian, wang, li, wang & dang, 2019) . the total score of sas is the cumulative score of each item. the higher the score is, the more severe the anxiety will be. online survey (via a questionnaire website platform) was send to the heads of each batch of nurses from guangxi who are supporting in wuhan, whom were asked to send on to nurses. the participants could complete the questionnaire via computer or smartphone that can open a website link or scan a quick response code. the online survey was sent to the potential participants with an invitation letter containing information regarding purpose, anonymity and confidentiality. consent was implied if participants connected to the website link and completed the questionnaire. counting data were expressed by frequency and percentage, and the measurement data were expressed by x ± s. comparisons between two groups were performed using two independent-sample t tests, and comparisons between multiple groups were performed using single-factor anova. the correlation between stress load and anxiety was analysed using the pearson correlation analysis, and multiple linear regression analysis was used for multivariate analysis. all statistical analyses were performed with spss for windows 22.0, with two-tailed p < .05 to be considered statistically significant. of the 180 nurses who participated in the survey, 18 were male (10%) and 162 were female (90%). the age of these nurses ranged from 21 to 48 (32.71 ± 6.52) years, with years of working ranging from 2 to 32 (8.45 ± 3.86) years. the education profile of the participants is as follows: 34 (18.89%) junior college students, 143 (79.44%) undergraduates and 3 (1.67%) masters. the professional qualification is as follows: 7 (3.89%) primary nurses, 102 (56.67%) senior nurses, 59 (32.78%) supervisors and 12 (6.67%) deputy chief nurses. the marital status of the participants is as follows: 89 (49.44%) married, 86 (47.78%) unmarried and 5 (2.78%) divorced. the fertility status of the participants is as follows: 82 (45.56%) nurses are fertile, and 98 (54.44%) have no children. the survey showed that the total stress load score of 180 nurses who assisted in combating the covid-19 was 39.91 ± 12.92, with a score rate of 39.91%, of which the event load score was 19.32 ± 6.52 points, and the individual vulnerability score was 20.59 ± 6.61 points. the total sas score was 32.19 ± 7.56 points, which was higher than the national standard points (29.78 + 0.46), and the difference was statistically significant (t = 4.27, p < .001). according to the pearson correlation analysis, the total stress load score and each dimension were positively correlated with sas (the r values were 0.676, 0.667 and 0.663); that is, the higher the stress load is, the higher the total anxiety score is, and the more evident the anxiety mood will be. the results showed that different professional qualifications, whether the participants are the only child in their families, the severity of patients, working hours per week, diet and sleep status had impacts on nurses' stress load scores (p < .05), as shown in table 1 . when the total stress load was used as a dependent variable, the single-factor analysis of the stress load that had statistically significant titles (primary nurse = 1, senior nurse = 2, nurse in charge = 3 and deputy chief nurse = 4), whether the participants are the only child in their families (yes = 1, no = 2), the severity of patients (suspected = 1, mild = 2, common = 3, severe = 4 and critically ill = 5), working hours per week (<20 hr = 1, 20-25 hr = 2, 26-30 hr = 3, 31-35 hr = 4, and >35 hr = 5), whether they adapted to daily diet (yes = 1, no = 2), sleep status (very good = 1, good = 2, average = 3, not very good = 4 and very bad = 5) and sas total score (substituting the actual value) were used as independent variables for multiple linear regression analysis. the results showed that whether the participants are the only child in their families, working hours per week and anxiety were the main factors influencing the stress load of nurses assisting in the fight against covid-19, which can explain 52.1% of the total variation, as shown in table 2 . the results of this study showed that the total stress load of nurses who assisted in fighting against covid-19 was 39.91 ± 12.92 points, with a score rate of 39.91%, and those with a score > 50 nursing team to assist in hubei. given unknown and uncontrollable nature of the epidemic rescue work, coupled with being far away from their hometown and loved ones, the nurses helping in hubei had certain psychological pressure. the pressure load of the nurses in hubei who participated in this study was at a moderately low level, which was slightly lower than that in the study of wu et al. (2020) and other studies (kane, 2009; lin et al., 2014) , which may be attributed to the high the knowledge of covid-19 is limited, but it is highly contagious. in order to better care for patients and protect nurses, the training of the nursing team's business capabilities should be strengthened, training plans of the covid-19 epidemic should be formulated, the training content should be rationally set, and multimedia network platforms should be used to promote the participation of all staff in training and improve the knowledge and skills reserve of the nursing staff and epidemic response ability. the stress load score of nurses who are the only child in their families in the present study was 50.87 ± 10.47 points and that of nurses who are the non-only child in their families was 38.91 ± 12.68 points (p < .05), which indicated that nurses who are the only child in their families were more stressful. this result may be correlated with role conflict and social support system. they worry about the health of their family members and fear that if they died of covid-19, their parents will lose their only child. when multiple roles are in conflict, certain psychological pressure will be present. social support is an important protective factor for psychological resilience that alleviates mental stress and lifts psychological barriers (su & guo 2015) . strengthening social support among nurses could also mitigate the effect of job strain on health, as has been mentioned in the literature (garcia-rojas, choi, & krause, 2015; schmidt, 2013) . thus, the social support system of nurses should be actively mobilized. nurses should keep in touch with their families and friends so as to achieve spiritual support. at the same time, nurses should encourage one another, discuss and share our feelings and experiences with their colleagues in a timely manner, and vent negative emotions. hu, hu, yang , han, yanmei (2014) reported that the social support of the nurses who are the only child in their families maintains their mental health. furthermore, the worries of the front-line nurses should be reafter wearing a full set of protective clothing, nurses' breathing will be limited to a certain extent. to save the use of isolation clothing during work, nurses do not drink water or go to the toilet, thereby increasing the difficulty of nursing work. in this case, the longer the working time per week is, the higher the consumption of body and mind will be. hence, the body is in a state of tension and fatigue. if tension cannot be released for a long time, then the nurse is prone to burnout. burnout is correlated with the physical and mental health of nurses and affects the quality and safety of nurses. stress from work moderately affects burnout (liu & aungsuroch, 2019) . thus, nurse managers should strengthen the allocation and management of human resources, scientifically arrange shifts, reduce the work intensity of nurses and decrease work pressure. in the case of sufficient human resources, nurses' participation in the treatment of covid-19 is for less than 1 month. at the same time, the support of medical protective equipment and other related materials should be increased, and conditions to provide medical staff with shower and bath facilities should be actively created, thereby ensuring that the staff can thoroughly bathe when leaving the isolated ward after work and reducing the possibility of infection. anxiety is a negative emotional state perceived by individual subjectively and one of the most common psychological obstacles of nurses (gao et al., 2012; dongbo et al., 2018) . in this survey, the average score of sas was 32.19 ± 7.56, which was significantly higher than the national standard anxiety level (p < .05). this result showed that nurses had evident anxiety, which was similar to the results of wu et al. (2020) and zhang, li, zheng, zhang, (2020) . the results of a multifactor analysis showed that anxiety is an important factor affecting nurses' stress load. the correlation analysis also shows that anxiety is positively correlated with stress load. the more evident the anxiety is, the more intense the pressure that the nurses will feel. many previous studies have also shown that nurses with high stress lead to anxiety, frustration, depression and other psychological disorders and emotions (malinauskiene et al., 2011; teles, barbosa, & vargas, 2014) . covid-19 is highly infectious and spread rapidly, with suspected and confirmed patients increasing daily. nurses feel anxiety and helplessness due to so many patients. the government of china has implemented policies to address these mental health problems. medical workers infected with covid-19 due to the performance of their duties, they shall be identified as industrial injury and enjoy the benefits of industrial injury insurance according to law (e.g., social network or clinical setting; occupational injury insurance supports occupational injury 'protection umbrella' for prevention and rescue personnel in the fight against new coronavirus pneumonia, 2020). online platforms with medical advice have been provided to share information on how to decrease the risk of transmission between the patients in medical settings, which aims to eventually reduce the anxiety and pressure on medical workers (kang et al., 2019) . nurses should maintain their psychological health to ensure the quality of care for patients (hsiao & tseng 2020) . nurse managers should guide the nurses to adjust their psychological state scientifically. leisure activities and training on how to relax should be properly arranged to help staff reduce stress. the results of this study showed a widespread pressure on nurses who are supporting in wuhan to fight against covid-19. maintaining the mental health of nursing staff is essential to control covid-19. nurse leaders should pay attention to the work stress and the related factors of the clinical nurses. nurse managers should try the best to provide safe working conditions for nurses, while offering financial subsidies and rewards, so as to mobilize the enthusiasm and conscientiousness of nurses. the knowledge of covid-19 is limited, but it is highly contagious. nurses who received covid 19 epidemic training had higher mental health levels than those who did not this work was supported by funds from the special project of guangxi department of science and technology on emergency treatment of covid-19 (grant no. 2020ab39028) . the authors thank the research participants for their participation in the study and heads of each batch of nurses who distributed the questionnaires to the nurses. we would like to extend our deepest gratitude to professor chuanyi ning for his language checking. hh and mq conceived the study. ym created and performed the literature search strategy. ld and ql built the data extraction file. ym and lz performed the data extraction. hh and mq supervised the process. ym performed the results. all authors contributed extensively to this work, interpreted the data and contributed substantially to the writing and revision of the manuscript, and read and approved the final version of the manuscript. the procedures of this study were reviewed and approved by the stress overload: a new approach to the assessment of stress national support wuhan medical staff "zero infection global challenges in health and health care for nurses and midwives everywhere job stress and burnout in hospital employees: comparisons of different medical professions analysis of nurse anxiety and its influencing factors conscientiousness, openness to experience and extraversion as predictors of nursing work performance: a facet-level analysis anxiety symptoms among chinese nurses and the associated factors: a cross sectional study psychosocial job factors and 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elsewhere? early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the impact of shift work on nurses' job stress, sleep quality and self-perceived health status work stress, perceived social support, self-efficacy and burnout among chinese registered nurses associations between self-rated health and psychosocial conditions, lifestyle factors and health resources among hospital nurses in lithuania occupational injury insurance supports occupational injury "protection umbrella" for prevention and rescue personnel in the fight against new coronavirus pneumonia reliability and validity test of pressure load scale in chinese nurses relationship between psychological elasticity, work stress and social support of clinical female nurses demand-control model and occupational stress among nursing professionals: integrative review psychosocial work conditions and quality of life among primary health care employees: a cross sectional study reliability and validity evaluation of anxiety and depression scale in clinical application of patients with liver cirrhosis use of assessment scales, turnover and job strain in nursing staff: a study in a colombian hospital how to provide an effective primary health care in fighting against severe acute respiratory syndrome: the experiences of two cities mwo9p dl29d mkmh5 npzp2 00312.shtml world health organization (2020, march20) survey of sleep quality of clinic-al front-line nurses and its influencing factors in the fight against new coronavirus pneumonia timely mental health care for the 2019 novel coronavirus outbreak is urgently needed investigation and counter-measures of nurse anxiety in a hospital with a new coronavirus pneumonia in hangzhou key: cord-351600-bqw9ks4a authors: zhang, shuai; guo, mengfei; duan, limin; wu, feng; hu, guorong; wang, zhihui; huang, qi; liao, tingting; xu, juanjuan; ma, yanling; lv, zhilei; xiao, wenjing; zhao, zilin; tan, xueyun; meng, daquan; zhang, shujing; zhou, e; yin, zhengrong; geng, wei; wang, xuan; zhang, jianchu; chen, jianguo; zhang, yu; jin, yang title: development and validation of a risk factor-based system to predict short-term survival in adult hospitalized patients with covid-19: a multicenter, retrospective, cohort study date: 2020-07-16 journal: crit care doi: 10.1186/s13054-020-03123-x sha: doc_id: 351600 cord_uid: bqw9ks4a background: coronavirus disease 2019 (covid-19) has become a public health emergency of global concern. we aimed to explore the risk factors of 14-day and 28-day mortality and develop a model for predicting 14-day and 28-day survival probability among adult hospitalized patients with covid-19. methods: in this multicenter, retrospective, cohort study, we examined 828 hospitalized patients with confirmed covid-19 hospitalized in wuhan union hospital and central hospital of wuhan between january 12 and february 9, 2020. among the 828 patients, 516 and 186 consecutive patients admitted in wuhan union hospital were enrolled in the training cohort and the validation cohort, respectively. a total of 126 patients hospitalized in central hospital of wuhan were enrolled in a second external validation cohort. demographic, clinical, radiographic, and laboratory measures; treatment; proximate causes of death; and 14-day and 28-day mortality are described. patients’ data were collected by reviewing the medical records, and their 14-day and 28-day outcomes were followed up. results: of the 828 patients, 146 deaths were recorded until may 18, 2020. in the training set, multivariate cox regression indicated that older age, lactate dehydrogenase level over 360 u/l, neutrophil-to-lymphocyte ratio higher than 8.0, and direct bilirubin higher than 5.0 μmol/l were independent predictors of 28-day mortality. nomogram scoring systems for predicting the 14-day and 28-day survival probability of patients with covid-19 were developed and exhibited strong discrimination and calibration power in the two external validation cohorts (c-index, 0.878 and 0.839). conclusion: older age, high lactate dehydrogenase level, evaluated neutrophil-to-lymphocyte ratio, and high direct bilirubin level were independent predictors of 28-day mortality in adult hospitalized patients with confirmed covid-19. the nomogram system based on the four factors revealed good discrimination and calibration, suggesting good clinical utility. since december 2019, an ongoing outbreak of coronavirus disease 2019 (covid-19) has struck wuhan, hubei province, china [1] [2] [3] [4] . human-to-human transmission has occurred through respiratory droplets or likely feces [5, 6] . epidemiological and clinical characteristics of patients with covid19 in china have been reported [2] [3] [4] 7] . the number of cases grew quickly since january 2020. as of june 9, 2020, 7,039,918 confirmed cases of covid-19 have occurred, resulting in 404,396 deaths [8] . outbreaks of covid-19 infection imposed a great burden on the healthcare system of many countries. to guide the allocation of limited healthcare resources, as well as the timely recognition and intervention of patients who were at high risk of mortality, efficient prognosis of the disease is needed. previous reports have shown age, sequential organ failure assessment (sofa) score, d-dimer, preexisting concurrent cardiovascular or cerebrovascular diseases, amounts of cd3 + cd8 + t cells, and cardiac troponin i to be risk factors for mortality of adult inpatients with covid-19 [9] [10] [11] . meanwhile, several prognostic models for predicting mortality risk have been developed [12, 13] . the most common predictors included in this prognostic model were age, sex, c-reactive protein (crp), lactate dehydrogenase (ldh), and lymphocyte count. however, most of these studies have relatively few outcome events, showed a high risk of model overfitting, and failed to clearly describe the intended use of these models. in this study, we investigated 828 patients with confirmed covid-19 who were admitted to wuhan union hospital west area and central hospital of wuhan between january 12 and february 9, 2020. since the median time to death from illness onset was reported to be 18.5 days, we believed 28-day could be an appropriate time point for the inclusion of mortality events and administrative censoring [10] . we aimed to explore the risk factors of 28-day mortality and develop a nomogram scoring system for predicting 28-day survival probability among patients with covid-19. this multicenter, retrospective, cohort study (clinical trial identifier chictr2000029770) was conducted at wuhan union hospital west area and central hospital of wuhan. the study was approved by the institutional ethics committee of union hospital, tongji medical college, huazhong university of science and technology (20200036); the requirement for informed consent was exempted by the ethics committee. the inclusion criterion was adult patients with confirmed covid-19. those who lacked laboratory findings and ct images or lost 28-day follow-up were excluded. besides, patients with hematological diseases had abnormal blood routine test due to their hematologic disorders, which made the analysis of blood routine test unfeasible, and were also excluded. in the training cohort, we retrospectively analyzed 604 consecutive patients with confirmed or suspected covid-19 who were admitted in wuhan union hospital west area between january 12, 2020, and february 7, 2020. eighty-eight of the 604 cases were excluded from the study; among them, 71 were suspected cases, 9 lacked laboratory findings and ct images due to their death or being transferred to other hospitals within 24 h after admission, and 8 patients were with hematological diseases. finally, a total of 516 patients were enrolled in the training cohort (union hospital training cohort, 420 survivors and 96 non-survivors, 87 patients died within 28 days of admission, fig. 1 ). next, another 194 consecutive patients were admitted in wuhan union hospital west area between february 8, 2020, and february 9, 2020. among them, 3 were suspected cases, 4 lacked laboratory findings and ct images due to their death within 24 h after admission, and one patient had hematological diseases; 8 patients were excluded from the study. finally, 186 patients with confirmed covid-19 were included as external validation cohort 1 (union hospital external validation cohort, 156 survivors and 30 non-survivors, 26 patients died within 28 days of admission). a total of 158 patients with confirmed or suspected covid-19 who were admitted in central hospital of wuhan between january 12, 2020, and february 6, 2020, were selected by simple random sampling. of the158 patients, 31 were suspected cases and one died within 24 h after admission, all of whom were excluded from the study, and the remaining 126 confirmed patients were included as the external validation cohort 2 (central hospital external validation cohort, 106 survivors and 20 non-survivors). a total of 46 deceased patients had been reported in a previous submission, and 18 patients participated in a phase 3 randomized, double-blind, placebo-controlled, multicenter study for evaluating the efficacy and safety of remdesivir in hospitalized adult patients with severe covid-19 [14, 15] . the diagnosis and clinical classification of covid-19 were based on the guidelines of the diagnosis and clinicians from the hospital identified patients who satisfied the study inclusion criteria through surveillance of all patients. we collected all available information from patients, their families, physicians, and the electronic medical records in the hospital, including the epidemiological history; clinical, laboratory, and ct findings; treatment (i.e., antiviral therapy, corticosteroid therapy, respiratory support, kidney replacement); and outcomes. all clinical data used in this study were collected from the first day of hospital admission unless indicated otherwise. electronic medical data were inputted onto a local server. a team of trained physicians searched the patient charts for all the information recorded. for patients discharged within 28 days after admission, patients or their families were followed up to obtain the information about their 14-day and 28-day outcomes by telephone interviews. the primary outcome of this study was mortality at 14 days and 28 days after admission. to avoid overfitting in our model, we calculated the numbers of variables allowed to enroll in our multivariable cox regression model based on a previous study for guidance on sample size requirements for prediction models [17] . in our multivariable model, by setting nagelkerke's r 2 = 0.18, we found that our sample size was sufficient to estimate the overall outcome risk and 6 variables could be enrolled in the multivariable analyses. considering a total number of 516 patients (with 96 decreased patients within 28 days after admission), the final nagelkerke's r 2 = 0.163, the cox-snell r squared statistic (r 2 cs ) = 0.099, and the candidate predictor parameter (epp) = 14.46, with 95% ci for overall risk = 0.138 and 0.203. among a dozen of indicators, which were associated with 28-day mortality in unavailable cox regression analyses (p < 0.001), variables included into the multivariable cox regression model were selected mainly based on the previous evidence, clinical significance, the correlation between predictors, and availability of data [18] . previous studies have shown older age, dyspnea, and higher levels of ldh, crp, and direct bilirubin (dbil) to be associated with severe disease at admission [19, 20] . elevated neutrophil-to-lymphocyte ratio (nlr) value was observed in patients who died of covid-19 and found to be able to predict severe cases of covid-19 at its early stage [20, 21] . meanwhile, these risk factors, including older age and higher ldh levels, have been reported to be associated with adverse clinical outcomes in adults with sars [22, 23] . other important indicators such as ct images, d-dimer, and ferritin might be unavailable in emergency circumstances. therefore, we chose age, nlr, ldh, crp, and dbil as the five variables for our multivariable cox regression model. all these variables included in the cox regression analyses were measured at admission. we converted these indicators including respiratory rate, breaths per minute, nlr, platelets count, alanine aminotransferase (alt), prothrombin time (pt), and ldh to binary variables and converted these indicators including total bilirubin, white blood cell count, dbil, urea nitrogen, d-dimer, and crp to trichotomous variables when performing univariable cox regression analyses in the training cohort. in addition, variables including ldh and nlr were dichotomized, and direct bilirubin was trichotomous when performing multivariate cox regression analyses to obtain risk factors for 28-day mortality in the training cohort. these predictors were eventually selected by forward stepwise regression. categorical variables were presented as frequency rates and percentages, and continuous variables were expressed as mean ± standard deviation (sd) if they were normally distributed or median (interquartile range [iqr]) if they were not. proportions for categorical variables were compared using the χ 2 test or fisher's exact test. means for continuous variables were compared using independent group t test when the data were normally distributed. otherwise, the wilcoxon rank-sum test was employed. 95% confidence interval (ci) of mortality was analyzed by wilson score ci. for the training cohort and the union hospital validation cohort, missing data have been mentioned in the relevant tables, and there was no other missing data, unless otherwise noted. and for the central hospital external validation cohort, 6 out of 126 missed ldh information, and these missing data were handled by multiple imputations [24] . the nomogram was used to visually score the patients' various parameters according to the results of multivariable cox regression analyses, and then to compute the probability of the event based on the patients' total score. c-index was calculated to evaluate the distinguishing power, and the calibration curve was used to evaluate the calibration of the nomogram. all statistics were two-tailed, and a p value less than 0.05 was considered as significant. all statistical analyses were performed by using the sas software package (version 9.4). the demographic and clinical characteristics at admission for the union hospital training cohort (n = 516), union hospital external validation cohort (n = 186), and central hospital of wuhan external validation cohort (n = 126) are listed in table 1 . among the 828 patients, 381 were females and 447 were males. on admission, 289 were mild and 539 were severely ill cases. the median age of non-survivors was older than that of survivors in both 3 cohorts. the median duration from illness onset to admission for all the patients was estimated to be 10 days (iqr, 7.0-13.0), and no difference was seen between the non-survivor and survivor groups (p = 0.484). the treatments, outcomes, and complications of the 828 cases were shown in table 2 . a total of 681 (82.25%) patients received oxygen therapy, 149 (18.00%) patients received mechanical ventilation, and 75 (9.06%) patients received invasive mechanical ventilation. antiviral therapies were used in 739 (89.25%) patients, systematic corticosteroids in 375 (45.29%) patients, and hydroxychloroquine in 57 (6.88%) patients. as of may 18, 2020, 682 (82.37%) patients have been discharged and 146 (17.63%) patients died. the median duration from illness onset to death in 146 deceased patients was estimated to be 20.0 days (iqr, 14.0-26.0). figure 2 shows the 28-day kaplan-meier survival curves for all patients and the two subgroups categorized by the severity of illness. of 146 non-survivors, 143 (97.95%) of the non-survivors developed ards; the most common complication was acute cardiac injury (40, 27.40%) followed by acute renal injury (32, 21.92%), septic shock (31, 21.23%), and acute liver injury (15, 10 .27%). next, we analyzed the risk factors for 28-day mortality in the training cohort by using cox regression model. eighty-seven decreased patients within 28 days were enrolled in the cox regression analyses. univariable cox regression analyses showed age, male, dyspnea, respiratory rate, curb-65 pneumonia severity score (curb-65 score), quick sepsis related organ failure assessment (qsofa) score, reticular patterns, and 15 laboratory factors were associated with 28-day mortality ( table 3 ). the comparison between survivors and non-survivors in laboratory and ct findings were also displayed in table s1 and figure 3 showed the temporal changes of the three independent laboratory risk factors from hospital admission in survivors and nonsurvivors. compared with survivors, non-survivors showed a significantly higher nlr, ldh, and dbil value at all time points. development and validation of nomogram for 14-day and 28-day mortality next, we worked out a nomogram scoring system for predicting the 14-day and 28-day survival probability of patients with covid-19 on the basis of the four independent predictors of mortality (fig. 4a) . to help physicians better understand the scoring system, we explained how to calculate the score in the legend of fig. 4 . figure 4b and c shows the calibration plot for the prediction model, in which the predicted probability of 14-day and 28-day survival is plotted against the observed data. the curves of predictive 14-day and 28-day survival probability were closely approximated to the observed probability, which means the nomogram scoring system exhibited good calibration. the discrimination of the constructed nomogram was evaluated with the c-index (0.886, 95% ci, 0.873-0.899), suggesting a favorable discriminative power. we also compared the nomogram score in our study with the curb-65 score and qsofa score. in the training cohort, the discrimination c-index of curb-65 and qsofa scores were 0.781 (95% ci, 0.757-0.805) and 0.672 (95% ci, 0.644-0.699), respectively. as indicated by the lack of overlap in the confidence intervals, the discrimination power of the nomogram score developed in the training categorical variables were presented as frequency rates and percentages continuous variables were expressed median (iqr) ci confidence interval cohort was significantly higher than that of the curb-65 and qsofa scores. to further verify the nomogram scoring system, two external cohorts were included. the external validation cohort 1 was performed by using the union hospital external validation set. in the union hospital external validation set, the final multivariable model for 28-day mortality showed strong external validity, with a discrimination c-index of 0.879 (95% ci, 0.856-0.900) indicating an 87.9% correct model identification of the 28-day survival probability across all possible pairs of patients. in the central hospital of wuhan validation set, the nomogram also exhibited a good discrimination power (c-index, 0.839, 95% ci [0.798-0.880]). calibration of the nomogram predicted 14-day and 28-day survival probability corresponding with the actual survival in both external validation cohorts (fig. 4d-g) . in this study, we employed the clinical and laboratory features of covid-19 patients to work out an effective and easy tool for predicting 28-day mortality. univariate analyses revealed that these factors including age, male sex, dyspnea, respiratory rate, curb-65 score, qsofa score, reticular patterns, leukocyte count, lymphocyte count, nlr, and several other biochemical parameters were associated with mortality. multivariate analyses found that older age, nlr over 8.0, dbil levels higher than 5.0 μmol/l, and ldh levels higher than 360 u/l at admission were four independent predictors of 28-day mortality in adult hospitalized patients with covid-19. many more patients developed fever and had comorbidities including hypertension and diabetes than those in guan et al.'s study with a relatively large sample size [7] . however, patients in our study were all from wuhan city, while patients in guan et al.'s study were from 30 provinces, autonomous regions, and municipalities in mainland china. since a great shortage of medical resources existed in wuhan city, the hardest-hit area of the covid-19 outbreak at the early stage of this pandemic, this regional difference should be noted. when compared with other studies, patients in which were also from wuhan, the proportions of patients with fever and comorbidities were comparable [4, 25] . the overall crude mortality rate in our series was higher than that in the previous report [26] . on the basis of a statistical model involving 72,314 patients, zhong and his colleagues estimated that the case mortality rate was 2.3% in patients with confirmed covid-19, 2.9% in hubei province, and 49% in severely ill patients. however, shang et al. reported that the mortality rate in severely ill patients with covid-19 was about 49% [27] . the discrepancies in the mortality rates might be ascribed to proportions of patients of different severities in different cohorts, given that all death events in our cohort were observed in severely ill patients. thus, the proportion of severe cases in our study should be taken into account. in fact, after a mandatory hierarchical management was introduced, more severe covid-19 patients were transferred to our hospitals, while mild cases were re-directed to the "mobile cabin hospitals." compared with survivors, more non-survivors were older, male, and were complicated with more chronic conditions. this result was coincident with the finding of a previous study focusing on critically ill covid-19 patients [27] . as aforementioned, all the non-survivors except two were those who were categorized as severely ill at admission in our study. this result suggested that mild patients could be treated by home quarantine or in our mobile cabin hospitals, given their satisfactory survival and the shortage of medical resources. of note, reticular patterns were more frequently found on ct images at presentation in non-survivors and were reportedly the predominant imaging finding on ct images 3 weeks after symptom onset [28] . previous studies have reported that older male patients were more subject to covid-19 infection, and severe patients were older than their non-severe counterparts [4, 7] . compared with survivors, non-survivors were reported to be older in two observational studies [9, 27] . in this study, we found that age was an independent risk factor for 28-day mortality in patients with covid-19. a higher level of ldh was suggested to indicate more extensive lung tissue injury and reported to be linked with poor outcomes in patients with severe acute respiratory syndrome (sars) [25, 29] . in patients with covid-19, plasma ldh level was reported to be higher in severe, icu, and deceased covid-19 patients than in mild, non-icu-patients, and survivors [27, 30] . our study showed that ldh could serve as a valuable predictor of mortality in covid-19 patients, with its hazard ratio being the highest. reminiscent of a previous mortality prediction model developed by yan et al., ldh higher than 365 u/l was also reported to be a risk factor for mortality in patients with covid-19 [31] . meanwhile, this previous model highlighted the crucial role of [20, 21] . this study confirmed that it could act as a predictor of mortality in covid patients. dbil was reported to be associated with severe covid-19 in a multicenter retrospective study [19] , now identified as one independent risk factor for 28-day mortality. although the presence of preexisting comorbidities seems to increase the odds of death, the association was not significant in our study. we also employed the four independent predictors to construct a predictive model which was shown in a form of nomogram scoring system. our prediction mode was constructed based on a reasonable size and consecutive cohort of adult patients with confirmed covid-19. this kind of sample selection minimized the selection bias. however, the proportion of severely ill patients was large in our hospital since wuhan union hospital was a designated hospital for severely ill covid-19 patient treatment. this made the cohort in our study less representative of adult hospitalized patients with confirmed covid-19 in wuhan. however, it should be highlighted that our model not only showed good discrimination and calibration in an external validation from the same hospital, but also performed well in an external validation cohort consisting of patients from another hospital, which was not a designated hospital for severely ill covid-19 patient treatment. therefore, our prediction models are based on and validated in wuhan hospitalized populations with covid-19 infection and should therefore be applicable to other sites within wuhan. compared with the curb-65 and qsofa scores, our scoring system displayed better discrimination ability in the training cohort. by employing our model, once the fig. 4 the nomogram scoring system for predicting patients' survival probability based on age, ldh level, dbil, and nlr. a nomogram for predicting the probability of 14-day and 28-day survival. the number of points for each factor is in the top row. for each factor, the absence is assigned 0 points. the presence of factors is associated with the number of points. the points for each factor are summed together to generate a total point score. the total points correspond to the respective 14-day and 28-day survival probabilities. the ability of this model to distinguish between low-risk and high-risk patients can be demonstrated by considering two hypothetical individuals who might be encountered in practice: patient a is 60 years old with nlr of 10, dbil of 4 μmol/l, and ldh of 400 u/l, getting a total score of 144.23; patient b is 40 years old with nlr of 3, dbil of 10 μmol/l, and ldh 100 u/l, getting a total score of 41.06. our model predicts that patient a's 14-day survival probability is 75%, and his 28-day survival probability is 63%. for patient b, his 14-day survival probability and 28-day survival probability are more than 95%. b-g the calibration plot of survival probabilities at 14 days and 28 days. nomogram-predicted survival probability is plotted on the x-axis, with observed survival probability on the y-axis. dashed lines along the 45°line through the origin point represent the perfect calibration models in which the predicted probabilities are identical to the actual probabilities. the training cohort calibration plot of survival probabilities at 14 days (b) and 28 days (c). d, e the external validation cohort 1 calibration plot of survival probabilities at 14 days (d) and 28 days (e). f, g the external validation cohort 2 calibration plot of survival probabilities at 14 days (f) and 28 days (g) target patients' data on the four risk factors were measured at admission, their risk of 14-day and 28-day mortality can be calculated by our model to guide the decision of clinical physicians. considering that the outcome events outside wuhan are different, when trying to apply this prediction mode into other provinces in china or other countries, this mode might need to be updated and adjusted to the local setting before it can safely be applied. our study had several limitations. first, it was of retrospective nature, and all data were collected from case records. therefore, important information might be missed and further prospective studies are needed. second, it is worth pointing out that the amount of missing data differed between the survivor and non-survivor groups, especially for ferritin and d-dimer. even though we believe these differences were attributed to different physicians' decisions in their clinical practice due to the absence of guideline recommendations, the resulting potential bias should be noted and further prospective studies can be also helpful to decrease this discrepancy in missing data. third, this study included a high population of patients who were severely ill; there may be a selection bias when identifying the risk factors of mortality. since physicians should evaluate the patients' condition at admission, we focused on the information of patients at admission, other important factors during hospitalization that might influence case mortality, such as the use of non-invasive assisted ventilation or other medications and timing, as well as longitudinal observations of clinical and laboratory variables, were not covered. more detailed analyses involving these factors should be undertaken. in conclusion, our study demonstrated that older age, high lactate dehydrogenase level, 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respiratory syndrome: retrospective analysis advanced statistics: missing data in clinical research--part 2: multiple imputation clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in china clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study radiological findings from 81 patients with covid-19 pneumonia in wuhan, china: a descriptive study usefulness of lactate dehydrogenase and its isoenzymes as indicators of lung damage or inflammation clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china an interpretable mortality prediction model for covid-19 patients publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations we thank all the patients who consented to donate their data for analysis and the medical staff members who are on the front line of caring for patients.authors' contributions yj, yz, and jc designed the study. fw, gh, jx, ym, zl, dm, xw, and jz collected the epidemiological and clinical data. sz, mg, ld, gh, zw, qh, tl, zz, xt, sz, ez, zy, and wg summarized all the data. sz, mg, and ld analyzed and drafted the manuscript. all authors revised the final manuscript. the authors read and approved the final manuscript. the data that support the findings of this study are available from the corresponding authors upon reasonable request. the study was approved by the institutional ethics committee of union hospital, tongji medical college, huazhong university of science and technology (20200036); the requirement for informed consent was exempted by the ethics committee. no individual participant data is reported that would require consent to publish from the participant. the authors declare no competing interests. supplementary information accompanies this paper at https://doi.org/10. 1186/s13054-020-03123-x. key: cord-354095-4sweo53l authors: qiu, yun; chen, xi; shi, wei title: impacts of social and economic factors on the transmission of coronavirus disease 2019 (covid-19) in china date: 2020-05-09 journal: j popul econ doi: 10.1007/s00148-020-00778-2 sha: doc_id: 354095 cord_uid: 4sweo53l this study models local and cross-city transmissions of the novel coronavirus in china between january 19 and february 29, 2020. we examine the role of various socioeconomic mediating factors, including public health measures that encourage social distancing in local communities. weather characteristics 2 weeks prior are used as instrumental variables for causal inference. stringent quarantines, city lockdowns, and local public health measures imposed in late january significantly decreased the virus transmission rate. the virus spread was contained by the middle of february. population outflow from the outbreak source region posed a higher risk to the destination regions than other factors, including geographic proximity and similarity in economic conditions. we quantify the effects of different public health measures in reducing the number of infections through counterfactual analyses. over 1.4 million infections and 56,000 deaths may have been avoided as a result of the national and provincial public health measures imposed in late january in china. the first pneumonia case of unknown cause was found close to a seafood market in wuhan, the capital city of hubei province, china, on december 8, 2019. several clusters of patients with similar pneumonia were reported through late december 2019. the pneumonia was later identified to be caused by a new coronavirus (severe acute respiratory syndrome coronavirus 2, or sars-cov-2) (zhu et al. 2020), later named coronavirus disease 2019 by the world health organization (who). 1 while the seafood market was closed on january 1, 2020, a massive outflow of travelers during the chinese spring festival travel rush (chunyun) in mid-january 2 led to the rapid spread of covid-19 throughout china and to other countries. the first confirmed case outside wuhan in china was reported in shenzhen on january 19 ). as of april 5, over 1.2 million confirmed cases were reported in at least 200 countries or territories. 3 two fundamental strategies have been taken globally, one focused on mitigating but not necessarily stopping the virus spread and the other relying on more stringent measures to suppress and reverse the growth trajectories. while most western countries initially implemented the former strategy, more and more of them (including most european countries and the usa) have since shifted towards the more stringent suppression strategy, and some other countries such as china, singapore, and south korea have adopted the latter strategy from the beginning. in particular, china has rolled out one of the most stringent public health strategies. that strategy involves city lockdowns and mandatory quarantines to ban or restrict traffic since january 23, social distance-encouraging strategies since january 28, and a centralized treatment and isolation strategy since february 2. this study estimates how the number of daily newly confirmed covid-19 cases in a city is influenced by the number of new covid-19 cases in the same city, nearby cities, and wuhan during the preceding 2 weeks using the data on confirmed covid-19 case counts in china from january 19 to february 29. by comparing the estimates before and after february 2, we examine whether the comprehensive set of policies at the national scale delays the spread of covid-19. besides, we estimate the impacts of social distancing measures in reducing the transmission rate utilizing the closed management of communities and family outdoor restrictions policies that were gradually rolled out across different cities. as covid-19 evolves into a global pandemic and mitigating strategies are faced with growing pressure to flatten the curve of virus transmissions, more and more nations are considering implementing stringent suppression measures. therefore, examining the factors that influence the transmission of covid-19 and the effectiveness of the large-scale mandatory quarantine and social distancing measures in china not only adds to our understanding of the containment of covid-19 but also provides insights into future prevention work against similar infectious diseases. in a linear equation of the current number of new cases on the number of new cases in the past, the unobserved determinants of new infections may be serially correlated for two reasons. first, the number of people infected by a disease usually first increases, reaches a peak, and then drops. second, there are persistent, unobservable variables, such as clusters that generate large numbers of infections, people's living habits, and government policies. serial correlations in errors give rise to correlations between the lagged numbers of cases and the error term, rendering the ordinary least square (ols) estimator biased. combining insights in adda (2016) , the existing knowledge of the incubation period of covid-19 (world health organization 2020b) , and data on weather conditions that affect the transmission rates of covid-19 (lowen and steel 2014; wang et al. 2020b ), we construct instrumental variables for the number of new covid-19 cases during the preceding 2 weeks. weather characteristics in the previous third and fourth weeks do not directly affect the number of new covid-19 cases after controlling for the number of new covid-19 cases and weather conditions in the preceding first and second weeks. therefore, our estimated impacts have causal interpretations and reflect population transmission rates. meanwhile, we estimate the mediating effects of socioeconomic factors on the transmission of covid-19 in china. these factors include population flow out of wuhan, the distance between cities, gdp per capita, the number of doctors, and contemporaneous weather conditions. we examine whether population flows from the origin of the covid-19 outbreak, which is a major city and an important transportation hub in central china, can explain the spread of the virus using data on real-time travel intensity between cities that have recently become available for research. realizing the urgency of forestalling widespread community transmissions in areas that had not seen many infections, in late january, many chinese cities implemented public health measures that encourage social distancing. we also examine the impacts of these measures on curtailing the spread of the virus. we find that transmission rates were lower in february than in january, and cities outside hubei province had lower transmission rates. preventing the transmission rates in non-hubei cities from increasing to the level observed in late january in hubei caused the largest reduction in the number of infections. apart from the policies implemented nationwide, the additional social distancing policies imposed in some cities in late january further helped reduce the number of infections. by mid february, the spread of the virus was contained in china. while many socioeconomic factors moderated the spread of the virus, the actual population flow from the source posed a higher risk to destinations than other factors such as geographic proximity and similarity in economic conditions. our analysis contributes to the existing literature in three aspects. first, our analysis is connected to the economics and epidemiological literature on the determinants of the spread of infectious diseases and prevention of such spread. existing studies find that reductions in population flow zhang et al. 2020; fang et al. 2020 ) and interpersonal contact from holiday school closings (adda 2016) , reactive school closures (litvinova et al. 2019) , public transportation strikes (godzinski and suarez castillo 2019), strategic targeting of travelers from high-incidence locations (milusheva 2017) , and paid sick leave to keep contagious workers at home (barmby and larguem 2009; pichler and ziebarth 2017) can mitigate the prevalence of disease transmissions. in addition, studies show viruses spread faster during economic booms (adda 2016) , increases in employment are associated with increased incidence of influenza (markowitz et al. 2019) , and growth in trade can significantly increase the spread of influenza (adda 2016) and hiv (oster 2012) . vaccination (maurer 2009; white 2019) and sunlight exposure (slusky and zeckhauser 2018) are also found effective in reducing the spread of influenza. second, our paper adds to the epidemiological studies on the basic reproduction number (r 0 ) of covid-19, i.e., the average number of cases directly generated by one case in a population where all individuals are susceptible to infection. given the short time period since the beginning of the covid-19 outbreak, research is urgently needed to assess the dynamics of transmissions and the implications for how the covid-19 outbreak will evolve (wu et al. 2020b, c) . liu et al. (2020) identify 12 studies that estimated the basic reproductive number in the wide range of 1.4 to 6.5 (with a mean of 3.28 and a median of 2.79) for wuhan, hubei, china, or overseas during january 1 through january 28, 2020. 4 our r 0 estimate relies on spatially disaggregated data during an extended period (until february 29, 2020) to mitigate potential biases, and the instrumental variable approach we use isolates the causal effect of virus transmissions and imposes fewer restrictions on the relationship between the unobserved determinants of new cases and the number of cases in the past. simultaneously considering a more comprehensive set of factors in the model that may influence virus spread, we find that one case generates 2.992 more cases within 2 weeks (1.876 if cities in hubei province are excluded) in the sub-sample from january 19 to february 1. in the sub-sample from february 2 to february 29, the transmission rates fall to 1.243 (0.614 excluding hubei province). our estimate of r 0 for the period in late january 2020 that overlaps with existing studies falls well within the range of the estimated r 0 in the emerging covid-19 literature . third, our study contributes to the assessments of public health measures aiming at reducing virus transmissions and mortality. through a set of policy simulations, we report initial evidence on the number of avoided infections through the end of february 2020 for cities outside hubei province. specifically, the stringent health policies at the national and provincial levels reduced the transmission rate and resulted in 1,408,479 (95% ci, 815,585 to 2,001,373) fewer infections and poten-tially 56,339 fewer deaths. 5 in contrast, the effects of the wuhan lockdown and local non-pharmaceutical interventions (npis) are considerably smaller. as a result of the wuhan lockdown, closed management of communities, and family outdoor restrictions, 31,071 (95% ci, 8296 to 53,845), 3803 (95% ci, 1142 to 6465), and 2703 (95% ci, 654 to 4751) fewer cases were avoided, respectively. these three policies may respectively avoid 1,243 deaths, 152 deaths, and 108 deaths. making some additional assumptions, such as the value of statistical life and lost productive time, these estimates may provide the basis for more rigorous cost-benefit analysis regarding relevant public health measures. this paper is organized as follows. section 2 introduces the empirical model. section 3 discusses our data and the construction of key variables. section 4 presents the results. section 5 documents the public health measures implemented in china, whose impacts are quantified in a series of counterfactual exercises. section 6 concludes. the appendix contains additional details on the instrumental variables, data quality, and the computation of counterfactuals. our analysis sample includes 304 prefecture-level cities in china. we exclude wuhan, the capital city of hubei province, from our analysis for two reasons. first, the epidemic patterns in wuhan are significantly different from those in other cities. some confirmed cases in wuhan contracted the virus through direct exposure to huanan seafood wholesale market, which is the most probable origin of the virus 6 . in other cities, infections arise from human-to-human transmissions. second, covid-19 cases were still pneumonia of previously unknown virus infections in people's perception until early january so that wuhan's health care system became overwhelmed as the number of new confirmed cases increased exponentially since mid-january. this may have caused severe delay and measurement errors in the number of cases reported in wuhan, and to a lesser extent, in other cities in hubei province. to alleviate this concern, we also conduct analyses excluding all cities in hubei province from our sample. 5 we assume a case fatality rate of 4%, the same as china's current average level. of course, the eventual case fatality rate may be different from the current value, and it depends on many key factors, such as the preparedness of health care systems and the demographic structure of the population outside hubei province in comparison to china as a whole. also importantly, among patients who have died from covid-19, the time from symptom onset to outcome ranges from 2 to 8 weeks (world health organization 2020b), which is partially beyond the time window of this analysis. therefore, we defer more rigorous estimates about avoided fatality to future studies. 6 document the exposure history of the first 425 cases. it is suspected that the initial cases were linked to the huanan seafood wholesale market in wuhan. to model the spread of the virus, we consider within-city spread and between-city transmissions simultaneously (adda 2016 where c is a city other than wuhan, and y ct is the number of new confirmed cases of covid-19 in city c on date t. regarding between-city transmissions, d cr is the log of the distance between cities c and r, and r =c d −1 cr y rt is the inverse distance weighted sum of new infections in other cities. considering that covid-19 epidemic originated from one city (wuhan) and that most of the early cases outside wuhan can be traced to previous contacts with persons in wuhan, we also include the number of new confirmed cases in wuhan (z t ) to model how the virus spreads to other cities from its source. we may include lagged y ct , y rt , and z t up to 14 days based on the estimates of the durations of the infectious period and the incubation period in the literature 7 . x ct includes contemporaneous weather controls, city, and day fixed effects 8 . ct is the error term. standard errors are clustered by province. to make it easier to interpret the coefficients, we assume that the transmission dynamics (α within,s , α between,s , ρ s ) are the same within s = 1, · · · , 7 and s = 8, · · · , 14, respectively, but can be different across weeks. specifically, we take averages of lagged y ct , y rt , and z t by week, asȳ τ ct = 1 7 7 s=1 y ct−7(τ −1)−s , y τ rt = 1 7 7 s=1 y rt−7(τ −1)−s , andz τ t = 1 7 7 s=1 z t−7(τ −1)−s , in which τ denotes the preceding first or second week. our main model is (1) we also consider more parsimonious model specifications, such as the model that only considers within-city transmissions, 7 the covid-19 epidemic is still ongoing at the time of writing, and the estimates are revised from time to time in the literature as new data become available. the current estimates include the following. the incubation period is estimated to be between 2 and 10 days (world health organization 2020a), 5.2 days , or 3 days (median, guan et al. (2020) ). the average infectious period is estimated to be 1.4 days (wu et al. 2020a there are several reasons thatȳ τ ct ,ȳ τ rt , andz τ t may be correlated with the error term ct . the unobserved determinants of new infections such as local residents' and government's preparedness are likely correlated over time, which causes correlations between the error term and the lagged dependent variables. as noted by the world health organization (2020b), most cases that were locally generated outside hubei occurred in households or clusters. the fact that big clusters give rise to a large number of cases within a short period of time may still be compatible with a general low rate of community transmissions, especially when measures such as social distancing are implemented. therefore, the coefficients are estimated by two-stage least squares in order to obtain consistent estimates on the transmission rates in the population. in eq. 2, the instrumental variables include averages of daily maximum temperature, total precipitation, average wind speed, and the interaction between precipitation and wind speed, for city c in the preceding third and fourth weeks. detailed discussion of the selection of weather characteristics as instruments is in section 3.2. the timeline of key variables are displayed in fig. 1 . the primary assumption on the instrumental variables is that weather conditions before 2 weeks do not affect the likelihood that a person susceptible to the virus contracts the disease, conditional on weather conditions and the number of infectious people within the 2-week window. on the other hand, they affect the number of other persons who have become infectious within the 2-week window, because they may have contracted the virus earlier than 2 weeks. these weather variables are exogenous to the error term and another objective of this paper is to quantify the effect of various socioeconomic factors in mediating the transmission rates of the virus, which may identify potential behavioral and socioeconomic risk factors for infections. for within-city transmissions, we consider the effects of local public health measures (see section 5 for details) and the mediating effects of population density, level of economic development, number of doctors, and environmental factors such as temperature, wind, and precipitation. for between-city transmissions, apart from proximity measures based on geographic distance, we also consider similarity in population density and the level of economic development. to measure the spread of the virus from wuhan, we also include the number of people traveling from wuhan. the full empirical model is as follows: whereh kτ ct includes dummies for local public health measures and the mediating factors for local transmissions.m kτ crt andm kτ c,wuhan,t are the mediating factors for between-city transmissions and imported cases from wuhan. january 19, 2020, is the first day that covid-19 cases were reported outside of wuhan, so we collect the daily number of new cases of covid-19 for 305 cities from january 19 to february 29. all these data are reported by 32 provincial-level health commissions in china 10 . figure 2 shows the time patterns of daily confirmed new cases in wuhan, in hubei province outside wuhan, and in non-hubei provinces of mainland china. because hubei province started to include clinically diagnosed cases into new confirmed cases on february 12, we notice a spike in the number of new cases in wuhan and other cities in hubei province on this day (fig. 2) . the common effects of such changes in case definitions on other cities can be absorbed by time fixed effects. as robustness checks, we re-estimate models a and b without the cities in hubei province. in addition, since the number of clinically diagnosed cases at the city level was reported for the days of february 12, 13, and 14, we recalculated the daily number of new cases for the 3 days by removing the clinically diagnosed cases from our data and re-estimate models a and b. our main findings still hold (appendix b). regarding the explanatory variables, we calculate the number of new cases of covid-19 in the preceding first and second weeks for each city on each day. to estimate the impacts of new covid-19 cases in other cities, we first calculate the geographic distance between a city and all other cities using the latitudes and longitudes of the centroids of each city and then calculate the weighted sum of the number since the covid-19 outbreak started from wuhan, we also calculate the weighted number of covid-19 new cases in wuhan using the inverse of log distance as the weight. furthermore, to explore the mediating impact of population flow from wuhan, we collect the daily population flow index from baidu that proxies for the total intensity of migration from wuhan to other cities 11 . figure 3 plots the baidu index of population flow out of wuhan and compares its values this year with those in 2019. we then interact the flow index with the share that a destination city takes (fig. 4) to construct a measure on the population flow from wuhan to a destination city. other mediating variables include population density, gdp per capita, and the number of doctors at the city level, which we collect from the most recent china city statistical yearbook. table 1 presents the summary statistics of these variables. on average, gdp per capita and population density are larger in cities outside hubei province than those in hubei. compared with cities in hubei province, cities outside hubei have more doctors. we rely on meteorological data to construct instrumental variables for the endogenous variables. the national oceanic and atmospheric administration (noaa) provides average, maximum, and minimum temperatures, air pressure, average and maximum wind speeds, precipitation, snowfall amount, and dew point for 362 weather stations at the daily level in china. to merge the meteorological variables with the number of new cases of covid-19, we first calculate daily weather variables for each city on each day from 2019 december to 2020 february from station-level weather records following the inverse distance weighting method. specifically, for each city, we draw a circle of 100 km from the city's centroid and calculate the weighted average daily weather variables using stations within the 100-km circle 12 . we use the inverse of the distance between the city's centroid and each station as the weight. second, we match the daily weather variables to the number of new cases of covid-19 based on city name and date. the transmission rate of covid-19 may be affected by many environmental factors. human-to-human transmission of covid-19 is mostly through droplets and contacts (national health commission of the prc 2020). weather conditions such as rainfall, wind speed, and temperature may shape infections via their influences on social activities and virus transmissions. for instance, increased precipitation 11 baidu migration (https://qianxi.baidu.com). 12 the 100-km circle is consistent with the existing literature. most studies on the socioeconomic impacts of climate change have found that estimation results are insensitive to the choice of the cutoff distance (zhang et al. 2017) . transmissions. in addition, increased rainfall and lower temperature may also reduce social activities. newly confirmed covid-19 cases typically arise from contracting the virus within 2 weeks in the past (e.g., world health organization 2020b). the extent of human-to-human transmission is determined by the number of people who have already contracted the virus and the environmental conditions within the next 2 weeks. conditional on the number of people who are infectious and environmental conditions in the previous first and second weeks, it is plausible that weather conditions further in the past, i.e., in the previous third and fourth weeks, should not directly affect the number of current new cases. based on the existing literature, we select weather characteristics as the instrumental variables, which include daily maximum temperature, precipitation, wind speed, and the interaction between precipitation and wind speed. we then regress the endogenous variables on the instrumental variables, contemporaneous weather controls, city, date, and city by week fixed effects. table 2 shows that f-tests on the coefficients of the instrumental variables all reject joint insignificance, which confirms that overall the selected instrumental variables are not weak. the coefficients of the first stage regressions are reported in table 9 in the appendix. this table reports the f -tests on the joint significance of the coefficients on the instrumental variables (iv) that are excluded from the estimation equations. our iv include weekly averages of daily maximum temperature, precipitation, wind speed, and the interaction between precipitation and wind speed, during the preceding third and fourth weeks, and the averages of these variables in other cities weighted by the inverse of log distance. for each f statistic, the variable in the corresponding row is the dependent variable, and the time window in the corresponding column indicates the time span of the sample. each regression also includes 1-and 2-week lags of these weather variables, weekly averages of new infections in the preceding first and second weeks in wuhan which are interacted with the inverse log distance or the population flow, and city, date and city by week fixed effects. coefficients on the instrumental variables for the full sample are reported in table 15 in the appendix we also need additional weather variables to instrument the adoption of public health measures at the city level. since there is no theoretical guidance from the existing literature, we implement the cluster-lasso method of belloni et al. (2016) and ahrens et al. (2019) to select weather characteristics that have good predictive power. details are displayed in appendix a. our sample starts from january 19, when the first covid-19 case was reported outside wuhan. the sample spans 6 weeks in total and ends on february 29. we divide the whole sample into two sub-samples (january 19 to february 1, and february 2 to february 29) and estimate the model using the whole sample and two sub-samples, respectively. in the first 2 weeks, covid-19 infections quickly spread throughout china with every province reporting at least one confirmed case, and the number of cases also increased at an increasing speed (fig. 2 ). it is also during these 2 weeks that the chinese government took actions swiftly to curtail the virus transmission. on january 20, covid-19 was classified as a class b statutory infectious disease and treated as a class a statutory infectious disease. the city of wuhan was placed under lockdown on january 23; roads were closed, and residents were not allowed to leave the city. many other cities also imposed public policies ranging from canceling public events and stopping public transportation to limiting how often residents could leave home. by comparing the dynamics of virus transmissions in these two sub-samples, we can infer the effectiveness of these public health measures. in this section, we will mostly rely on model a to interpret the results, which estimates the effects of the average number of new cases in the preceding first and second week, respectively, and therefore enables us to examine the transmission dynamics at different time lags. as a robustness check, we also consider a simpler lag structure to describe the transmission dynamics. in model b, we estimate the effects of the average number of new cases in the past 14 days instead of using two separate lag variables. table 3 reports the estimation results of the ols and iv regressions of eq. 2, in which only within-city transmission is considered. after controlling for time-invariant city fixed effects and time effects that are common to all cities, on average, one new infection leads to 1.142 more cases in the next week, but 0.824 fewer cases 1 week later. the negative effect can be attributed to the fact that both local authorities and residents would have taken more protective measures in response to a higher perceived risk of contracting the virus given more time. information disclosure on newly confirmed cases at the daily level by official media and information dissemination on social media throughout china may have promoted more timely actions by the public, resulting in slower virus transmissions. we then compare the transmission rates in different time windows. in the first sub-sample, one new infection leads to 2.135 the dependent variable is the number of daily new cases. the endogenous explanatory variables include the average numbers of new confirmed cases in the own city in the preceding first and second weeks (model a) and the average number in the preceding 14 days (model b). weekly averages of daily maximum temperature, precipitation, wind speed, the interaction between precipitation and wind speed, and the inverse log distance weighted sum of each of these variables in other cities, during the preceding third and fourth weeks, are used as instrumental variables in the iv regressions. weather controls include contemporaneous weather variables in the preceding first and second weeks. standard errors in parentheses are clustered by provinces. *** p <0.01, more cases within a week, implying a fast growth in the number of cases. however, in the second sub-sample, the effect decreases to 1.077, suggesting that public health measures imposed in late january were effective in limiting a further spread of the virus. similar patterns are also observed in model b. many cases were also reported in other cities in hubei province apart from wuhan, where six of them reported over 1000 cumulative cases by february 15 13 . their overstretched health care system exacerbates the concern over delayed reporting of confirmed cases in these cities. to mitigate the effect of such potential measurement errors on our estimates, we re-estimate (2) excluding all cities in hubei province. the bottom panel of table 3 reports these estimates. comparing the iv estimates in columns (4) and (6) between the upper and lower panels, we find that the transmission rates are lower in cities outside hubei. in the january 19-february 1 sub-sample, one new case leads to 1.483 more cases in the following week, and this is reduced to 0.903 in the february 2-february 29 sub-sample. we also find a similar pattern when comparing the estimates from model b. people may contract the virus from interaction with the infected people who live in the same city or other cities. in eq. 1, we consider the effects of the number of new infections in other cities and in the epicenter of the epidemic (wuhan), respectively, using inverse log distance as weights. in addition, geographic proximity may not fully describe the level of social interactions between residents in wuhan and other cities since the lockdown in wuhan on january 23 significantly reduced the population flow from wuhan to other cities. to alleviate this concern, we also use a measure of the size of population flow from wuhan to a destination city, which is constructed by multiplying the daily migration index on the population flow out of wuhan (fig 3) with the share of the flow that a destination city receives provided by baidu (fig. 4) . for days before january 25, we use the average destination shares between january 10 and january 24. for days on or after january 24, we use the average destination shares between january 25 and february 23 14 . table 4 reports the estimates from iv regressions of eq. 1, and table 5 reports the results from the same regressions excluding hubei province. column (4) of table 4 indicates that in the first sub-sample, one new case leads to 2.456 more cases within 1 week, and the effect is not statistically significant between 1 and 2 weeks. column (6) suggests that in the second sub-sample, one new case leads to 1.127 more cases within 1 week, and the effect is not statistically significant between 1 and 2 weeks. the comparison of the coefficients on own city between different sub-samples indicates that the responses of the government and the public have effectively decreased the risk of additional infections. comparing table 4 with table 3 , we find that although the number of new cases in the preceding second week turns insignificant (3) table 6 . each estimation sample contains 14 days with the starting date indicated on the horizontal axis and smaller in magnitude, coefficients on the number of new cases in the preceding first week are not sensitive to the inclusion of terms on between-city transmissions. as a robustness test, table 5 reports the estimation results excluding the cities in hubei province. column (4) of table 5 indicates that in the first sub-sample, one new case leads to 1.194 more cases within a week, while in the second sub-sample, one new case only leads to 0.899 more cases within a week. besides, in the second subsample, one new case results in 0.250 fewer new infections between 1 and 2 weeks, which is larger in magnitude and more significant than the estimate (−0.171) when cities in hubei province are included for estimation (column (6) of table 4 ). the time varying patterns in local transmissions are evident using the rolling window analysis (fig. 5) . the upper left panel displays the estimated coefficients on local transmissions for various 14-day sub-samples with the starting date labelled on the horizontal axis. after a slight increase in the local transmission rates, one case generally leads to fewer and fewer additional cases a few days after january 19. besides, the transmission rate displays a slight increase beginning around february 4, which corresponds to the return travels and work resumption after chinese spring festival, but eventually decreases at around february 12. such decrease may be partly attributed to the social distancing strategies at the city level, so we examine the impacts of relevant policies in section 5. moreover, the transmission rates in cities outside hubei province have been kept at low levels throughout the whole sample period (columns (4) and (6) of table 5 ). these results suggest that the policies adopted at the national and provincial levels soon after january 19 prevented cities outside hubei from becoming new hotspots of infections. overall, the spread of the virus has been effectively contained by mid february, particularly for cities outside hubei province. in the epidemiology literature, the estimates on the basic reproduction number of covid-19 are approximately within the wide range of 1.4 ∼ 6.5 ). its value depends on the estimation method used, underlying assumptions of modeling, time period covered, geographic regions (with varying preparedness of health care systems), and factors considered in the models that affect disease transmissions (such as the behavior of the susceptible and infected population). intuitively, it can be interpreted as measuring the expected number of new cases that are generated by one existing case. it is of interest to note that our estimates are within this range. based on the results from model b in tables 4 and 5 , one case leads to 2.992 more cases in the same city in the next 14 days (1.876 if cities in hubei province are excluded). in the second sub-sample (february 2-february 29), these numbers are reduced to 1.243 and 0.614, respectively, suggesting that factors such as public health measures and people's behavior may play an important role in containing the transmission of covid-19. while our basic reproduction number estimate (r 0 ) is within the range of estimates in the literature and is close to its median, five features may distinguish our estimates from some of the existing epidemiological estimates. first, our instrumental variable approach helps isolate the causal effect of virus transmissions from other confounded factors; second, our estimate is based on an extended time period of the covid-19 pandemic (until the end of february 2020) that may mitigate potential biases in the literature that relies on a shorter sampling period within 1-28 january 2020; third, our modeling makes minimum assumptions of virus transmissions, such as imposing fewer restrictions on the relationship between the unobserved determinants of new cases and the number of cases in the past; fourth, our model simultaneously considers comprehensive factors that may affect virus transmissions, including multiple policy instruments (such as closed management of communities and shelter-at-home order), population flow, within-and between-city transmissions, economic and demographic conditions, weather patterns, and preparedness of health care system. fifth, our study uses spatially disaggregated data that cover china (except its hubei province), while some other studies examine wuhan city, hubei province, china as a whole, or overseas. regarding the between-city transmission from wuhan, we observe that the population flow better explains the contagion effect than geographic proximity (table 4 ). in the first sub-sample, one new case in wuhan leads to more cases in other cities receiving more population flows from wuhan within 1 week. interestingly, in the second sub-sample, population flow from wuhan significantly decreases the transmission rate within 1 week, suggesting that people have been taking more cautious measures from high covid-19 risk areas; however, more arrivals from wuhan in the preceding second week can still be a risk. a back of the envelope calculation indicates that one new case in wuhan leads to 0.064 (0.050) more cases in the destination city per 10,000 travelers from wuhan within 1 (2) week between january 19 and february 1 (february 2 and february 29) 15 . note that while the effect is statistically significant, it should be interpreted in context. it was estimated that 15,000,000 people would travel out of wuhan during the lunar new year holiday 16 . if all had gone to one city, this would have directly generated about 171 cases within 2 weeks. the risk of infection is likely very low for most travelers except for few who have previous contacts with sources of infection, and person-specific history of past contacts may be an essential predictor for infection risk, in addition to the total number of population flows 17 . a city may also be affected by infections in nearby cities apart from spillovers from wuhan. we find that the coefficients that represent the infectious effects from nearby cities are generally small and not statistically significant (table 4 ), implying that few cities outside wuhan are themselves exporting infections. this is consistent with the findings in the world health organization (2020b) that other than cases that are imported from hubei, additional human-to-human transmissions are limited for cities outside hubei. restricting to cities outside hubei province, the results are similar (table 5 ), except that the transmission from wuhan is not significant in the first half sample. we also investigate the mediating impacts of some socioeconomic and environmental characteristics on the transmission rates (3). to ease the comparison between different moderators, we consider the mediating impacts on the influence of the average number of new cases in the past 2 weeks. regarding own-city transmissions, we examine the mediating effects of population density, gdp per capita, number of doctors, and average temperature, wind speed, precipitation, and a dummy variable of adverse weather conditions. regarding between-city transmissions, we consider the mediating effects of distance, difference in population density, and difference in gdp per capita since cities that are similar in density or economic development level may be more closely linked. we also include a measure of population flows from wuhan. table 6 reports the estimation results of the iv regressions. to ease the comparison across various moderators, for the mediating variables of within-city transmissions that are significant at 10%, we compute the changes in the variables so that the effect of new confirmed infections in the past 14 days on current new confirmed cases is reduced by 1 (columns (2) and (4)). 15 it is estimated that 14,925,000 people traveled out of wuhan in 2019 during the lunar new year holiday (http://www.whtv.com.cn/p/17571.html). the sum of baidu's migration index for population flow out of wuhan during the 40 days around the 2019 lunar new year is 203.3, which means one index unit represents 0.000013621 travelers. the destination share is in percentage. with one more case in wuhan, the effect on a city receiving 10,000 travelers from wuhan is 0.00471 × 0.000013621 × 100 × 10000 = 0.064. 16 http://www.whtv.com.cn/p/17571.html 17 from mid february, individual specific health codes such as alipay health code and wechat health code are being used in many cities to aid quarantine efforts. the dependent variable is the number of daily new confirmed cases. the sample excludes cities in hubei province. columns (2) and (4) report the changes in the mediating variables that are needed to reduce the impact of new confirmed cases in the preceding 2 weeks by 1, using estimates with significance levels of at least 0.1 in columns (1) and (3), respectively. the endogenous variables include the average numbers of new cases in the own city and nearby cities in the preceding 14 days and their interactions with the mediating variables. weekly averages of daily maximum temperature, precipitation, wind speed, the interaction between precipitation and wind speed, and the inverse log distance weighted sum of these variables in neighboring cities, during the preceding third and fourth weeks, are used as instrumental variables in the iv regressions. additional instrumental variables are constructed by interacting them with the mediating variables. weather controls include these variables in the preceding first and second weeks. standard errors in parentheses are clustered by provinces *** p <0.01, ** p <0.05, * p <0.1 in the early phase of the epidemic (january 19 to february 1), cities with more medical resources, which are measured by the number of doctors, have lower transmission rates. one standard deviation increase in the number of doctors reduces the transmission rate by 0.12. cities with higher gdp per capita have higher transmission rates, which can be ascribed to the increased social interactions as economic activities increase 18 . in the second sub-sample, these effects become insignificant probably because public health measures and inter-city resource sharing take effects. in fact, cities with higher population density have lower transmission rates in the second sub-sample. regarding the environmental factors, we notice different significant mediating variables across the first and second sub-samples. the transmission rates are lower with adverse weather conditions, lower temperature, or less rain. further research is needed to identify clear mechanisms. in addition, population flow from wuhan still poses a risk of new infections for other cities even after we account for the above mediating effects on own-city transmission. this effect is robust to the inclusion of the proximity measures based on economic similarity and geographic proximity between wuhan and other cities. nevertheless, we do not find much evidence on between-city transmissions among cities other than wuhan. as the 2002-2004 sars outbreak has shown, non-pharmaceutical interventions (npis) or public health measures may decrease or effectively stop the transmission of covid-19 even without vaccines. although the effectiveness of a single intervention strategy can be limited, multiple interventions together may generate substantial impacts on containing the spread of the virus. figure 6 depicts the timeline for a series of policies enacted at the national, provincial, and city levels in china since january 19. after the official confirmation of human-to-human transmission by the chinese authorities on january 20, china has adopted a variety of npis to contain the covid-19 outbreak. at the national level, covid-19 was classified as a statutory class b infectious disease on january 20, and prevention and control measures for class a infectious diseases have been taken. government agencies across the country were mobilized. the joint prevention and control mechanism of the state council was established on january 20, and the central leadership group for epidemic response was established on january 25. on january 23, national healthcare security administration announced that expenses related to covid-19 treatments would be covered by the medical insurance and the government if necessary, in order that all covid-19 cases could be hospitalized 19 . at the provincial level, 30 provinces declared level i responses to major public health emergencies from january 23 to 25, and all provinces had declared level i responses by january 29 20 . level i responses in china are designed for the highest state of emergencies. measures taken include enhanced isolation and contact tracing of cases, suspension of public transport, cancelling public events, closing schools and entertainment venues, and establishment of health checkpoints (tian et al. 2020) . these policies together represent population-wide social distancing and case isolation (ferguson et al. 2020) . early detection of covid-19 importation and prevention of onward transmission are crucial to all areas at risk of importation from areas with active transmissions (gilbert et al. 2020) . to contain the virus at the epicenter, wuhan was placed under lockdown with traffic ban for all residents starting on january 23. the lockdown is not expected to be lifted until april 8. local buses, subways, and ferries ceased operation. ridehailing services were prohibited, and only a limited number of taxis were allowed on road by january 24. residents are not permitted to leave the city. departure flights and trains were canceled at the city airport and train stations. checkpoints were set up at highway entrances to prevent cars from leaving the city. since january 22, it became mandatory to wear masks at work or in public places. 19 there was insufficient hospital capacity in hubei (and wuhan in particular) in late january. most patients in wuhan were hospitalized and isolated around mid february with the completion of new hospitals, makeshift health facilities, and increased testing capacity. see section 5.1 for details. 20 we should note that the summary of china's policy responses here is not a comprehensive list. other entities have also made efforts to help curtail the spread of covid-19. for example, on january 27, the state grid corporation of china declared that it would continue supplying electricity to resident users even if payment was not received on time. school and universities were closed already because of lunar new year holidays. in addition, all cities in hubei province implemented the lockdown policy, and most hubei cities had also adopted measures commensurate with class a infectious diseases by january 28 21 . residents in those areas were strongly encouraged to stay at home and not to attend any activity involving public gathering. health facilities in wuhan had been extremely overstretched with shortage in medical supplies and high rates of nosocomial infections until february 2 when (1) two new hospitals, i.e., huoshenshan and leishenshan, were built to treat patients of covid-19 with severe symptoms, and (2) 14 makeshift health facilities were converted to isolate patients with mild symptoms and to quarantine people suspected of contracting covid-19, patients with fever symptoms, and close contacts of confirmed patients. this centralized treatment and isolation strategy since february 2 has substantially reduced transmission and incident cases. however, stringent public health measures within hubei province enforced after the massive lockdown may have little to do with virus transmissions out of hubei province due to the complete travel ban since january 23. quarantine measures have been implemented in other provinces that aim at restricting population mobility across cities and reducing the risk of importing infections 22 . seven cities in zhejiang, henan, heilongjiang, and fujian provinces had adopted the partial shutdown strategy by february 4 (fang et al. 2020) 23 . in wenzhou, most public transportation was shut down, and traffic leaving the city was banned temporarily. on january 21, the ministry of transport of china launched level 2 responses to emergencies in order to cooperate with the national health commission in preventing the virus spread. on january 23, the ministry of transport of china, civil aviation administration of china, and china state railway group company, ltd. (csrgc) declared to waive the change fees for flight, train, bus, and ferry tickets that were bought before january 24. later, the csrgc extended the fee waiver policy to train tickets that were bought before february 6. by february 2, all railway stations in china had started to monitor body temperature of travelers when they enter and exit the station. across the whole country, transportation departments set up 14,000 health checkpoints at bus and ferry terminals, at service centers and toll gates on highways, monitoring the body temperature of passengers and controlling the inflow of population (world health organization 2020b). recent visitors to high covid-19 risk areas are required to self-quarantine for 14 days at home or in designated facilities. on february 2, china's exit and entry administration temporarily suspended the approval and issuance of the travel permits to hong kong and macau. on january 23, wuhan municipal administration of culture and tourism ordered all tour groups to cancel travels to wuhan. on january 27, the ministry of education of china postponed start of the spring semester in 2020, and on february 7, it further announced that students were not allowed to return to school campus without approvals from school. recent studies suggest that there is a large proportion of asymptomatic or mildsymptomatic cases, who can also spread the virus (dong et al. 2020; mizumoto et al. 2020; nishiura et al. 2020; wang et al. 2020a ). thus, maintaining social distance is of crucial importance in order to curtail the local transmission of the virus. the period from january 24 to 31, 2020, is the traditional chinese spring festival holiday, when families are supposed to get together so that inter-city travel is usually much less. people were frequently reminded by official media (via tv news and phone messages) and social media to stay at home and avoid gathering activities. on january 26, china state council extended this holiday to february 2 to delay people's return travel and curtail the virus spread. nevertheless, economic activities are still supposed to resume after the spring festival, bringing people back to workplaces, which may increase the risk of virus spread. to help local residents keep social distance and decrease the risk of virus transmissions, many cities started to implement the "closed management of communities" and "family outdoor restrictions" policies since late january (table 7) , encouraging residents to restrict nonessential travels. from january 28 to february 20, more than 250 prefecture-level cities in china implemented "closed management of communities," which typically includes (1) keeping only one entrance for each community, (2) allowing only community residents to enter and exit the community, (3) checking body temperature for each entrant, (4) testing and quarantining cases that exhibit fever immediately, and (5) tracing and quarantining close contacts of suspicious cases. meanwhile, residents who had symptoms of fever or dry cough were required to report to the community and were quarantined and treated in special medical facilities. furthermore, local governments of 127 cities also imposed more stringent "family outdoor restrictions"-residents are confined or strongly encouraged to stay at home with limited exceptions, e.g., only one person in each family may go out for shopping for necessities once every 2 days 24 . exit permits were usually distributed to each family in advance and recollected when residents reenter the community. contacts of those patients were also traced and quarantined. table 7 summarizes the number of cities that had imposed "closed management of communities" or "family outdoor restrictions" by different dates in february. in order to help inform evidence-based covid-19 control measures, we examine the effect of these local quarantine measures in reducing the virus transmission rates. dummy variables for the presence of closed management of communities or family outdoor restrictions are created, and they are interacted with the number of infections in the preceding 2 weeks. several factors may contribute to the containment of the epidemic. the transmission dynamics may change during the course of this epidemic because of improved medical treatments, more effective case isolation and contact tracing, increased public awareness, etc. therefore, we have split the sample into two sub-samples, and the estimated coefficients can be different across the sub-samples (section 4). npis such as closed management of communities, city lockdowns, and restrictions on population flow out of areas with high infection risks may also directly affect the transmission rates. while many public health measures are implemented nationwide, spatial variations exist in the adoption of two types of measures: closed management of communities (denoted by closed management) and family outdoor restrictions (denoted by stay at home), which allow us to quantify the effect of these npis on the transmission dynamics. because most of these local npis are adopted in february and our earlier results indicate that the transmission of covid-19 declines during late january, we restrict the analysis sample to february 2-february 29. we also exclude cities in hubei province, which modified the case definition related to clinically diagnosed cases on february 12 and changed the case definition related to reduced backlogs from increased capacity of molecular diagnostic tests on february 20. these modifications coincide with the adoption of local npis and can significantly affect the observed dynamics of confirmed cases. the adoption of closed management or stay at home is likely affected by the severity of the epidemic and correlated with the unobservables. additional weather controls that have a good predictive power for these npis are selected as the instrumental variables based on the method of belloni et al. (2016) . details are displayed in appendix a. the estimation results of ols and iv regressions are reported in table 8 . effects of local non-pharmaceutical interventions the sample is from february 2 to february 29, excluding cities in hubei province. the dependent variable is the number of daily new confirmed cases. the instrumental variables include weekly averages of daily maximum temperature, wind speed, precipitation, and the interaction between wind speed and precipitation, in the preceding third and fourth weeks, and the inverse log distance weighted averages of these variables in other cities. additional instrumental variables are constructed by interacting these excluded instruments with variables that predict the adoption of closed management of communities or family outdoor restrictions (table 17 ). the weather controls include weather characteristics in the preceding first and second weeks. standard errors in parentheses are clustered by provinces. *** p <0.01, ** p <0.05, we find that closed management and stay at home significantly decrease the transmission rates. as a result of closed management of communities, one infection will generate 0.244 (95% ci, −0.366 ∼ −0.123) fewer new infections in the first week. the effect in the second week is also negative though not statistically significant. family outdoor restrictions (stay at home) are more restrictive than closing communities to visitors and reduce additional infections from one infection by 0.278 (95% ci, −0.435 ∼ −0.121) in the first week. the effect in the second week is not statistically significant. to interpret the magnitude of the effect, it is noted that the reproduction number of sars-cov-2 is estimated to be around 1.4 ∼ 6.5 as of january 28, 2020 . many cities implement both policies. however, it is not conclusive to ascertain the effect of further imposing family outdoor restrictions in cities that have adopted closed management of communities. when both policies are included in the model, the ols coefficients (column (5)) indicate that closed management reduces the transmission rate by 0.547 (95% ci, −0.824 ∼ −0.270) in the first week, and by 0.259 (95% ci, −0.485 ∼ −0.032) in the second week, while the additional benefit from stay at home is marginally significant in the second week (−0.124, 95% ci, −0.272 ∼ 0.023). the iv estimates indicate that closed management reduces the transmission rate in the first week by 0.193 (95% ci, −0.411 ∼ 0.025), while the effect in the second week and the effects of stay at home are not statistically significant. additional research that examines the decision process of health authorities or documents the local differences in the actual implementation of the policies may offer insights into the relative merits of the policies. we further assess the effects of npis by conducting a series of counterfactual exercises. after estimating (3) by 2sls, we obtain the residuals. then, the changes in y ct are predicted for counterfactual changes in the transmission dynamics (i.e., coefficients α k within,τ ) and the impositions of npis (i.e.,h kτ ct , and the lockdown of wuhanm kτ c,wuhan,t ). in scenario a, no cities adopted family outdoor restrictions (stay at home). similarly, in scenario b, no cities implemented closed management of communities. we use the estimates in columns (2) and (4) of table 8 to conduct the counterfactual analyses for scenarios a and b, respectively. in scenario c, we assume that the index of population flows out of wuhan after the wuhan lockdown (january 23) took the value that was observed in 2019 for the same lunar calendar date (fig. 3) , which would be plausible had there been no lockdown around wuhan. it is also likely that in the absence of lockdown but with the epidemic, more people would leave wuhan compared with last year (fang et al. 2020) , and the effect would then be larger. in scenario d, we assume that the within-city transmission dynamics were the same as those observed between january 19 and february 1, i.e., the coefficient of 1-week lag own-city infections was 2.456 and the coefficient of 2-week lag own-city infections was −1.633 (column (4) of table 4 ), which may happen if the transmission rates in cities outside hubei increased in the same way as those observed for cities in hubei. appendix c contains the technical details on the computation of counterfactuals. in fig. 7 , we report the differences between the predicted number of daily new cases in the counterfactual scenarios and the actual data, for cities outside hubei province. we also report the predicted cumulative effect in each scenario at the bottom of the corresponding panel in fig. 7 . had the transmission rates in cities outside hubei province increased to the level observed in late january, by february 29, there would be 1,408,479 (95% ci, 815, 585 ∼ 2, 001, 373) more cases (scenario d). assuming a fatality rate of 4%, there would be 56,339 more deaths. the magnitude of the effect from wuhan lockdown and local npis is considerably smaller. as a result of wuhan lockdown, 31,071 (95% ci, 8296 ∼ 53, 845) fewer cases would be reported for cities outside hubei by february 29 (scenario c). closed management of communities and family outdoor restrictions would reduce the number of cases by 3803 (95% ci, 1142 ∼ 6465; or 15.78 per city with the policy) and 2703 (95% ci, 654 ∼ 4751; or 21.98 per city with the policy), respectively. these estimates, combined with additional assumptions on the value of statistical life, lost time from work, etc., may contribute to cost-benefit analyses of relevant public health measures. our counterfactual simulations indicate that suppressing local virus transmissions so that transmission rates are kept well below those observed in hubei in late january is crucial in forestalling large numbers of infections for cities outside hubei. our retrospective analysis of the data from china complements the simulation study fig. 7 counterfactual policy simulations. this figure displays the daily differences between the total predicted number and the actual number of daily new covid-19 cases for each of the four counterfactual scenarios for cities outside hubei province in mainland china. the spike on february 12 in scenario c is due to a sharp increase in daily case counts in wuhan resulting from changes in case definitions in hubei province (see appendix b for details) of ferguson et al. (2020) . our estimates indicate that suppressing local transmission rates at low levels might have avoided one million or more infections in china. chinazzi et al. (2020) also find that reducing local transmission rates is necessary for effective containment of covid-19. the public health policies announced by the national and provincial authorities in the last 2 weeks in january may have played a determinant role (tian et al. 2020) in keeping local transmission rates in cities outside hubei at low levels throughout january and february. among the measures implemented following provincial level i responses, shen et al. (2020) highlight the importance of contact tracing and isolation of close contacts before onset of symptoms in preventing a resurgence of infections once the covid-19 suppression measures are relaxed. we also find that travel restrictions on high-risk areas (the lockdown in wuhan), and to a lesser extent, closed management of communities and family outdoor restrictions, further reduce the number of cases. it should be noted that these factors may overlap in the real world. in the absence of the lockdown in wuhan, the health care systems in cities outside hubei could face much more pressure, and local transmissions may have been much higher. in china, the arrival of the covid-19 epidemic coincided with the lunar new year for many cities. had the outbreak started at a different time, the effects and costs of these policies would likely be different. this paper examines the transmission dynamics of the coronavirus disease 2019 in china, considering both within-and between-city transmissions. our sample is from january 19 to february 29 and covers key episodes such as the initial spread of the virus across china, the peak of infections in terms of domestic case counts, and the gradual containment of the virus in china. changes in weather conditions induce exogenous variations in past infection rates, which allow us to identify the causal impact of past infections on new cases. the estimates suggest that the infectious effect of the existing cases is mostly observed within 1 week and people's responses can break the chain of infections. comparing estimates in two sub-samples, we observe that the spread of covid-19 has been effectively contained by mid february, especially for cities outside hubei province. data on real-time population flows between cities have become available in recent years. we show that this new source of data is valuable in explaining between-city transmissions of covid-19, even after controlling for traditional measures of geographic and economic proximity. by april 5 of 2020, covid-19 infections have been reported in more than 200 countries or territories and more than 64,700 people have died. behind the grim statistics, more and more national and local governments are implementing countermeasures. cross border travel restrictions are imposed in order to reduce the risk of case importation. in areas with risks of community transmissions, public health measures such as social distancing, mandatory quarantine, and city lockdown are implemented. in a series of counterfactual simulations, we find that based on the experience in china, preventing sustained community transmissions from taking hold in the first place has the largest impact, followed by restricting population flows from areas with high risks of infections. local public health measures such as closed management of communities and family outdoor restrictions can further reduce the number of infections. a key limitation of the paper is that we are not able to disentangle the effects from each of the stringent measures taken, as within this 6-week sampling period, china enforced such a large number of densely timed policies to contain the virus spreading, often simultaneously in many cities. a second limitation is that shortly after the starting date of the official data release for confirmed infected cases throughout china, i.e., january 19, 2020, many stringent measures were implemented, which prevents researchers to compare the post treatment sub-sample with a pre treatment subsample during which no strict policies were enforced. key knowledge gaps remain in the understanding of the epidemiological characteristics of covid-19, such as individual risk factors for contracting the virus and infections from asymptotic cases. data on the demographics and exposure history for those who have shown symptoms as well as those who have not will help facilitate these research. adjustment in covid-19 case definitions in hubei province in february. section a contains details on the computation of the counterfactuals. weather conditions affect disease transmissions either directly if the virus can more easily survive and spread in certain environment, or indirectly by changing human behavior. table 9 reports results of the first stage of the iv regressions (table 4 ) using the full sample. in columns (1) and (2), the dependent variables are the numbers of newly confirmed covid-19 cases in the own city in the preceding first and second weeks, respectively. in columns (3) and (4), the dependent variables are the sum of inverse log distance weighted numbers of newly confirmed covid-19 cases in other cities in the preceding first and second weeks, respectively. these are the endogenous variables in the iv regressions. the weather variables in the preceding first and second weeks are included in the control variables. the weather variables in the preceding third and fourth weeks are the excluded instruments, and their coefficients are reported in the table. because the variables are averages in 7-day moving windows, the error term may be serially correlated, and we include city by week fixed effects. also included in the control variables are the average numbers of new cases in wuhan in the preceding first and second weeks, interacted with the inverse log distance or the population flow. because the spread of the virus depends on both the number of infectious people and the weather conditions, the coefficients in the first stage regressions do not have structural interpretations. the wald tests on the joint significance of the excluded instruments are conducted and their f statistics are reported. the excluded instruments have good predictive power. the implementation of local public health measures is likely correlated with the extent of the virus spread, so weather conditions that affect virus transmissions may also affect the likelihood that the policy is adopted. the influence of weather conditions on policy adoption may be complicated, so we use the cluster-lasso method of belloni et al. (2016) to select the weather variables that have good predictive power on the adoption of closed management of communities or family outdoor restrictions. let d ct be the dummy variable of the adoption of the local public health measure, i.e., d ct = 1 if the policy is in place in city c at day t. q ct is a vector of candidate weather variables, including weekly averages of daily mean temperature, maximum temperature, minimum temperature, dew point, stationlevel pressure, sea-level pressure, visibility, wind speed, maximum wind speed, snow depth, precipitation, dummy for adverse weather conditions, squared terms of these variables, and interactions among them. first, city and day fixed effects are removed. d ct = d ct − 1 n c d ct − 1 t t d ct + 1 nt ct d ct andq ct is defined similarly. the cluster-lasso method solves the following minimization problem: 1 nt ct d ct −q ct b 2 + λ nt k φ k |b k |. (ahrens et al. 2019) , which implements the cluster-lasso method of belloni et al. (2016) . city and date fixed effects are included. candidate variables include weekly averages of daily mean temperature, maximum temperature, minimum temperature, dew point, station-level pressure, sea-level pressure, visibility, wind speed, maximum wind speed, snow depth, precipitation, dummy for adverse weather conditions, squared terms of these variables, and interactions among them λ and φ are penalty parameters. a larger penalty value forces more coefficients to zero. the penalty parameters are picked using the theoretical result of belloni et al. (2016) . the estimation uses the stata package by ahrens et al. 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importance of additional climatic variables other than temperature and precipitation impact of population movement on the spread of preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak we are grateful to editor klaus zimmermann and three anonymous referees for valuable comments and suggestions which have helped greatly improve the paper. we received helpful comments and suggestions from hanming fang and seminar participants at institute for economic and social research of jinan university and voxchina covid-19 public health and public policy virtual forum. pei yu and wenjie wu provided excellent research assistance. all errors are our own. conflict of interests the authors declare that they have no conflict of interest.open access this article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons licence, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons licence, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this licence, visit http://creativecommonshorg/licenses/by/4.0/. the appendix consists of three sections. section a provides details on the first stage of the iv regressions and the selection of the instrumental variables for the local public health policies. section b shows that our main findings are not sensitive to the covid-19 case definitions were changed in hubei province on february 12 and february 20. starting on february 12, covid-19 cases could also be confirmed based on clinical diagnosis in hubei province, in addition to molecular diagnostic tests. this resulted in a sharp increase in the number of daily new cases reported in hubei, and in particular wuhan (fig. 2) . the use of clinical diagnosis in confirming cases ended on february 20. the numbers of cases that are confirmed based on clinical diagnosis for february 12, 13, and 14 are reported by the health commission of hubei province and are displayed in table 11 . as a robustness check, we re-estimate the model after removing these cases from the daily case counts (fig. 8 ). our main findings still hold (table 12 ). the transmission rates are significantly lower in february compared with january. population flow from the epidemic source increases the infections in destinations, and this effect is slightly delayed in february. it is convenient to write it in vector form,where y nt = y 1t · · · y nt and nt are n × 1 vectors. assuming that y ns = 0 if s ≤ 0, because our sample starts on january 19, and no laboratory confirmed case was reported before january 19 in cities outside wuhan. x nt = x 1t · · · x nt is an n × k matrix of the control variables. h nt,s (α within ) is an n × n y. qiu et al.diagonal matrix corresponding to the s-day time lag, with parameters α within = {α k within,τ } k=1,··· ,k within ,τ =1,2 . for example, for s = 1, · · · , 7, the ith diagonal element of h nt,s (α within ) is 1 7 k within k=1 α k within,1h k1 ct,i , and for s = 8, · · · , 14, the ith diagonal element of h nt,s (α within ) is 1 7 k within k=1 α k within,2h k2 ct,i . m nt,s (α between ) is constructed similarly. for example, for s = 1, · · · , 7 and i = j , the ij th element of m nt,s (α between ) is 1 7 k between k=1 α k between,1m k1 ij t . z τ nt is an n × k wuhan matrix corresponding to the transmission from wuhan. for example, the ikth element of z 1 nt is m k1 i,wuhan,tz 1 t . we first estimate the parameters in eq. 4 by 2sls and obtain the residualŝ n1 , · · · ,ˆ nt . let· denote the estimated value of parameters and· denote the counterfactual changes. the counterfactual value of y nt is computed recursively,the counterfactual change for date t is y nt =ỹ nt − y nt . the standard error of y nt is obtained from 1000 bootstrap iterations. in each bootstrap iteration, cities are sampled with replacement and the model is estimated to obtain the parameters. the counterfactual predictions are obtained using the above equations with the estimated parameters and the counterfactual scenario (e.g., no cities adopted lockdown).publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. key: cord-259149-svryhcgy authors: su, yue; xue, jia; liu, xiaoqian; wu, peijing; chen, junxiang; chen, chen; liu, tianli; gong, weigang; zhu, tingshao title: examining the impact of covid-19 lockdown in wuhan and lombardy: a psycholinguistic analysis on weibo and twitter date: 2020-06-24 journal: int j environ res public health doi: 10.3390/ijerph17124552 sha: doc_id: 259149 cord_uid: svryhcgy many countries are taking strict quarantine policies to prevent the rapid spread of covid-19 (corona virus disease 2019) around the world, such as city lockdown. cities in china and italy were locked down in the early stage of the pandemic. the present study aims to examine and compare the impact of covid-19 lockdown on individuals’ psychological states in china and italy. we achieved the aim by (1) sampling weibo users (geo-location = wuhan, china) and twitter users (geo-location = lombardy, italy); (2) fetching all the users’ published posts two weeks before and after the lockdown in each region (e.g., the lockdown date of wuhan was 23 january 2020); (3) extracting the psycholinguistic features of these posts using the simplified chinese and italian version of language inquiry and word count (liwc) dictionary; and (4) conducting wilcoxon tests to examine the changes in the psycholinguistic characteristics of the posts before and after the lockdown in wuhan and lombardy, respectively. results showed that individuals focused more on “home”, and expressed a higher level of cognitive process after a lockdown in both wuhan and lombardy. meanwhile, the level of stress decreased, and the attention to leisure increased in lombardy after the lockdown. the attention to group, religion, and emotions became more prevalent in wuhan after the lockdown. findings provide decision-makers timely evidence on public reactions and the impacts on psychological states in the covid-19 context, and have implications for evidence-based mental health interventions in two countries. the covid-19 (corona virus disease 2019) pandemic is a global health emergency that is having a profound impact on the physical and mental health of people [1] [2] [3] . many countries have taken strict quarantine measures as an intervention: cities locked down, school closure, mass gathering ban, public event prohibition, and self-isolation. a study conducted in china shows that lockdown has been effective in postponing the spread of covid-19 [4] . however, strict quarantine interventions may have negative impacts on mental health [5, 6] . it is essential to investigate the psychological effects of the lockdown which could make an influence on the execution of measures on epidemic containment. studies find that public reactions to sars (severe acute respiratory syndrome) in 2003 and the ebola virus disease in 2014 have impeded infection control to an extent [7, 8] . moreover, quarantine measures are making psychosocial impact on individuals more severe [9] . this study intends to explore how the lockdown affects the psychological states. the "first case" of covid-19 was identified in wuhan [10] , which was the epicenter of the coronavirus outbreak in china. to stop the spread of covid-19, china declared the lockdown of wuhan on 23 january 2020, which was the first city placed on lockdown during this pandemic in china and affected over 11 million people [11] . in europe, italy was the first country facing the pandemic [12] and taking actions (e.g., banned flights) [13] . lombardy in italy was the most affected area by covid-19 [14] . on 8 march 2020, the italian government announced a quarantine zone that covered most of northern italy, including lombardy. lombardy had a population of over 10 million, which was comparable with wuhan. this quarantine measure was considered as the most aggressive response taken in any region beyond china [15] . taken all these together, we chose wuhan and lombardy as research regions to investigate the impacts of the lockdown. recent studies used the self-report questionnaire approach to examine the psychological responses during the lockdown in different countries, including italy, india, and china [12, 16, 17] . however, these studies rely on retrospective and time-lagged surveys and interviews. these approaches have limitations in accessing psychological statuses before the lockdown. that is, there is recall bias inevitably when people are required to recall a past period in the retrospective study. social media plays a vital role in recording the reactions, opinions, and mental health features of social media users [18] previous studies suggest that the language use and psychosocial expressions on social media data provide indicators of mental health [19] [20] [21] . in china, sina weibo is the leading social media service provider. upon the end of 2019, the number of daily active users of sina weibo reached 222 million. twitter is one of the most-used social media platforms in italy. weibo and twitter provide vast amounts of user's online behavioral records for researchers. although there are some differences between weibo and twitter when comparing the functions and other features of platforms, they both serve as the online environment of expression and communication, providing us features of contents related to this study. thus, we collected chinese social media data from weibo and used twitter to acquire italian social media data. existing studies have widely used the language inquiry and word count (liwc) and confirmed it as a valid tool for psychometric analysis [22] . the liwc dictionary has multiple versions of different languages, including english [23] , french [24] , italian [25] , and dutch [26] . the liwc dictionary includes many word categories of linguistic features that are related to mental processes and human behaviors [22] . for example, the word category of personal pronouns reflects attentional allocation [22] . in this study, we used the simplified chinese version of liwc and italian liwc to measure people's psychological status before and after the lockdown in wuhan and lombardy, respectively. by using psycholinguistic analysis, we aim to identify the psychological effects of the lockdown on individuals in wuhan and lombardy. we downloaded active user's posts from weibo and twitter as our dataset. the research protocol was approved in advance by the ethics committee of the institute of psychology, chinese academy of sciences (approved number: h15009). we extracted the linguistic features using the simplified chinese liwc dictionary (scliwc) [27] and the italian liwc dictionary [25] . given both scliwc and italian liwc share liwc dictionary structure, there are many common words in scliwc and liwc. to make the result of wuhan and lombardy comparable, we only analyzed the common word categories between scliwc and italian liwc. the selection procedure of common categories is as follows: a native italian speaker who is fluent in english translated the names of italian liwc word categories into english. we translated the chinese names of scliwc word categories into english. 3. we selected the common names between two translation versions. as for the names sharing similar meanings, such as "tentative" from scliwc and "possibility" from italian liwc, we checked the meaning of words belonging to this word category in italian liwc and scliwc to determine whether the two names represented the same kind of word category. some word categories are unique in scliwc or italian liwc. by comparing, there are 26 word categories only existing in scliwc, such as quantity unit, interjunction, and tense mark words. in italian, people conjugate verbs when they follow different subjects. moreover, people can infer the subject of the sentence from verb conjugation. as the subject in a sentence is dropped sometimes, conjugations (i_verb, we_verb, you_verb, you_plural_verb, heshe_verb, they_verb) can reveal the use of pronouns more accurately compared to pronouns (i, we, you, you plural, heshe, them). thus, we regard the use of conjugations, the same as pronouns in our study. additionally, we found that 28 word categories only exist in italian liwc. in this study, we kept the common word categories in both scliwc and italian liwc and got 51 common word categories for further analysis. the chinese samples are from the weibo data pool containing 1.16 million active weibo users [28] . in this study, we selected active weibo users from the data pool by the following criteria: 1. published at least one original post on average each day from 9 january 2020 to 5 february 2020 (i.e., two weeks before and after the lockdown); 2. individual users only, excluding any organizations; 3. locate at "wuhan, hubei" by the geo-location in the user profile. we finally got 850 weibo users and downloaded their posts published from 9 january 2020 to 5 february 2020. for each weibo user, we divided the posts into two groups. for example, all posts published before the date 23 january 2020, are labeled as "before lockdown" group. in contrast, those posts published after the data 23 january 2020 (23 january included) are labeled as "after lockdown" group. we employed the textmind system to extract linguistic features [29] in each of the two groups for all sampled weibo users. then, we used the liwc dictionary containing 51 common word categories to extract psycholinguistic features and calculated word frequencies of each word category in the dictionary. the final dataset included the word frequencies of two groups from 850 weibo users. we sampled italian twitter users' messages as our twitter data. we downloaded tweets of users whose location authentication is lombardia, italy. there are 3,650,380 tweets acquired. we then selected italian twitter users as follows: 1. published at least one original tweet (not retweet) from 23 february 2020 to 21 march 2020 (that is, two weeks before and after the lockdown); 2. all tweets in italian only. we acquired 14,269 tweets from 188 unique twitter users. we divided these tweets into two groups as well. we gathered each user's tweets and labeled the tweets posted before 8 march 2020, as "before lockdown" tweets and tweets posted after 8 march 2020 (march 8 included) as "after lockdown" tweets, respectively. we filtered out the users if only emoji, numbers, web links, "@" and "#" were published in either "before lockdown" or "after lockdown" tweets. we finally acquired 120 twitter users. then, we extracted every user's linguistic features from "before" and "after" tweets by using the same dictionary used in weibo data and calculated word frequencies of each word category. we conducted wilcoxon tests to examine the differences between linguistic characteristics before and after the lockdown. spss (statistical product and service solutions) 26.0 (international business machines corporation, armonk, ny, usa). released 2019. ibm spss statistics for macintosh, version 26.0. was used during data analysis, which was published by ibm (international business machines corporation, armonk, ny, usa). in this study, we compared the word frequencies of 51 liwc categories before lockdown with after lockdown in wuhan. results showed that the frequencies of 39 word categories were statistically significantly different before and after wuhan lockdown. we identified 16 out of 39 significant categories with absolute values of effect size greater than 0.2, including function words (e.g., i, we), relative words (motion, time), personal concerns words (home, money, religion), affective process words (negative emotion, affect), social words (humans, social), and cognitive mechanism words (e.g., certain, inhibition). as shown in table 1 , the first-person plural pronoun is of high effect size (p < 0.001, effect size d = 0.674), which means users used more words of the first-person plural pronoun significantly after the lockdown. in addition, weibo users mentioned more in religion, social, negative emotion, home, affect after wuhan lockdown. meanwhile, we found significant decreases in the frequencies of some word categories, such as motion, i, money, and time after the lockdown. table 1 . word categories with significant differences between "before" and "after" in weibo (n = 850). dictionary; m1-the mean of the "before lockdown" group; sd1-the standard deviation of the "before lockdown" group; m2-the mean of the "after lockdown" group; sd2-the standard deviation of the "after lockdown" group. we compared the word frequencies of the 51 liwc categories before and after lombardy lockdown (8 march 2020) . results showed that the frequencies of 10-word categories were significantly changed. among them, the number of word categories with absolute values of effect size greater than 0.2 is five-word categories, including personal concerns words (leisure, home), affective process words (anxiety), and cognitive mechanism words (discrepancy, possibility). as shown in table 2 , there are increases in the frequencies of discrepancy, home, leisure, and possibility. meanwhile, we observed significant decrease in the frequency of anxiety after the lockdown. table 2 . words with significant changes between "before lockdown" and "after lockdown" in lombardy (n = 120). english liwc-language inquiry and word count; m1-the mean of the "before lockdown" group; sd1-the standard deviation of the "before lockdown" group; m2-the mean of the "after lockdown" group; sd2-the standard deviation of the "after lockdown" group. we presented the word categories whose frequencies significantly changed after the lockdown both in wuhan and lombardy in table 3 , including home and discrepancy. in both wuhan and lombardy, the frequencies of home and discrepancy words increased after a lockdown. the present study uses the chinese version of liwc and italian version of liwc to extract the psycholinguistic features from social media users' posts. examinations of the features allow us to access the changes of psychological status before and after the lockdown in wuhan and lombardy. the frequencies of some word categories increase in both wuhan and lombardy after the lockdown, including discrepancy and home words. these linguistic features imply that social media users' psychological states were impacted after the covid-19 lockdown, in both wuhan and lombardy. the increased use of home words is related to mobility control after the lockdown in wuhan and lombardy. researchers estimated that mobility and social contacts in china during the lockdown dropped about 80%, concerning a baseline set on 1 january 2020 [30] . moreover, google reported a 23% increase in residential location activity in lombardy during lockdown compared to baseline [31] . these reports indicate people spend more time at home and spend less time outdoors during a lockdown, which is consistent with more use of home words. the frequency of discrepancy words increases after the lockdown in wuhan and lombardy. besides, we observe the increased use of inhibition and certain words after the lockdown in wuhan. previous study suggests that the uses of discrepancy, inhibition, and certain words reflect the change of degree of cognitive processing [32] . furthermore, cognitive processing indicates that individuals make efforts to make sense of the environment [32] . residents in wuhan and lombardy attempt to figure out what has happened after the lockdown. thus, they could adjust their attitudes and lifestyles to accommodate new circumstances during the covid-19 pandemic. we observe there are some differences between wuhan and lombardy after a lockdown in the use of liwc word categories. we find significant changes in three-word categories in lombardy, including tentative, anxiety, and leisure words. the use of tentative words increases after a lockdown in lombardy. the previous study shows that people may use tentative language (e.g., maybe, perhaps, guess) when they feel uncertain or insecure about their topic [22] . our findings suggest that people tend to use tentative words during the lockdown. losing direct social contacts during the lockdown contributes to make residents feel losses of recreation, freedoms, and supports [1] . such a sense of loss means losing control of their healthy life, and people are likely to feel uncertain about the upcoming situation. tweets reveal that people in lombardy express such feelings on social media. however, we do not observe such change in wuhan, suggesting that people in wuhan do not convey the emotions of uncertainty in their posts on weibo. our results show that twitter users in lombardy use more leisure words in their posts after the lockdown. the increased use of leisure words implies more focus on leisure activities after a lockdown in lombardy. according to the news reports from cnbc (consumer news and business channel), italians turn to music to boost morale during lockdown [33] , which might be expressed in the use of leisure in tweets. on the contrary, we do not find the same change in the use of leisure words in wuhan. with the rapid growth of the pandemic, some people might focus more attention on the latest news of this disease on weibo and discuss less about leisure after the lockdown. moreover, some people may talk more about leisure and recreation after the lockdown, considering that the lunar new year holiday was in the lockdown period (25 january 2020, is the spring festival in china). considering these two facets, we may find it reasonable to observe no change in the use of leisure words in wuhan. the use of anxiety words decreases in lombardy. anxiety reveals self-reported stress [34] . our results imply that people feel less stressed after lombardy lockdown. however, people do not experience any change of stress in wuhan. researchers find that unrealistic optimism is more evident for european north americans [13] , which might be related to the different responses in the level of stress between lombardy and wuhan after the lockdown. however, our results are not consistent with existing studies [12, 35] . rossi and colleagues consider that the strict measures of the lockdown in italy serve as an unprecedented stressful event [12] . besides, ahmed and colleagues find that 29% of respondents report different levels of anxiety related to lockdown at home in china [35] . such differences could be due to different research methods, design, measurements, and timeframe used in the study. some word categories are changing significantly after the lockdown only in wuhan. the uses of first-person plural pronouns, second-person plural pronouns, religion, social, negative emotions, humans, certainty, affect, inhibition, and prepositions words increase. in contrast, the uses of motion, first-person singular pronouns, time, and money words decrease after the lockdown in wuhan. in wuhan, the uses of the first-person plural pronouns, second-person plural pronoun increase after a lockdown, while the use of first-person singular pronoun decreases. previous reports confirm that first-person singular pronouns show attention to the self, whereas most other pronouns suggest attention to other individuals [36] . moreover, "we" implies a sense of group identity sometimes [37] . results suggest that people switch their attention from themselves to others and the communities after the lockdown. besides, the increased use of "we" indicates that people focus more on the group, become more united, and share more group identity after a lockdown, which is consistent with some researchers' opinions [1] . china has a collectivistic culture, and italy has an individualistic culture [38] . results show that the increased use of other pronouns and decreased use of first-person singular pronouns suggest a collectivistic culture in china. at the same time, the absence of such a consequence in lombardy might be related to the individualist culture. researchers find that people sharing collectivist values stress more communal coping as a resource to cope with collective traumatic events [39] , which is consistent with our research conducted in the context of the lockdown. holmes and colleagues find that higher levels of the use of emotion words indicate more immersion in the negative event [40] . in the study, we find that a higher degree of immersion [22] evidenced by the frequent use of emotion words (negative emotion and affective process words). therefore, people in wuhan might get more emotional and are at a deeper level of immersion in negative emotions after the lockdown. however, we do not observe such a situation in lombardy. besides, we also find a decrease in the use of motion words after a lockdown in wuhan. our results are consistent with the previous mobility study of wuhan [41] , suggesting that stringent mobility control leads to the reduction of movement in wuhan. google's location mobility report in lombardy shows an 85% decrease in activities at transit stations, a 57% drop in activities at workplaces, an 86% drop in activities at parks, and a 94% drop in activities at retail and recreation from 15 march 2020 to 26 april 2020. however, our results do not identify a significant change of mobility in the use of motion words in lombardy. the increased use of social words in wuhan after the lockdown suggests the focus on social concerns and social support [22] . social support can make people feel better about their situation and reinforce the belief that they have access to support resources [16, 42] . thus, seeking social support is considered adaptive for people during a lockdown. in contrast, we do not observe such a change in lombardy. table 1 shows increases in the uses of religion and humans words, while decreases in the uses of money and time words after wuhan lockdown. content word categories explicitly reveal where individuals are focusing, including death, sex, and money [22] . moreover, our results suggest people focus more on humans and religion, while less on money and time during the lockdown. the previous study finds that religion can bring more positive and comforting emotions, and people tend to use it when suffering from emergencies such as stress or death [43] . the increases in the use of religion words suggest an adaptive behavior during the lockdown. moreover, the decreased use of money words may relate to fewer transactions under strict restrictions. in contrast, we do not identify any changes in these word categories among lombardy tweets. this result in lombardy tweets suggests that residents in lombardy do not change their focus level on religion, human, time, and money after lockdown. besides, we find an increase in the use of prepositions. previous research shows that prepositions signal more complex expression and detailed information about a topic [44] . the increased use of prepositions in wuhan indicates broader and more in-depth discussions that occurred on weibo after lockdown. however, such a change is not identified in lombardy. study findings have implications for decision-makers, public health authorities, and practitioners. first, considering the efforts of adjusting to the changing environment in both wuhan and lombardy after the lockdown, decision-makers should ensure the supply chain functions as usual to ensure people's confidence in having the control of their lives. besides, public health authorities and practitioners could adjust their focus of service given the changes in residents' attention after lockdown. for example, people in wuhan expressed more stress and negative emotions, public health authorities and practitioners should take interventions to comfort them and relieve stress, such as the online consulting service and indoor activities. notably, the support for individuals with pre-existing mental or physical health issues is also needed. meanwhile, people did not show significant stress in lombardy. public health communities and practitioners might focus more on the popularization of pandemic prevention knowledge and the reinforcement of protection awareness. there are several limitations. first, our samples were from selected active social media users only. the results have a limitation in generalizing to the whole population. second, language differences exist between chinese and italian. while processing italian text, some inevitable errors may occur because of the apostrophe. third, we do not have access to the users' ip, and location authentication is self-reported. there are some studies also applying self-reported location authentication to identify users' locations [45] . fourth, the bias existing in two different platforms possibly influences the results of our study. twitter users generally use more hashtags than weibo users, which shows that twitter users seem to be more eager to publicize their posts [46] . in addition, weibo users have a stronger tendency to post positive content compared to twitter users [46] . considering these differences between twitter and weibo, future studies should find methods to deal with these differences to avoid biases when employing data from weibo and twitter. this study examined the changes in psycholinguistic features before and after a lockdown in wuhan and lombardy. we compared the differences in frequencies of liwc word categories before and after lockdown and found that the number of word categories whose frequencies were significantly changed is more in wuhan than in lombardy. we found significant changes in the use of function words, relative words, personal concerns words, affective process words, social words, and cognitive mechanism words among wuhan users' posts. we also found significant changes in the frequencies of personal concerns words, affective process words, and cognitive mechanism words in lombardy. individuals focus more on home and express more levels of the cognitive process after a lockdown in both wuhan and lombardy. in lombardy, the level of stress decreases, the use of leisure increases. in wuhan, people convey more emotion expressions, more feelings of uncertainty, and more focus on groups after the lockdown. results inform decision-makers, public health authorities, and practitioners the potentially different impacts of city lockdown on individuals in the two countries, and contribute to the cultural-based psychological responses. author contributions: t.z., j.x., and y.s. were responsible for study design. x.l., j.c., and w.g. were responsible for data collection. y.s., p.w., c.c., and t.l. were responsible for data analysis. y.s., j.x., and t.z. were responsible for data interpretation. y.s. wrote the first draft of the manuscript. y.s., j.x., and t.z. contributed to the final draft. all authors have read and agreed to the published version of the manuscript. multidisciplinary research priorities for the covid-19 pandemic: a call for action for mental health science timely mental health care for the 2019 novel coronavirus outbreak is urgently needed mental health and psychosocial considerations during the covid-19 outbreak an 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nederlandse versie van de 'linguistic inquiry and word count'(liwc) developing simplified chinese psychological linguistic analysis dictionary for microblog predicting active users' personality based on micro-blogging behaviors improving user profile with personality traits predicted from social media content covid-19 outbreak response: a first assessment of mobility changes in italy following national lockdown covid-19 community mobility reports analyzing songs used for lyric analysis with mental health consumers using linguistic inquiry and word count (liwc) software. theses diss coronavirus italy: italians are singing songs during lockdown detecting well-being via computerized content analysis of brief diary entries epidemic of covid-19 in china and associated psychological problems the psychological functions of function words pronouns in marital interaction: what do "you" and "i" say about marital health? self-esteem and its association with depression among chinese, italian, and costa rican adolescents: a cross-cultural study comparison of expressive writing after the terrorist attacks of september 11th and march 11th cognitive and emotional processing in narratives of women abused by intimate partners human mobility restrictions and the spread of the novel coronavirus (2019-ncov) in china the relationship between social support and psychological problems among students a social cognitive perspective on religious beliefs: their functions and impact on coping and psychotherapy abstracts, introductions and discussions: how far do they differ in style? the impact of covid-19 epidemic declaration on psychological consequences: a study on active weibo users a comparative study of users' microblogging behavior on sina weibo and twitter the authors thank fiorella foscarini at university of toronto for fruitful discussions in the analysis of italian texts, and sijia li at institute of psychology, chinese academy of sciences for helpful suggestions in the data analysis. the authors declare no conflict of interest. key: cord-353862-7xe3fvd5 authors: li, na; han, lefei; peng, min; lv, yuxia; ouyang, yin; liu, kui; yue, linli; li, qiannan; sun, guoqiang; chen, lin; yang, lin title: maternal and neonatal outcomes of pregnant women with covid-19 pneumonia: a case-control study date: 2020-03-30 journal: clin infect dis doi: 10.1093/cid/ciaa352 sha: doc_id: 353862 cord_uid: 7xe3fvd5 background: the ongoing epidemics of coronavirus disease 2019 (covid-19) have caused serious concerns about its potential adverse effects on pregnancy. there are limited data on maternal and neonatal outcomes of pregnant women with covid-19 pneumonia. methods: we conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without covid-19 pneumonia. results: during january 24 to february 29, 2020, there were sixteen pregnant women with confirmed covid-19 pneumonia and eighteen suspected cases who were admitted to labor in the third trimester. two had vaginal delivery and the rest took cesarean section. few patients presented respiratory symptoms (fever and cough) on admission, but most had typical chest ct images of covid-19 pneumonia. compared to the controls, covid-19 pneumonia patients had lower counts of white blood cells (wbc), neutrophils, c-reactive protein (crp), and alanine aminotransferase (alt) on admission. increased levels of wbc, neutrophils, eosinophils, and crp were found in postpartum blood tests of pneumonia patients. there were three (18.8%) and three (16.7%) of the mothers with confirmed or suspected covid-19 pneumonia had preterm delivery due to maternal complications, which were significantly higher than the control group. none experienced respiratory failure during hospital stay. covid-19 infection was not found in the newborns and none developed severe neonatal complications. conclusion: severe maternal and neonatal complications were not observed in pregnant women with covid-19 pneumonia who had vaginal delivery or caesarean section. mild respiratory symptoms of pregnant women with covid-19 pneumonia highlight the need of effective screening on admission. in december 2019, an outbreak of the 2019 coronavirus disease (covid-19) associated pneumonia was reported in wuhan, a mega city with an 11 million population in central china, and soon spread to other cities in china and overseas [1] . the causative pathogen was identified as a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (sars-cov-2) [1] . as of 25 march 2020, covid-19 has caused more than 420,000 confirmed cases and 18,887 deaths globally, including 81,852 confirmed cases and 3,287 deaths in china [2] . in response to this fast-spreading epidemic, the chinese government has locked down the epicenter wuhan city since 23 january 2020, and implemented a series of social distancing measures such as strict traffic restrictions, forbidden social gatherings, closure of residential communities [3] . the epidemiological data in china showed that most cases had mild symptoms, with the overall case fatality rate of 2.3%. although sars-cov-2 appears less virulent than two previous zoonotic coronaviruses sars-cov and mers-cov, it was far more efficient to transmit between close contacts [4] . particularly, this novel coronavirus has caused special concerns in pregnant women, because both sars-cov and mers-cov have been found to cause severe complications in pregnant women [5, 6] . several reports on suspicious vertical transmission of this virus have further increased such concerns [7] . although recent laboratory studies and clinical reports did not find strong evidence to support a vertical transmission route, the possibility still cannot be completely ruled out [8] [9] [10] . clinical and epidemiological features of covid-19 infection have been widely reported [11] [12] [13] [14] [15] . however, clinical reports on maternal and neonatal outcomes of pregnant women with sars-cov-2 infection remain sparse. an earlier study by chen et al reported nine pregnant women with covid-19 pneumonia, who took cesarean section in a tertiary hospital of wuhan [8] . these patients showed clinical symptoms similar to non-pregnant patients with covid-19 pneumonia. they also claimed that there was no evidence of vertical transmission. to date, none of previous studies have investigated the adverse effects of covid-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with covid-19 pneumonia to those without pneumonia. we retrospectively reviewed medical records of pregnant women who were admitted into the hubei provincial maternal and child health center, a tertiary hospital in wuhan with 1,900 hospital beds, during january 24 -february 29, 2020. we followed the clinical diagnosis criteria for covid-19 pneumonia in the new coronavirus pneumonia prevention and control program (5th edition) by the national health commission of china [16] . throat swabs were collected from all these patients and sent to the laboratory of the wuhan center for disease control and prevention for tests of sars-cov-2 using the standard kit (biogerm, shanghai, china). diagnosis criteria of covid-19 infection include 1) typical chest ct imaging of patchy shadowing and ground-glass opacity, and 2) positive in reverse transcription polymerase chain reaction (rt-pcr) tests for sars-cov-2. however, previous studies argued that false negative cases might be common for covid-19 infection cases due to low virus titers, sampling at late stage of illness, and inappropriate swabbing sites [8] . given overloaded healthcare systems and limited test capacities during our study period, we might have missed some covid-19 cases if solely relying on laboratory tests. therefore, in this study we also included the suspected patients with typical chest ct imaging but negative in rt-pcr tests. eleven pregnant women who were tested positive for sars-cov-2 were classified as laboratory confirmed case group, and eighteen with typical chest ct imaging but tested negative in rt-pcr tests as suspected case group. the control group of pregnant women without pneumonia during hospital stay were randomly selected from the medical records by an investigator (mp), who was not involved in statistical analysis. only those aged 25-35 years were selected to match the age range of cases. we selected 121 women who were admitted during the same period (control 2020 group). considering the potential adverse effects of mental stress caused by city lockdown and severe epidemics, we also included the second control group of 121 women admitted during january 24 -february 11, 2019 (control 2019 group). blood test results were also retrieved from medical records. two case groups underwent blood tests every three days but two control groups only took once on admission. clinical characteristics, laboratory test results, maternal and neonatal outcomes were collected from medical records and reviewed independently by two investigators (yxl and yo). fisher's exact tests and mann-whitney u tests were used to compare the group difference for categorical and continuous variables, respectively. friedman tests were used to test for the difference of blood test results across time within the same subjects. all data analysis was conducted using r version 3.6.2. demographic characteristics of two case groups and two control groups are shown in table 1 . the age of confirmed cases ranged 26-37 years and all were in the third trimester. two confirmed cases (12.5%) and one suspected case had chronic conditions of hypertension, polycystic ovary syndrome and hepatitis b. their gestational weeks on admission ranged from 33 weeks plus 6 days to 40 weeks plus 4 days. around 70% of two case groups had other maternal complications, significantly higher than the controls (31-33%). all these complications were developed before diagnosis of pneumonia. fourteen patients had caesarean section, because confirmed or suspected covid pneumonia has become one indication for caesarean section in our hospital since 24 january 2020. two patients had vaginal delivery because neither presented any respiratory symptoms when admitted for full-term labor. one of them had fever two days after childbirth and another had ct images of patchy shadowing in the right lung on the same day of labor. there were 22 patients who took emergency cesarean section (12 confirmed and 10 suspected cases) because of active labor at the time of admission, and eight had scheduled cesarean section (3 confirmed and 5 suspected cases). in addition to pneumonia, eleven out of 16 confirmed cases had gestational complications on admission, including gestational diabetes mellitus (n=3), premature rupture of membranes (1), gestational hypertension (3), hypothyroidism (2), preeclampsia (1) and sinus tachycardia (1) . only one of them had more than one complications (gestational diabetes mellitus and hypertension). among three confirmed cases with preterm delivery, two were caused by premature rupture of membranes, and one by placental bleeding. two suspected cases had preterm delivery due to gestational hypertension/preeclampsia, and one suspected case due to placenta previa. none of confirmed covid-19 patients reported an exposure history. four were admitted with fever for investigation and eight developed fever after childbirth ( table 2) . none presented other respiratory symptoms on admission nor during hospital stay. two of the patients with suspected covid-19 pneumonia reported cough, sore throat, dyspnea, diarrhea and vomiting. all patients took chest ct scans. seven of confirmed cases had typical image of pneumonia in both lungs and eight in single lung. seventeen out of eighteen suspected patients had either both lungs or single lung affected. compared to the controls, two case groups had slightly lower counts of white blood cells (wbc), neutrophils, c-reactive protein (crp) and alanine aminotransferase (alt) on admission, although none reached statistical significance and most were marginally beyond the normal range (table 3) . lymphocytes, eosinophils and aspartate aminotransferase (ast) were comparable between the cases and controls. an increase of wbc, neutrophils, and crp were observed in the first postpartum blood test of confirmed cases, followed by a decrease in the second postpartum test (figure 1 ). but this transient change was not found in suspected cases. lymphocytes remained at the lower end of normal range in two case groups. all covid-19 pneumonia patients received antibiotics and four patients received antivirals during hospital stay. all of them have been discharged or transferred to the designated hospitals for covid-19 patients, and the length of stay in our hospital ranged from 3 to 26 days, with a median of 6.5 days. none were admitted into the intensive care unit (icu) because of covid-19 pneumonia or severe maternal complications. sixteen patients with confirmed covid-19 pneumonia gave birth to seventeen babies (fifteen singletons and two twins). two singletons were born prematurely due to premature rupture of membranes and placental abruption. there were 23.5% and 21.1% premature birth among the newborns born to mothers with confirmed or suspected covid-19 pneumonia, significantly higher than those from the controls (5.8% and 5.0% in the 2020 and 2019 controls) ( table 4 ). low birth weight also occurred more often in infants of two case groups (17.6% and 10.5%) than in those of two control groups (2.5%). newborns from the cases and controls showed no significant differences in key neonatal indicators including gestational age at birth, apgar score at 5 minutes, and intrauterine fetal distress. of three newborns with intrauterine fetal distress, two were from the covid-19 confirmed mothers, one of whom also had sinus tachycardia. one case of fetal distress was from the mother who had suspected covid-19 pneumonia but no other comorbidity. no events of severe neonatal asphyxia and deaths occurred in these newborns. to reduce contact transmission, all covid-19 patients were immediately moved to isolation wards after delivery or cesarean section, and their newborns were taken care by other family members. three newborns (including two twins), who were delivered by caesarean section, took throat swabs at 4 and 14 days after birth. all of them tested negative for sars-cov-2. to our best knowledge, this is the first case-control study to comprehensively compare maternal and neonatal outcomes of pregnant women with covid-19 pneumonia, to those with non-covid-19 pneumonia and without pneumonia. we found that sars-cov-2 infection caused generally mild respiratory symptoms in pregnant women. clinical signs and symptoms mainly included fever and pneumonia, but other respiratory symptoms were less common. our results echo the findings of a previous study in pregnant women with sars in hong kong, reporting that fever was the dominant presenting symptom [17] . however, it is of note that most patients did not have any symptoms on admission. for the purpose of screening for suspected cases, we asked all pre-laboring pregnant women to take low-dose chest ct scans with their abdominal region covered, and found that 2.1% fulfilled the criteria of covid-19 pneumonia (patchy shadowing and ground glass opacity in single or both lungs). this highlights the need of enhancing screening for covid-19 pneumonia on admission, as well as strengthening infection control measures in obstetric wards during the epidemics. compared to other covid-19 pneumonia patients, pregnant women generally had no or mild respiratory symptoms. none of our patients developed severe respiratory complications to require critical care. laboratory investigations on admission found lower counts of wbc, neutrophils, crp, and alt in pregnant women, compared to the non-pneumonia controls. these findings are consistent with those reported in other hospitalized covid-19 patients who often had lymphopenia and decreased wbc [11] . slightly increased wbc, neutrophils, eosinophils and crp were found in postpartum blood tests. we also notice that confirmed and suspected cases shared similar dynamic profiles, suggesting that laboratory test results might not be very useful in making differential diagnosis. cesarean section in one tertiary hospital in wuhan [8] . in our study, in addition to fourteen cesarean section patients, we also reported two pregnant woman who had a full-term vaginal delivery and were confirmed with covid-19 pneumonia on the day of delivery. we observed a higher incidence rate of premature delivery in confirmed cases (18.8%), but none was due to severe maternal respiratory failure. this rate was higher than in suspected patients (16.7%) and in two control groups (~5%) of our study, but lower than the rate of 44% in confirmed covid-19 pneumonia patients reported by chen et al. [8] all these events of preterm delivery were triggered by gestational complications such as premature rupture of membranes and placental bleeding, which might not be directly related to covid-19 pneumonia. we did not observe any deaths or events of severe complications associated with covid-19 pneumonia that required critical care in the pregnant women and newborns. hence, the adverse effects of covid-19 pneumonia on pregnancy appear less severe than those of sars-cov and mers-cov. there were three pregnant women died during the 2003 sars outbreak in hong kong, and preterm delivery was as high as 80% [18] . although no maternal deaths were recorded in the mers-cov outbreak, more than half of their newborns required critical care and nearly 30% eventually died [19] . zhu et al reported ten newborns born to mothers with covid-19 pneumonia in wuhan, and there was one newborn who died from multiple organ failure and disseminated intravascular coagulation (dic), and another had dic but recovered. however, none of these ten newborns tested positive for sars-cov-2 [20] . a previous study also reported that sars-cov infection could increase the risk of preterm delivery in the second trimester and spontaneous abortion in the first trimester [17] . since all patients in our study and others were in the third trimester, the potential adverse effect of sars-cov-2 infection in the first and second trimesters remains to be investigated. in response to this unprecedented covid-19 outbreak in wuhan, confirmed and suspected covid-19 infection has been included as one indication for cesarean section in our hospital, because there was only one negative pressure operation room suitable for airborne precautions. two patients had vaginal delivery in positive pressure labor rooms before they were diagnosed with covid-19 pneumonia. no transmission events occurred in the doctors and midwives, who were wearing a full set of personal protective equipment (n95 respirators, protective gown, coveralls, gloves and goggles) during the delivery procedure. healthcare workers need to stay vigilant against covid-19 infection when there is an epidemic in neighborhood or pregnant women have a travel history to an epidemic area within 14 days. as suggested by favre et al, vaginal delivery could be considered for the benefit of patients, when there is a labor room properly equipped for airborne precautions [21] . all healthcare workers in close contacts should strictly adhere to contact and airborne precautions in addition to standard precautions. similar to two previous reports of nine and one pregnant women with confirmed covid-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of sars-cov-2 from mother to fetus via placenta or during cesarean section. however, there was one newborn in wuhan who was born to the mother with covid-19 pneumonia under emergent cesarean section and tested positive for sars-cov-2 at 36 hours after birth [23] . none of these studies have detected the virus in breast milk, cord blood or placenta. therefore, there is limited evidence of vertical transmission via placenta or during cesarean section. our study also added some evidence to suggest that the risk of vertical transmission during vaginal delivery might also be trivial. there were two patients with vaginal delivery, one of them had symptom onset two days after delivery and another had delivery during the course of illness. neither of their newborns had respiratory systems after birth. unfortunately, none of them gave us the consent to collect the respiratory specimens of their neonates. given the small sample size of our study, the possibility of vertical transmission during vaginal delivery still cannot be ruled out. there are a few caveats in our study. first, this is a retrospective case control study from one single center, which could be subject to recall bias and selection bias. second, we collected the data of sixteen pregnant women with laboratory confirmed covid-19 pneumonia and eighteen suspected cases with typical ct imaging. although this is the largest number of pregnant women with covid-19 pneumonia in literature so far, the sample size is still relatively small. nevertheless, given the ongoing global pandemic caused by sars-cov-2, we believe our study could be one of important clinical studies to guide clinical diagnosis and treatment to this vulnerable group. in this study, we did not find any evidence to suggest that covid-19 pneumonia causes lyang and mp originated and designed the study. ylv, kl lyue, ql and yo contributed to data collection and clean. lh conducted data analysis. nl, lh, gs, lc and lyang interpreted the findings and drafted the manuscript. all the authors proved the final version of this manuscript. all authors have completed the icmje uniform disclosure form at www.icmje.org/coi_disclosure.pdf . ly is supported by the alibaba (china) -hong kong polytechnic university collaborative research fund. other authors declare: no support from any organisation for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work. the ethical approval has been obtained from the ethics committee of the hubei provincial maternal and child health center. apgar score at 5 minutes after birth, mean (sd) intrauterine fetal distress (n, %) 2 (11.7%) 1 (5.3%) 0.593 6 (5.0%) 0.256 6 (5.0%) 0.256 a p value of fisher's exact tests and mann-whitney u tests, the laboratory confirmed cases as reference group. b babies who were born weighing less than 2,500 grams. c babies who were born before the start of the 37th week of pregnancy of mothers. a novel coronavirus from patients with pneumonia in china coronaviruses: genome structure, replication, and pathogenesis the novel coronavirus originating in wuhan, china: challenges for global health governance characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china summary of a report of 72 314 cases from the chinese center for disease control and prevention 2019-ncov epidemic: what about pregnancies? the lancet potential maternal and infant outcomes from (wuhan) coronavirus 2019-ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections newborns in wuhan were diagnosed with novel coronavirus infection, experts warned the possibility of vertical transmission. reuters clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding what are the risks of covid-19 infection in pregnant women? the lancet clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with 2019 novel coronavirus in wuhan, china. the lancet early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical characteristics of coronavirus disease 2019 in china new coronavirus pneumonia prevention and control program a case-controlled study comparing clinical course and outcomes of pregnant and non-pregnant women with severe acute respiratory syndrome severe acute respiratory syndrome and pregnancy middle east respiratory syndrome coronavirus during pregnancy: report of two cases & review of the literature clinical analysis of 10 neonates born to mothers with 2019-ncov pneumonia guidelines for pregnant women with suspected sars-cov-2 infection. the lancet infectious diseases a case of 2019 novel coronavirus in a pregnant woman with preterm delivery a case report of neonatal covid-19 infection in china all data and materials used in this work are available based on reasonable request to the corresponding author. key: cord-029100-gxn15jgt authors: clark, anthony e. title: conclusion date: 2020-07-14 journal: china&#x02019;s catholics in an era of transformation doi: 10.1007/978-981-15-6182-5_5 sha: doc_id: 29100 cord_uid: gxn15jgt this conclusion of the compendium of essays by anthony e. clark summarizes the content and significance of his research on the history of catholicism in china. it was written as the covid-19 virus was sweeping across the globe, and clark reflects upon the comparisons between the virus’ outbreak at wuhan in 2019 and two french catholic missionaries, françois-régis clet, and jean-gabriel perboyre, who were martyred in the wuchang district of wuhan in the mid-nineteenth century. also considered in this conclusion is the trend among scholars to depict china’s relationship with the west and christianity as one of “conflict” or “cooperation,” highlighting the two extremes of either irreconcilable difference or congruous sameness. clark concludes this collection of essays with the suggestion that the historical exchange between china and the west has been rather an admixture of conflict and cooperation, but defined mostly as a relationship of friendship. writing about china is sometimes an exercise in useful superfluity-as one completes a line of commentary on an historical moment, even if it bears utility in understanding trends and events, one realizes that the vicissitudes of china's historical trajectories are so varied that any single interpretation seems canceled by the era that follows. the essays in this volume may at first appear overly varied, as if one essay proves the previous one outmoded, but even so, such transformations in the historical tableau accurately represent the rapid fluctuations that describe china's past, and its present. it was recommended to me that i provide a brief conclusion to this compendium of research essays and reflections, and the first thing that came to mind was the now hackneyed, but still useful, chinese saying, hua she tian zu, or "when drawing a snake, add a foot." the chinese hearer of this saying immediately knows the implication; one should avoid ruining the effect by adding something superfluous. there is no need, i first assumed, to add concluding remarks to the essays included in this volume about the long history of china's catholics and their place within the history of sino-western intellectual and religious exchange. but as i pondered what i might say by way of a conclusion, i observed the swaying branches of the blossoming cherry trees outside my office window, where i spend long hours reading due to the "shelter in place" rules enforced as the covid-19 virus sweeps across the globe. i recalled that several years ago i was in wuhan, the origin of this virus, conducting research on two catholic missionaries who died there in 1820 and 1840, respectively. it struck me that both of these missionaries, françois-régis clet (1748-1820) and jean-gabriel perboyre (1802-1840), were executed in a fashion uniquely relevant to the way in which this particular virus attacks those whom it infects, and that their stories might help explain how the contours of china's christian history connect to our own time. clet and perboyre were executed by slow strangulation-they died because they could not breathe. it occurred to me that china's catholic history bears deeper relevance to china's present than many assume. in fact, many of the covid-19 patients treated in wuhan were admitted into hospitals that were founded by roman catholic missionaries. research often carries scholars to unexpected locations, locations that few people have heard of. while i was in wuhan conducting research on the french lazarist martyrs of that area, i was certain that almost no-one from my native us had ever heard of that city, and i also assumed that they never would hear of wuhan. i was mistaken. "wuhan" is now in the common lexicon of everyone who has followed the disquieting history of the covid-19 virus and its origin in wuhan. to be precise, the catholic missionary martyrs of wuhan died in wuchang, the urban core of the thirteen districts of the large prefectural-level city of wuhan. in my essay of december 2008, included in this compendium, i recount my time in wuhan, during which i met with priests who complained of tapped phones and unremitting interference in diocesan affairs by local officials. in that essay i also describe the deaths of clet and perboyre and my search for the execution ground where they died, but in these concluding remarks i would like to offer a few more reflections on how their lives and deaths largely echoes the situation that emerged from wuhan in november of 2019. françois-régis clet and jean-gabriel perboyre lived in considerable anxiety because of the political chaos that churned around them, they were isolated, and they died from strangulation. they are among the few canonized catholic saints who died because they could not breathe. accounts of their martyrdoms were disseminated widely throughout france, and when the famous carmelite nun, thérèse of lisieux (1873-1897), read about them she was so transfixed what they endured in wuhan that she kept in her personal prayer-book a holy card of perboyre. four characteristics of their lives attracted the interest of french catholics during the late nineteenth century, and these same characteristics have attracted the interest of scholars presently living through the suffering and social unrest caused by what in china is known as the wuhan ganmao, or "wuhan flu." first, they lived within politically fraught times; second, they expressed a great deal of fear and anxiety in their epistolary exchanges; third, they spent their final months in forced isolation; and fourth, they experienced remarkable agony due to strangulation as they died on the wuhan execution ground during the late qing dynasty. françois-régis clet was born tenth in a family of fifteen children, and when he was twenty-one years old he entered the lazarists because of his admiration for saint vincent de paul's (1581-1660) affection for the poor and overlooked. he was in paris when intense anti-clericalism erupted during the french revolution (1789-1799), and when priests were being exiled from their native france he volunteered to go to china where he felt certain he would confront more of the same oppression. as anticipated, once he was in china clet encountered disagreements between the missionaries and local officials, but what most exasperated him during his early years within the qing empire was his initial struggle to learn chinese. in one letter home, he wrote quite pejoratively of the mandarin dialect: "no word except barbarous describes the chinese language. its written characters represent, not sounds, but thoughts, and their number is incalculable." 1 he began his life as a missionary in china in 1789, and three decades later he was tied onto a wooden pole in wuhan; a rope was wrapped around his throat and he was slowly deprived of the air his body required to remain alive. jean-gabriel perboyre, like his confrere, father clet, was born into a large french catholic family, and four of his siblings, like him, became lazarists because of their desire to serve others following the pattern of saint vincent. 2 he entered the lazarists when he was only sixteen years old, and while he was in the seminary he displayed the usual french piety that was common in nineteenth-century france. perboyre spent long hours in front of the tabernacle in prayer and kneeling in thanksgiving after receiving holy communion. his brother, louis, was also a lazarist, and louis was sent to china before jean-gabriel. the two brothers were very close, and thus when the news reached jean-gabriel back in france that louis had died of illness en route to china it was a painful shock. while on his deathbed, father louis perboyre (d. 1831), wrote a letter to jean-gabriel: "i am dying before i can accomplish my goal-i hope that my priest brother can come and take my place." 3 jean-gabriel did take his brother's place; he left france five years after louis' death, and in 1835 he took his first steps as a missionary on chinese soil. for jean-gabriel, his time in china was short. he was tied to a pole and strangled, just as françois-régis clet was, only five years after his arrival. while clet and perboyre served as missionaries in china, the empire was strained with social disorder, and among the popular uprisings that afflicted several provinces was a rebellion led by a millenarian sect called the white lotus society. 4 unfortunately for the lazarists in hubei, local officials lumped christians into the same category as the white lotus followers, that is as a "heterodox religious sect." the result was terrifying for both the missionaries and chinese faithful; christians were loathed and attacked both by the white lotus group, as well as many magistrates within the provincial government. as catholics were accused of the same religious agenda as anti-court societies such as the white lotus adherents, anti-christian intrigues also precipitated official decrees ordering the suppression of christians. one such incident in 1818 forced françois-régis clet into hiding. on 25 may, the imperial palace in beijing was suddenly enveloped in "strong winds and torrential rains, while the sky turned red as thunder pealed above the city." 5 the emperor's advisors suggested that the strange occurrence was caused by the spiritual interference of the christian missionaries, and thus yamen runners were dispatched to arrest father clet. he was forced to remain in seclusion, hiding in small caves and remote places in the woods, and he eventually sought refuge in the home of a catholic family, where he "sheltered in place" for six lonely months. clet's location was revealed by an apostate christian and he was locked in chains, after which he was delivered to a local court where he was made to kneel on chains while his face was beaten with a leather strap. 6 when he was later transferred to the prison at wuhan, his clothes were, as one witness described them, "stained with blood from cuts and wounds caused by the blows and ill-usage to which he had been subjected during the journey." 7 he was condemned to death by slow suffocation on 17 february 1820, and he was taken to the execution ground in the wuchang district of the city, where he endured strangulation when a cord was tightened around his neck in three stages. his remains were collected by pious chinese catholics, and they were eventually sent to paris where they are today reserved at a side altar in the lazarist motherhouse. perboyre's arrest and execution in wuhan were quite similar to what françois-régis clet had undergone two decades previously. an anti-christian movement emerged in 1839 that compelled jean-gabriel to live in a state of isolation, and through this time he was hidden and protected by chinese christians who sheltered him despite the danger of losing their own lives if perboyre was discovered. after offering mass on 16 september 1839, a local christian arrived to inform perboyre that two officials and a large band of troops were quickly approaching the church. he fled only a few moments before the church was besieged and razed, and he survived temporarily by hiding in forests and the secreted rooms of chinese christian homes. he was eventually discovered and seized by patrolmen who dragged him away by his qing-style queue to be interrogated in tribunals. 8 jean-gabriel perboyre was summoned from his cell on 11 september 1840, and led to his execution while carrying a sign announcing his sentence. a lazarist record of his final moments is difficult to read, though the section that describes how he was executed in the wuchang district of wuhan provides the details regarding the particular nature of his martyrdom. the executioner then placed a cord around his neck and slipped a piece of bamboo into the knot. with a strong twist, he tightened the cord around the convict's neck, and then he loosened the cord to give the poor sufferer a moment to catch his breath. then he tightened the cord a second time, and relaxed it again. only after the third twist did he keep the cord tightened until death followed. 9 local christians bribed the officials to acquire the rope and clothes that remained on perboyre's body after his strangulation, and his corpse was interred beside the grave of françois-régis clet at a place called hong mountain near wuhan. i discuss clet and perboyre here in my concluding remarks because of their relevance to the present situation of china's catholic community, especially the "underground" and "aboveground" christians in and around wuhan, afflicted by the spread of the covid-19 virus. local chinese catholics still remember and commemorate the martyrdoms of clet and perboyre, and the detail that they were executed by strangulation, in the minds of some, serves as an historical precursor to the way the virus afflicts the infected by attacking their ability to breathe. wuhan's nineteenth-century catholic history has been compared with the city's twenty-first-century pandemic. seminarians now preparing for the priesthood in the wuhan seminary affectionately care for the two tombstones that formerly adorned the graves of clet and perboyre on hong mountain; the stone monuments are often seen surrounded by fresh flowers and seminarians praying for their intercession. these gravestones were previously relocated to the home of a local catholic where they were concealed and protected during the destructive years of the cultural revolution. the franciscan bishop of wuhan, bernadine dong guangqing, ofm (1917-2007) conducted a search for the gravestones after the cultural revolution had ended, and had them restored and installed at the huayuanshan catholic seminary. presently, they are displayed in the seminary courtyard and clet and perboyre are viewed as sympathetic intercessors as hospitals receive patients who bear such infectious diseases as the coronavirus. as i write this conclusion to the essays included in this volume, the catholic seminary, churches, and other catholic sites of wuhan are places of fervent prayer as many members of the christian community have suffered and died from covid-19. if anything, i trust that this compendium of research essays underscores how systemic was, and is, the roman catholic presence within the larger mass of chinese society. sino-christian exchange has at some level influenced the overall history of china since the appearance of franciscan mendicants during the yuan dynasty, but catholics were certainly not the only participants in china's early modern and modern transformation. secular diplomats and protestant missionaries, too, were lively interlocutors within the sino-western dialogue. the english explorer and naturalist, thomas wright blakiston (1832-1891), serves as a good example of a non-catholic westerner who participated in sino-western exchange in china. blakiston made his way of the yangze river in 1861, and when he encountered the catholic missionaries around wuhan, he believed a "disguised priest or two of the romish church" had surreptitiously concealed themselves within the chinese population. 10 as william t. rowe puts it, "roman catholic missionaries were not the only europeans who made their presence felt in hankow [district of wuhan] in pre-treaty-port days." 11 the cultural connections between westerners and chinese during the nineteenth, twentieth, and twenty-first centuries are ubiquitous and complex; these essays represent only a small portion of intellectual and religious encounters between east asia and the west. cultural dialectics are never homogenous, and i trust that this volume supports that assertion. to make one final point: while the word "conflict" has appeared throughout these essays, i do not suggest that conflict has monolithically defined sino-western encounters. far from it. just as often the word "friendship" appears throughout this compendium, and this is a much better term to describe the general nature of china's long relationship with the west. beatrice leung and william t. liu authored a fine book on the history of catholicism in modern china, and they chose to entitle their study, the chinese church in conflict, emphasizing the antagonisms that china's catholic christians have experienced with the state, as well as vatican tensions with beijing's post-1940 government. 12 other works in recent decades have sought to downplay the theme of conflict in their narratives, choosing instead an alternative nomenclature in their titles. such works use such terms as "cooperation" and "common ground" to depict the sino-christian and communist-christian dialogue. 13 in my own work i have attempted to portray the history of christianity in china as existing somewhere between what is implied in the terms, "conflict" and "cooperation." in 2015, i published a study of the catholics in shanxi, entitled heaven in conflict: franciscans and the boxer uprising in shanxi, and two years later, in 2017, i published an edited volume centering more on the theme of cooperation than conflict, entitled china's christianity: from missionary to indigenous church. 14 the essays in the present volume, i hope, tread cautiously between representing christianity in modern china as a church of mostly conflict, or one of mostly cooperation; it has historically been, and continues to be, a religious community that rests between these extremes. in his reflections on the end of the excruciating years of the cultural revolution, the now-deceased bishop of shanghai, aloysius jin luxian, wrote that while human beings are capable of "hatred and delighting in destruction, they are also able to preach benevolence, amity, and harmony. human progress is like the tides of the sea-waves advance and recede; we recede a single step, but we advance two steps." 15 this is an optimistic view of humanity, one that most of china's catholics, at least the ones i know, agree with. in several ways i remain an "outsider" of the church in china, but what i have observed over the decades is more advance than retreat, and in that way, i suppose, i am more inside than outside the mind of china's catholic community. two vincentian martyrs: blessed francis regis clet for an exhaustive biography of jean-gabriel perboyre, see life of blessed john gabriel perboyre: priest of the congregation of the mission, martyred in china martyr en chine for various popular movements of the late-qing, including the white lotus sect (bailian jiao), see jean chesneaux two vincentian martyrs two vincentian martyrs hankow: commerce and society in a chinese city the chinese church in conflict patriotic cooperation: the border services of the church of christ in china and chinese-church relations seeking the common ground: protestant christianity, the three-self movement, and china's united front heaven in conflict china's christianity: from missionary to indigenous church key: cord-279569-289fu2yb authors: lei, yu; lan, yunping; lu, jianli; huang, xiaobo; silang, bamu; zeng, fan title: clinical features of imported cases of coronavirus disease 2019 in tibetan patients in the plateau area date: 2020-03-13 journal: nan doi: 10.1101/2020.03.09.20033126 sha: doc_id: 279569 cord_uid: 289fu2yb abstract coronavirus disease 2019 (covid-19), caused by sars-cov-2, has rapidly spread throughout china, but the clinical characteristics of tibetan patients living in the qinghai-tibetan plateau are unknown. we aimed to investigate the epidemiological, clinical, laboratory and radiological characteristics of these patients. we included 67 tibetan patients with confirmed sars-cov-2 infection. the patients were divided into two groups based on the presence of clinical symptoms at admission, with 31 and 36 patients in the symptomatic and asymptomatic groups, respectively. the epidemiological, clinical, laboratory and radiological characteristics were extracted and analysed. no patient had a history of exposure to covid-19 patients from wuhan or had travelled to wuhan. the mean age of tibetan patients was 39.3 years and 59% of the patients were male. seven patients presented with fever on admission and lymphocytopenia was present in 20 patients. 47 patients had abnormal chest cts at admission instead of stating that 20 were unchanged. lactate dehydrogenase levels were increased in 31 patients. seven patients progressed to severe covid-19; however, after treatment, their condition was stable. no patients died. of the 36 asymptomatic patients, the mean age was younger than the symptomatic group (34.4vs 44.9 years, p=0.02). lymphocyte count and prealbumin levels were higher in the asymptomatic group than the group with clinical symptoms (1.6 vs 1.3 and 241.8 vs 191.9, respectively; p<0.05). imported cases of covid-19 in tibetan patients were generally mild in this high-altitude area. absence of fever or radiologic abnormalities on initial presentation were common corona virus disease 2019 (covid-19) has rapidly spread from wuhan to other areas of china and has now become a global threat. at the time of writing on march 2 nd 2020, covid-19 cases have been confirmed in 92 countries, with more than 100,000 cases globally. wuhan is thought to be the site of earliest covid-19 occurrence, and cases further afield were infected by sars-cov-2 carriers from wuhan. in particular, the mortality of patients in wuhan was higher than in any other city in china, at 4.3% compared with 0.8% in the rest of mainland china(updated data available at https://wp.m.163.com/163/page/news/virus_report/index.html?spss=feed&&spssid=a 64bed4d89174914f9792895db5b15e8&spsw=1). the clinical characteristics and outcome of patients seem to be different between wuhan and other areas. despite the publication of many articles regarding the clinical features of covid-19 patients, most of these patients were considered in the context of wuhan. daofu, located within the qinghai-tibetan plateau at an altitude of more than 3000 m, is a low-income county in sichuan province, china. there are more than 3000 tibetans living here. of those becoming infected, none of them had travelled to wuhan or had a history of all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in epidemiological, clinical laboratory and radiological characteristics, chronic medical histories, clinical symptoms, treatment and outcome data were obtained from electronic medical records and analysed by two independent researchers. when missing or uncertain records were encountered, the researchers communicated directly with patients or their families to collect and clarify the relevant data. the date of disease onset was defined as the day when symptoms were first noticed or the day when the real-time pcr test for nucleic acid in respiratory or blood samples from asymptomatic patients was positive. the patients were then divided into two groups based on the presence of clinical symptoms at time of admission. the symptomtic group was defined as those patients with any clinical symptoms such as fever, cough and headache. according to the diagnostic and treatment guidelines for covid-19 issued by the chinese national health committee, severe covid-19 was defined as all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033126 doi: medrxiv preprint the occurrence of either one of the following criteria: respiratory distress with respiratory frequency ≥30/min; oxygenation index (artery partial pressure of oxygen/inspired oxygen fraction, pao2/fio2) ≤300mmhg. importantly, oxygenation index should be corrected if the local altitude is higher than 1000 m using the corrector formula: pao2/fio2*atmospheric pressure/760. patient nasal and pharyngeal swabs or blood samples were collected for detection of sars-cov-2 viral nucleic acid using real-time pcr assay. laboratory confirmation of sars-cov-2 was performed by the local cdc as previously described 1 . categorical variables were summarized as frequencies and percentages. continuous variables were expressed as median + standard deviation (sd) or inter-quartile range (iqr). continuous variables were compared using student's t-test and the mann-whitney test. the chi-squared and fisher's tests were used for the frequencies of categorical variables. all statistical analyses were performed using spss software (version 24, ibm, armonk, ny). p-values less than 0.05 were considered to be statistically significant. a total of 67 patients diagnosed with covid-19 were included in this study. all of them were tibetans living in qinghai-tibetan plateau twenty-six were members of one family ,34 had a history of attending a funeral or temple; however, none had visited wuhan or had contact with wuhan residents. the first patient to be diagnosed with sars-cov-2 infection had travelled to chengdu，the city of westchina., 10 days before onset of symptoms but denied any contact with covid-19 patients. the clinical characteristics of the patients are shown in table 1 .2. thirty-nine of 67 all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033126 doi: medrxiv preprint patients (58.2%)were male, with a median age of 39.3 years. the youngest patient was 3 years old, with his family all confirmed as sars-cov-2-positive. twenty (29.9%)of the total cohort had chronic diseases. fever was present in only seven patients (10%) on admission and developed in a further nine (24%) during hospitalization. thirty-six patients (54%) showed no clinical symptoms when they were admitted to hospital. the remaining 31 patients (46%) presented with clinical symptoms, of which cough was the most common (13/67, 19%). other symptoms included fatigue, headache, muscle ache and dizziness. of note, the asymptomatic group was significantly younger than the symptomatic group, with median ages of 34 and 44 years (p=0.02), respectively. table 1 baseline characteristics on admission and clinical outcomes of patients with all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 13, 2020. table 3) . with advancing time, the medical history associated with case exposure to sars-cov-2 infected patients from wuhan has become less obvious. human to human transmission is now occurring, resulting in imported cases with no direct contact with patients in wuhan. in our study, we assessed 67 sars-cov-2 infected tibetan all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033126 doi: medrxiv preprint patients living in theqinghai-tibetan plateau. none of these patients had a history of exposure to covid-19 cases from wuhan or had travelled to wuhan. however, most of them had a history of attending a gathering or contact with a sars-cov-2-infected family. isolation of cases and contact tracing has been implemented for covid-19 2 . in our study, most patients did not present with typical clinical symptoms at time of admission. this is inconsistent with recent studies, which have most commonly found fever and cough to be the dominant symptoms 3, 4 . in our study, fever was only found in 10% of patients on admission and increased to13.5% during hospitalization. cough was only presented by 18% of patients. the absence of fever and cough was frequent in our study. unlike the other studies that included only the cases who actively sought medical attention 3 , our cohort included sub-or preclinical cases identified by local cdc collection of nasal and pharyngeal secretion samples from most residents to detect sars-cov-2 nucleic acid, even though the majority of residents had no clinical symptoms or any history of exposure to covid-19 cases. through active screening, we found 36 virus carriers without clinical symptoms. if surveillance relies on fever detection or on patients actively seeking medical advice due to clinical symptoms, many potential virus carriers may be missed. lymphocytopenia was common, especially in those with clinical symptoms, which is consistent with the data reported recently. nearly half of patients showed increased levels of ldh, while one-third of patients suffered liver injury and decreased levels of prealbumin. however, these changes were mild. angiotensin converting enzyme 2 (ace2) may act as a potential intermediate host receptor which transmitting sars-cov-2 to human. ace2 is expressed in liver tissue and an overactive inflammatory response in patients with sars-cov-2 infection may cause increased ace2 expression, and thus result in the observed liver tissue injury 5, 6 . therefore, in addition to the obvious target organ of the lungs, the liver is another important organ that is vulnerable following infection with sars-cov-2. in our study, the condition of most patients was mild, with only 10% of patients developing to severe disease. after antiviral and oxygen therapies, the patients' conditions gradually stabilized, with none succumbing to disease. the fatality rate all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033126 doi: medrxiv preprint was therefore lower than that reported by the national official statistics, which recorded a rate of death of 3100 among 80000 cases of covid-19 to date in china. one reason for this discrepancy may be that in our study, all the patients were imported cases resulting from serial human to human transmission rather than direct contact with cases in wuhan. in addition, the altitude at which our cohort lives is higher than 3000 m and so virus viability and virulence may be decreased. the second reason may be that the median age was 39.3 years in our study, which was younger than that reported by huang et al 7 . interestingly, the median age of patients with clinical symptoms was older than that of asymptomatic patients (44.9 vs 34.4 years, p=0.02). in general, older persons appear more susceptible to covid-19 and more likely to suffer severe disease, which may be due to underlying health issues and comorbidities 8 . in our study , the mean age of severe cases were 58.5 years. a further reason for the discrepancy in mortality rates between our study and the national figures may be that because the local cdc actively screened a large number of residents, approximately half of the patients were identified and admitted to hospital before clinical symptoms appeared. patients therefore received treatment at the earliest stages of disease. early identification and timely treatment are of crucial importance for effective prevention of severe disease. our study has some notable limitations. first, only 67 patients were included, although this study describes the largest cohort of tibetan patients. with the effective measures taken by the government, the number of new patients has decreased. second, some patients remained in hospital and the outcome is unknown at the time of data cutoff. we will continue to focus on the prognosis of these patients and report outcomes in due course. in conclusion, imported cases of sars-cov-2 infection in tibetan patients were generally mild in this high-altitude area. absence of fever or radiologic abnormalities on initial presentation was common. our findings highlight the importance of active screening for residents who live in areas with high incidence rate of covid-19. a rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-ncov) infected pneumonia (standard version) feasibility of controlling covid-19 outbreaks by isolation of cases and contacts. the lancet global epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of coronavirus disease 2019 in china exploring the mechanism of liver enzyme abnormalities in patients with novel coronavirus-infected pneumonia composition and divergence of coronavirus spike proteins and host ace2 receptors predict potential intermediate hosts of sars-cov-2 clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical characteristics of 140 patients infected with sars-cov-2 in wuhan all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in all rights reserved. no reuse allowed without permission. perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in the copyright holder for this this version posted march 13, 2020. . https://doi.org/10.1101/2020.03.09.20033126 doi: medrxiv preprint key: cord-343715-y594iewi authors: gavriatopoulou, maria; korompoki, eleni; fotiou, despina; ntanasis-stathopoulos, ioannis; psaltopoulou, theodora; kastritis, efstathios; terpos, evangelos; dimopoulos, meletios a. title: organ-specific manifestations of covid-19 infection date: 2020-07-27 journal: clin exp med doi: 10.1007/s10238-020-00648-x sha: doc_id: 343715 cord_uid: y594iewi although covid-19 presents primarily as a lower respiratory tract infection transmitted via air droplets, increasing data suggest multiorgan involvement in patients that are infected. this systemic involvement is postulated to be mainly related to the sars-cov-2 virus binding on angiotensin-converting enzyme 2 (ace2) receptors located on several different human cells. lung involvement is the most common serious manifestation of the disease, ranging from asymptomatic disease or mild pneumonia, to severe disease associated with hypoxia, critical disease associated with shock, respiratory failure and multiorgan failure or death. among patients with covid-19, underlying cardiovascular comorbidities including hypertension, diabetes and especially cardiovascular disease, has been associated with adverse outcomes, whereas the emergence of cardiovascular complications, including myocardial injury, heart failure and arrhythmias, has been associated with poor survival. gastrointestinal symptoms are also frequently encountered and may persist for several days. haematological complications are frequent as well and have been associated with poor prognosis. furthermore, recent studies have reported that over a third of infected patients develop a broad spectrum of neurological symptoms affecting the central nervous system, peripheral nervous system and skeletal muscles, including anosmia and ageusia. the skin, the kidneys, the liver, the endocrine organs and the eyes are also affected by the systemic covid-19 disease. herein, we provide a comprehensive overview of the organ-specific systemic manifestations of covid-19. the sars-cov-2 virus has caused a worldwide pandemic in the past few months with a major impact on health care systems and economies. since december 2019 when the first diagnosed case was identified in wuhan, china, the highly contagious virus has spread throughout the world with detrimental consequences. sars-cov-2 belongs to the coronaviruses family of enveloped, single-stranded rna viruses [1] . notably, the main hosts of these viruses are animals. to date, 39 different species of the viruses have been identified, including two highly contagious and pathogenic species that led to two different outbreaks the past 2 decades [severe acute respiratory syndrome coronavirus (sars-cov) in 2002 and middle east respiratory syndrome coronavirus (mers-cov) in 2012] [2] . patients infected with this new coronavirus present with a variety of symptoms, which range from asymptomatic disease to mild and moderate symptoms (mild pneumonia), severe symptoms (dyspnoea, hypoxia, or > 50% lung involvement on imaging) and symptoms of critical illness (acute respiratory distress syndrome, respiratory failure, shock or multiorgan system dysfunction). the disease affects mainly elderly adults; however, younger patients without comorbidities can also be diagnosed with severe disease. the virus presents primarily as a lower tract respiratory infection transmitted via air droplets, but the multisystemic nature of the disease is becoming increasingly apparent as more data are emerging. it is postulated that it is related to the tropism of the virus for the ace-2 receptors located on several different human cells. the occurrence of other symptoms can not only coexist, but may also precede the typical phenotype of covid19 . in a recent study, sars-cov-2 viral load was quantified in 22 post-mortem autopsy tissue samples [3] ; 17 patients (77%) had more than two coexisting conditions. the number of coexisting conditions was strongly associated with sars-cov-2 affinity to the kidneys, including patients without history of chronic kidney disease. the highest levels of sars-cov-2 copies were detected in the respiratory tract, while the levels detected in kidneys, liver, heart, brain and blood were lower. these findings indicate a possible organ tropism of sars-cov-2 that might influence the course of the disease leading potentially to underlying conditions aggravation. as our knowledge on the virus mechanisms increases, our understanding on the various complications will continue to evolve. this manuscript aims to review the available literature and provide further insight on multiorgan involvement of the disease (fig. 1 ). the severity of lung involvement associated with sars-cov-2 infection ranges from lack of symptoms or mild pneumonia (in 81%) to severe disease-associated hypoxia (seen in 14%), critical disease associated with shock, respiratory failure and multiorgan failure (in 5%) or death (2.3%) [4] . it is the most common serious disease manifestation. patients may present with dry cough, fever, sputum production, fatigue and dyspnea, and the reported frequency varies based on the cohort studied [5] [6] [7] . among hospitalized patients, 20-41% will develop acute respiratory distress . what is becoming increasingly apparent as our understanding of the mechanisms of covid-19 induced lung injury expands, are the distinct or "atypical" features of covid-19-associated ards [4, 8] . based on sars-cov virus data, the genome of which is highly homologous to the sars-cov-2 genome, it is hypothesized that the human angiotensin-converting enzyme 2 (ace2) receptor is the main functional receptor for the sars-cov-2 virus. the ace2 receptor is expressed on the apical side of type ii alveolar epithelial cells in the alveolar space, and the large surface area of the lung serves as a reservoir for viral binding and replication, providing an explanation for the tropism of the sars-cov-2 virus and the lung vulnerability observed [9, 10] . sars-cov-2 infection induces alveolar injury and interstitial inflammation. dendritic cells (dcs) and alveolar macrophages phagocytose the virus-infected apoptosed epithelial cells, and t cell responses are initiated activating innate and adaptive immune mechanisms [11] . levels of proinflammatory cytokines and chemokines, such as tumour necrosis factor (tnf)-α, interleukin 1β (il-1β), il-6, and more, are increased in patients with covid-19 infection [12] . the cytokine storm is hypothesized to play a central role in the immunopathology of covid-19, but the primary source or the exact virological mechanisms behind it have not been identified yet. there is extensive hemophagocytosis which shares features but is distinct from the well-described macrophage activation syndrome (mas) [13, 14] . in addition to the proinflammatory stage and immune system activation, an immune suppression stage follows which is characterized by lymphopenia, low cd4 and cd8 t cell counts, increasing the risk of bacterial infection [15, 16] . emerging data from covid-19 pneumonia autopsy studies demonstrate acute interstitial pneumonia and diffuse alveolar damage (dad) with macrophage infiltration, formation of hyaline membranes and alveolar wall oedema and thickening. there is also microvasculature involvement with pulmonary vessel (intra and extra) hyaline thrombosis, haemorrhage, vessel wall oedema, intravascular neutrophil trapping and immune cell infiltration. in one series, in 5 out of 23 patients, major pulmonary vessel thromboemboli and/or haemorrhage were reported [14, 17, 18] . mcgonagle et al. use the term diffuse pulmonary intravascular coagulopathy (pic) to describe this lungrestricted vascular immunopathology [19] driven probably by the close anatomical positioning of type ii pneumocytes and the pulmonary vasculature. at early stages of this process, there is no systemic coagulopathy (dic) which is seen, however, at later disease stages coupled with the presence of ards. extensive microthrombi formation within the vascular bed causes pulmonary infarction, haemorrhage, pulmonary hypertension and secondary ventricular stress [20] . hypoxemia and mechanical ventilation which forces immunostimulatory molecules in the microvasculature also seem to contribute to the development of pic. findings on chest radiograph imaging are not diseasespecific and usually include ground glass opacities with bilateral, peripheral or lower lung zone distribution with or without consolidation [21] [22] [23] . chest ct is more sensitive, but no finding can 100% establish or rule out the diagnosis [24] . according to the radiological society of north america, ct findings are categorized into typical, indeterminate or atypical for covid-19 demonstrating that specificity is low even for ct [25] . in one study using rt-pcr as a reference, sensitivity was 97% but specificity very low at 25% [26] . radiological abnormalities increase over the disease course, and the typical peak is at 10-12 days post-symptom initiation. at early stages or in mild disease, imaging may not reveal any pathology, but interestingly abnormal findings on imaging can be identified in some cases prior to symptom development or even prior to pcr rna detection [27] . using ct as a screening tool is not, however, recommended. improvement of the findings lags behind symptom or hypoxia improvement [28] . hypoxia is frequently a presenting feature of covid-19 pneumonia, but interestingly, it is often insidious and paradoxically well tolerated by the patients. this unusual clinical presentation, seen at early disease stages, is referred to as "silent hypoxia" and is linked to the "atypical" features of the ards syndrome associated with covid-19 pneumonia [29] . contrary to the typical ards, lung compliance is preserved and the hypoxia-driven tachypnea allows high volumes and hypocapnia which fails to stimulate the sensation of dyspnea. a similar pathophysiological mechanism is seen in hypobaric hypoxia at high altitude [30] . a model has been recently proposed which includes two timeassociated phenotypes. the severity of infection, patient comorbidities and physiological reserve, the time elapsed between disease onset and presentation to hospital and the host immune response all contribute. the l-phenotype is seen at early disease stages; there is high lung compliance, and the ventilation-to-perfusion ratio (va/q ratio) is low, but there is dysfunctional regulation of perfusion with hypoxic vasoconstriction. at this stage, the lung weight is low and lung recruitability is low with minimal amount of non-aerated lung tissue. this develops into the h-phenotype with decreased lung compliance due to oedema, increased fraction of cardiac output perfusing the non-aerated tissue and therefore a right-to-left shunt, increased lung volume due to oedema and consolidation and therefore high recruitability. type l patients usually remain stable for some time and can then either improve or worsen and transition into type h, secondary to evolution of the covid-19 pneumonia but also injury induced by high-stress ventilation [31] . management should be adapted based on the type of phenotype and timing/stage of lung injury. a high positive end-expiratory pressure (peep) on the ventilator, at early stages of poor lung recruitability, is not very effective, but in combination with gravitational forces (using prone positioning), it may allow for perfusion redistribution and increased oxygenation [32, 33] . the initial practice of early intubation was not supported by emerging data. l-phenotype patients should receive high-flow nasal cannula fio2, continuous positive airway pressure or non-invasive ventilation with close monitoring. awake or self-proning has been incorporated in many hospital protocols in an attempt to prevent intubation and reverse hypoxemia [34] . type h patients should be treated as severe ards with higher peep volumes, prone positioning and extracorporeal support. another factor that may predispose for severe and potentially fatal ards in patients with covid-19 is the excessive increase in circulating proinflammatory cytokines including interleukins (il-1, il-6), interferon and tnf-α. this "cytokine storm" results from an inflammatory over-reaction as a response to sars-cov-2 infection that ultimately leads to endothelial cell dysfunction, damage of the vascular barrier, capillary leak and diffuse alveolar damage [35] . in this context, anti-il-6 inhibitors, such as the monoclonal antibody tocilizumab, inhibitors of jak kinases, such as baricitinib, and corticosteroids, especially dexamethasone, have been evaluated in patients with severe covid-19 and have shown promising preliminary results [36] [37] [38] [39] . among patients with covid-19, underlying cardiovascular comorbidities including hypertension, diabetes, and especially cardiovascular disease, have been associated with adverse outcomes [4, [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] , whereas the emergence of cardiovascular complications, including myocardial injury, heart failure and arrhythmias, has been associated with poor survival [6, [40] [41] [42] [43] [44] [50] [51] [52] [53] [54] . the presence of obesity is also associated with adverse cardiovascular outcomes [55] . evidence of myocardial injury in patients with covid-19 has been a remarkable finding [40-42, 44, 50-53] . ace2 expression is significantly elevated in cardiac tissue [56] and may potentially facilitate direct myocardial damage induced by viral infection. there have been also reported isolated cases of covid-19-induced myocarditis, which support the hypothesis of direct myocardial injury by sars-cov-2 [57] [58] [59] [60] . furthermore, ace2 plays an important role in the renin-angiotensin system by catalysing the conversion of angiotensin ii to angiotensin 1-7, which exerts a protective effect on the cardiovascular system [61, 62] . importantly, the binding of sars-cov-2 to ace2 is anticipated to result in loss of the external ace2 catalytic effect [63, 64] . subsequently, the theoretical downregulation of ace2 and the decrease in angiotensin 1-7 levels in patients with covid-19 may also compromise heart function [65] . in addition to the above, a non-negligible proportion of patients with covid-19 seem to experience a hyperinflammatory state, in which inflammatory cytokines and other markers of systemic inflammation are markedly increased [40] [41] [42] 66] . the circulating cytokines can stimulate macrophages and leucocyte adhesion molecule expression on the endothelial cells of underlying atherosclerotic lesions, rendering them more vulnerable for disruption and increasing the possibility of a clinically evident acute coronary syndrome [67, 68] . systemic cytokines may also activate the microvascular endothelium and induce a dysfunction of the coronary microvasculature, which may result in myocardial ischaemia and myocardial injury [68] . inflammation and subsequent dysfunction of the endothelium in several organs are the result of both the direct effect of sars-cov-2 infection of endothelial cells and the indirect effects of the host inflammatory response [69] . myocardial injury can also result secondary to a mismatch between myocardial oxygen supply and demand, known as type 2 myocardial infarction. sars-cov-2 infection may be associated with myocardial damage through increased myocardial oxygen demand along with reduced myocardial oxygen supply. severe respiratory complications and associated hypoxia have been common findings in patients with covid-19 [41, 43, 45, 51, 70] . moreover, hypotension, which is a common clinical feature both in sepsis and during the cytokine storm syndrome, can also reduce myocardial oxygen supply [68] . furthermore, systemic infection and fever increase the metabolic needs of peripheral tissues and end-organs, which elevates the metabolic demands of the myocardial cells [71] . fulminant myocarditis may be a clinical manifestation of covid-19 [57, 58] and may result in left ventricular systolic dysfunction or even cardiogenic shock [72, 73] . among 176 chinese patients with covid-19, chen et al. reported heart failure as a complication in 24.4% (n = 43), using age-related amino-terminal pro-brain natriuretic peptide (ntprobnp) cut-points [53] . interestingly, there was a significant difference in the prevalence of heart failure between covid-19 survivors and non-survivors (3.2% vs. 49.4%) [53] . another study encompassing data from 191 patients reported a 23% (n = 44) incidence of heart failure, 63.6% (n = 28) of which was fatal [41] . a meta-analysis of 43 studies involving 3600 patients reported a prevalence of heart failure as a covid-19 complication of 17.1% (95%, ci 1.5-42.2) among critically ill patients compared to 1.9% (95% ci 0.0-26.0) among non-critically ill patients [54] . guo et al. reported sustained ventricular tachycardia or ventricular fibrillation in 5.9% (n = 11) of 187 patients treated in a covid-19 specialized centre in china [52] . another retrospective study including data from the 393 consecutive patients with covid-19 in two hospitals in new york city showed that patients who received mechanical ventilation were more likely to have atrial arrhythmias (18.5% versus 1.9%) [6] . it has to be noted that sustained ventricular arrhythmias have been reported as a frequent clinical feature of acute myocarditis [73] , which may be the case in patients with covid-19 complicated by myocarditis. importantly, arrhythmias may be also induced by medical treatment for covid-19, such as chloroquine phosphate, hydroxychloroquine sulphate and azithromycin [74] . these agents and their combinations may prolong the qtc interval and predispose for torsades de pointes or other ventricular arrhythmias [75] . another characteristic manifestation of covid-19 in the cardiovascular system that has been recently reported is a kawasaki-like syndrome, which is characterized by circulatory dysfunction and macrophage activation syndrome [76] . a single-centre study conducted in bergamo, italy, reported a 30-fold increase in the incidence of kawasaki-like disease during the covid-19 pandemic, as compared with the previous year [77] . the cytokine storm associated with infection by sars-cov-2 may be the predisposing mechanism for the kawasaki-like clinical phenotype, but further insight has to be shed by future preclinical studies. the underlying pathophysiologic mechanism for the occurrence of digestive symptoms is also thought to be related to the virus's affinity for ace2 receptors located in specific enterocytes in the ileum and colon [52, 78, 79] . ace2 receptors are involved partially in inflammation mechanisms and therefore could provide an explanation for the occurrence of diarrhoea in infected patients. importantly, the binding efficiency is stronger for sars-cov-2 than the sars-cov-1, and this might be one of the reasons of high rate of transmission [80] . binding to primary intestinal epithelial cells also raises the question on whether the virus can be transmitted through the faecal-oral route, which currently remains unconfirmed [78, 79] . the largest study evaluating digestive involvement in patients with covid-19 was performed in wuhan, china. the investigators evaluated 1141 retrospective cases admitted to one single hospital over a period of 7 weeks [81] . 16% (183) of patients presented only with gastrointestinal symptoms. the most common symptom reported was loss of appetite. vomiting and nausea occurred in approximately two-third of the patients, while diarrhoea and abdominal pain were present in 37% and 25%, respectively. the main study limitations were its retrospective design along with the relatively small sample size. another cross-sectional study from hubei province reported results on digestive symptoms from patients being admitted to one of three different hospitals during january and february 2020. in total, 99 patients (48.5%) had gastrointestinal symptoms. the symptoms included anorexia (83.8%), diarrhoea (29.3%), vomiting (8.1%) and abdominal pain (4.0%), while some patients reported symptoms combinations. notably, 7 patients presented only with digestive symptoms with no evidence of respiratory involvement. in this case, the diagnosis was delayed due to the non-specific symptoms they experienced [82] . another study in china included 1099 patients and demonstrated that the most common symptoms on admission were fever (43.8%) and cough (67.8%) [43] . gastrointestinal symptoms were less common-nausea or vomiting 5% and diarrhoea 3.8%, respectively. in a single-centre case series of 138 hospitalized patients with covid-19, 10.1% reported diarrhoea and/or nausea, but the proportion of patients only with digestive symptoms was not outlined [50] . in another recent study performed in china, gastrointestinal symptoms were reported in 74 of 651 (11.4%) patients [83] . nausea, vomiting and diarrhoea were the most common. importantly, it was demonstrated that gi symptoms were more common in patients with severe covid-19 disease (23% vs. 8.1%). further data are required to understand better the role of the gastrointestinal involvement of covid-19 and clarify whether it is correlated with worse outcomes. the abovementioned studies did not test for virus rna in the stool, so there is no proof that active viral rna replication can be found in the digestive tract. a recent report of a 25-year-old female who presented with respiratory symptoms and fever indicates that the virus might be excreted in faeces [84] . ten days after admission, she underwent real-time pcr of a pharyngeal sample that was negative for sars-cov-2. a separate faecal sample was tested and found positive. the next 7 days 4 additional samples from the respiratory tract were tested and were all negative. this suggests that the gastrointestinal tract was the only documented source of the virus infection. in a recent singaporean study, 50% of patients had sars-cov-2 detected in their stool samples, but detection did not correlate with the presence of digestive symptoms [85] . in another study, the duration of viral rna detection after recovery was examined [86] . the median time from symptoms onset to first negative rt-pcr test from oropharyngeal swab was 9.5 days, but 16 .7% of the patients tested positive for viral rna from stool specimens for a median of 11 days. this observation indicates that there might be a potential faecal-oral transmission risk many days after symptoms resolution. regarding the liver-related complications of covid-19, liver test abnormalities have been described in infected patients. in one study, it was demonstrated that total bilirubin, ast and alt were elevated in 10%, 21% and 22% of patients, respectively [43] . other case series have reported alt abnormalities in 16-53% [40, 51, [87] [88] [89] [90] . to date, cases of acute liver failure have not been reported. liver dysfunction is mainly described in patients with severe disease upon presentation. however, it is difficult to discriminate the independent effect of the infection from other treatment modalities, such as antibiotics and antiviral drugs administered to these patients. additionally, these abnormalities could be attributed to the infection itself, the induced sepsis or the concurrence of hypoxia. one patient underwent liver autopsy which revealed microvesicular steatosis, mild lobular and portal inflammation [91] . ace2 receptors are located in hepatocytes and cholangiocytes; therefore, it was anticipated that the liver would also be involved. however, cholestatic abnormalities have rarely been described. underlying pre-existing liver diseases could have contributed to liver enzyme abnormalities. the exact pattern of liver injury as well as its role in mortality needs to be further investigated. finally, very recently a systemic review and meta-analyses were published in lancet gastroenterology and hepatology in order to identify the prognosis and prevalence of digestive tract involvement and liver abnormalities in patients diagnosed with covid-19. in total, 35 studies with 6686 patients were included in the analyses. the study demonstrated that gastrointestinal symptoms and hepatic toxicity are not uncommon among patients with covid-19 disease [92] . covid-19 is a systemic infection with a significant impact on the haematopoietic system and homeostasis [93] . lymphopenia may be considered as a cardinal laboratory finding, with prognostic potential. approximately, 7-14 days from the onset of the initial symptoms, there is a surge in the clinical manifestations of the covid-19 disease with a pronounced systemic increase in inflammatory mediators and cytokines, which may even be characterized as a "cytokine storm" [94] . in this context, significant lymphopenia becomes evident. neutrophil/lymphocyte ratio and peak platelet/lymphocyte ratio may also have prognostic value in determining severe cases. lymphocytes express the ace2 receptor on their surface [81] ; thus, sars-cov-2 may directly infect those cells, whereas the cytokine surge may promote lymphocyte apoptosis [95] [96] [97] . substantial cytokine activation may be also associated with atrophy of lymphoid organs, including the spleen, and further impairs lymphocyte turnover [98] . abnormalities in haematological parameters have been more prominent among severe versus non-severe cases (96.1% versus 80.4% for lymphocytopenia, 57.7% versus 31.6% for thrombocytopenia and 61.1% versus 28.1% for leukopenia). these results were consistent in four other descriptive studies that were conducted during the same period in china and included 41, 99, 138 and 201 confirmed cases with covid-19, respectively [40, 42, 50, 87] . a meta-analysis of nine studies suggested that thrombocytopenia is significantly associated with the severity of the covid-19 disease, with very high between-studies heterogeneity, though a more sizeable drop in platelet counts was noted especially in non-survivors [99] . during the disease course, longitudinal evaluation of lymphocyte count dynamics and inflammatory indices, including ldh, crp and il-6, may help to identify cases with dismal prognosis and prompt intervention in order to improve outcomes [93] . biomarkers such as high serum procalcitonin, crp and ferritin have also emerged as poor prognostic factors [41, 43, 100] . more recently, high cortisol levels at presentation may reflect disease severity and have been recognized as an adverse prognostic factor associated with poor survival among patients with severe covid-19 [101] . furthermore, blood hypercoagulability is common among hospitalized covid-19 patients, especially among those with severe disease [41, 102, 103] . elevated d-dimer levels are consistently reported, whereas their gradual increase during disease course is associated with clinical deterioration [40, 43, 50, 87, 104] . other coagulation abnormalities such as pt and aptt prolongation, increasing fibrin degradation products, with severe thrombocytopenia lead to life-threatening disseminated intravascular coagulation (dic) which necessitates continuous vigilance and prompt intervention [41, 42, 52, [105] [106] [107] [108] . endothelial dysfunction and immune deregulation may be implicated in the underlying pathophysiology [109] . covid-19 infected patients are at high risk of venous thromboembolism (vte) (up to 10% for acutely ill hospitalized patients [110] ). comorbidities, along with the possibility of endothelial cell activation/damage due to the virus binding to ace2 receptor, collectively increase the risk of vte. prompt pharmacological thromboprophylaxis with low molecular weight heparin is highly recommended [93, 111, 112] . although coronaviruses mainly cause respiratory symptoms, they have been reported to be involved in direct cns infection as well as para-infectious complications [113] . recent studies reported that over a third of infected patients developed a broad spectrum of neurological symptoms affecting central nervous system (cns), peripheral nervous system (pns) and skeletal muscles [114, 115] . in each case, it has to be noted that the challenge lies in discriminating between causal relationship and incidental comorbidity [116] . a large retrospective observational study from china showed that among 214 hospitalized patients with confirmed sars-cov-2 infection, 36.4% had neurological manifestations [114] . most neurological symptoms occurred early during the first days after hospital admission. with regard to symptom category, 24.8% of infected patients presented symptoms from cns, 8.9% from pns and 10.7% developed skeletal muscle injury. the most common cns symptoms were dizziness (16.8%) and headache (13.1%), and the most commonly reported symptoms involving pns were taste impairment (5.6%) and anosmia (5.1%). other less frequent symptoms included impaired consciousness (7.5%), acute cerebrovascular disease (2.8%), ataxia (0.5%), seizure (0.5%), vision impairment (1.4%) and nerve pain (2.7%). notably among severely infected patients the prevalence of neurological manifestation was even higher, up to 45% compared to patients with less severe disease (30.2%). the correlation of disease severity with neurological symptoms was confirmed by another retrospective study from france, reporting a prevalence of 84% of neurological manifestations in 58 hospitalized patients with acute respiratory distress syndrome (ards) due to covid-19 [115] . of note, some of the reported symptoms such as inattention, disorientation and movement disorders persisted even after discharge. several mechanisms that may overlap have been proposed to explain the link between sars-cov-2 infection and nervous system injury [117] . clinical manifestations of covid-19 might be a consequence of the viral infection per se and/ or the adverse insult of the hyperinflammatory status and dysregulated metabolic function, in combination with the multiple organ damage observed in patients after covid-19 infection [113, 118] . direct viral damage of nervous tissue might be possible in different ways. as with sars and mers viruses, sars-cov-2 may enter the cns through the hematogenous or retrograde neuronal route. infection of olfactory neurons in the nose may enable the virus to enter the brain transneuronally and spread directly from the respiratory tract to the brain [118] . ace2 receptors are also found in the nervous system and skeletal muscles [119, 120] . the expression and distribution of ace2 in brain and endothelial cells may explain how sars-cov-2 may cause direct neurological symptoms and skeletal muscle damage. direct viral damage of nervous tissue resembling in some ways herpes simplex encephalitis might be also possible, although there is no definite evidence of direct injury of cns by sars-cov-2 virus. the excessive immune response which results in a hyperinflammatory status and cytokine storm may represent another alternative mechanism. cytokines can directly pass through the blood-brain barrier causing considerable damage such as acute necrotizing encephalopathy [121] . an indirect injury related to host immune response effects after acute coronavirus infection could also be possible, explaining to some extent the occurrence of guillain-barré syndrome (gbs) cases, transverse myelitis or acute disseminated encephalomyelitis in patients with covid-19 and other virus epidemics [113, 122, 123] . neurological symptoms caused by systemic illness especially in severely ill patients could also justify neurological manifestations of covid-19 infection [114] . patients admitted to intensive care unit (icu) often develop encephalopathy, myopathy, autonomic neuropathy and polyneuromyopathy related to critical illness [124] . cerebrovascular disease represents another mechanism explaining neurological signs and symptoms in covid-19 patients, although the rate of acute stroke admissions has been significantly reduced over the covid-19 pandemic [125] . a large retrospective study from china reported a rate of 5.4% for both haemorrhagic and ischaemic strokes among critically ill patients [114] . a recent study reported a rate of 0.9% imaging proven ischaemic stroke among 3556 hospitalized patients [126] , stressing that cerebrovascular events may have been underestimated in intubated and sedated patients with severe covid-19. in a recent study based on data from the global covid-19 stroke registry, it was shown that patients with stroke and concurrent covid-19 infection had a higher risk of severe disability (p < 0.001) and death (odds ratio 4.3, 95% ci 2.22-8.30) compared with patients without covid-19 [127] . severe sars-cov-2 infection is a hypercoagulable state and may predispose to both venous and arterial thromboembolic events. systemic inflammatory response triggers autoimmune mechanisms, leading to dysregulation of the coagulation cascade as reflected by elevated d-dimers, prolonged prothrombin time, high fibrinogen levels, low anti-thrombin levels, thrombocytopenia and diffuse intravascular coagulation in severely ill patients with covid-19 [83, 106, 128] . imbalance between procoagulant and anticoagulant homeostatic mechanisms may result in endothelial damage, microvascular thrombosis and vessel occlusion. in addition, cardiac dysregulation and cardiac arrhythmias/dysrhythmias attributed to excessive inflammation and to respiratory failure, may lead to cardiac strain and myocardial injury/dysfunction facilitating cardioembolism. among covid-19 patients who suffered a stroke, the rate of cryptogenic and embolic strokes was higher, and events were more severe and affected younger patients [126, 129] . finally, blood pressure alterations, hypotension or hypertension, may lead to impaired cerebral perfusion and cerebrovascular events. although not highlighted in the initial cohort studies, olfactory (od) and gustatory (gd) sense dysfunctions have been reported as common symptoms of covid-19 from several centres worldwide. prevalence of smell and taste disturbances varies considerably depending mainly on the assessment criteria and tools used and on the degree of sense dysfunction. in a recent multicentre european study [130] , it was shown that patients with mild-to-moderate forms of covid19 present commonly with od (anosmia or hyposmia) and gd (hypogeusia or ageusia), (86% and 88%, respectively), even without nasal symptoms. women were more likely to be affected, and there was an early olfactory recovery rate of 44%, while symptoms could last even 14 days after the resolution of symptoms. another study reported a high prevalence of od (61%) in covid-19 patients, with an early and severe occurrence and a high correlation with loss of taste. od was still found more prevalent in women, but also in younger patients, while there was an association with shortness of breath [131] . a pilot quantitative study has also shown that a moderate olfactory dysfunction is present in approximately threequarters of hospitalized covid-19 patients using an objective smelling identification test [132] . a multicentre prospective study demonstrated an under-reporting of od and gd manifestations in patients with more severe covid19 disease neglecting their symptomatology. these findings confirm that od and gd are not predictors of a milder disease but are also markedly present in covid19 severe infection [133] . the american academy of otolaryngology-head and neck surgery and the british association of otorhinolaryngology suggested that anosmia-hyposmia and hypogeusia-ageusia should be considered as "significant symptoms" even in the absence of other nasal manifestations (rhinorrhea or nasal congestion), which should be used as potential markers of otherwise asymptomatic carriers of covid-19 infection (i.e. as a screening tool). in particular, the sudden onset of olfactory dysfunction could represent an early indicator of covid-19 infection [134] . these findings make clear that clinicians should take into account self-reporting od and gd symptomatology and incorporate in their assessment, the evaluation of the olfactory nerve function [135] . despite the lack of a clear pathogenetic mechanism explaining od and gd manifestations in covid19 patients, it seems that there is a specific viral neuroinvasivity and neutropism via the olfactory nerves spreading rapidly to other brain structures such as the thalamus and the brainstem, but also possibly to the temporal lobe, the amygdala, insula, limbic lobe (psycho sensorial syndrome) [88] . neurotropism may also occur via circulation and/or an upper transnasal route covid-19 to reach the brain tissue, where covid-19 spike protein binds angiotensin-converting enzyme 2 (ace2) receptors [136] . interestingly, the presence of ace-2, in host olfactory and gustatory pathways, might provide a potential explanatory mechanism for the smell and taste disorders in covid-19 patients. the expression level of ace2 in different tissues and in particular neural cells might be also important in viral neurotropism differences between patients from different geographic regions. thus, the differential ace2 expression could give an explanation of the higher prevalence of od and gd observed in european compared to asian population [114] ; however, more studies are needed to confirm such hypothesis. in the kidney, ace2 is present in several cells such as podocytes, mesangial cells, epithelium of the bowman's capsule, proximal cells brush border and collecting ducts [119] . the most frequent abnormality in patients with covid-19 is mild-to-moderate proteinuria which is mediated via several mechanisms [137] . it has been reported that patients in the icu have higher levels of il-1β, il-8, ifn-γ and tnf-α [40] . this suggests a potential role of cytokine release syndrome (crs), also known as "cytokine storm" comparable with sepsis-associated aki (sa-aki), where the uncontrolled systemic inflammatory response leads to kidney injury [40] . other studies have confirmed tropism to monocytes as well as lymphocytes, where the virus induces proinflammatory responses and cell death [138] . in addition, alterations in renal haemodynamics can induce further dysfunction [139] . acute kidney injury (aki) is infrequent in patients with mildto-moderate disease (5%). in this patient subgroup, the abnormalities are mainly subclinical. a recent prospective study, which included 701 patients with moderate or severe disease, demonstrated that 43.9% presented with proteinuria and 26.7% with haematuria at hospital admission. thirteen percentage revealed elevated levels of either serum creatinine (scr), blood urea nitrogen (bun) or both. aki occurred in 5.1% of hospitalized patients. all these abnormalities conferred for higher death risk [140] . another recent report showed that aki was more common in critically ill patients. in 52 critically ill patients who were admitted to an intensive care unit (icu) in wuhan, aki was the most common extra-pulmonary complication, occurring in 15 patients (29%). eight patients (25%) required continuous renal replacement therapy, and 12 (80%) died with a median duration from admission to icu until death of 7 days [51] . in another study previously described, a in silico analysis of publicly available data sets of single-cell rna sequencing was performed. this analysis showed that rna for angiotensin-converting enzyme 2 (ace2), transmembrane serine protease 2 (tmprss2) and cathepsin l (ctsl) is enriched in several kidney cells. this enrichment may explain the relevant affinity that induces sars-cov-2 kidney injury [3] . following that, tissue microdissection was applied on 6 kidneys biopsied to define sars-cov-2 viral load in exact kidney compartments. three patients revealed detectable sars-cov-2 viral load in all compartments examined, mainly at the glomerular cells. these extremely interesting findings indicate that renal tropism is the obvious reason leading to kidney injury, even in the absence of severe disease. these data indicate that kidney abnormalities are common and are associated with worse clinical outcomes. kidney autopsies of sars-cov patients have also demonstrated that the virus was present in tubular epithelial cells [141] . a number of case reports on skin complications observed in patients with covid-19 have been published. skin abnormalities are seen in up to 20% of covid-19 patients in some series and are very heterogenous ranging from urticarial, vesicular, purpuric to papulosquamous lesions. it is, however, not clear currently whether these skin manifestations are caused directly by the virus invasion or secondary to host immune response or treatment administration. purpuric eruptions, livedo reticularis or retiform purpura could be part of the manifestations of the vasculopathy associated with covid-19 infection [142] . the nature of the association between covid-19 and skin lesions and the systemic implications of their presence remains to be determined and requires active input and effort from dermatologists [143] [144] [145] [146] . knocking down the host's response to cortisol stress is a strategy employed by many viruses, including sars-cov to evade the host immune system. sars-cov expresses key amino acids that act as molecular mimics to the host adrenocorticotropic hormone (acth) directing antibodies to these acth residues implying a relative cortisol insufficiency. data on serum cortisol levels in sars-cov-2 patients are scarce to date. a recent study among patients with no signs of adrenal insufficiency showed that high cortisol levels at presentation may reflect systemic disease severity and have associated with dismal survival among patients with severe covid-19 [101] . autopsy studies from sars-cov viral infection have demonstrated degeneration and necrosis of the adrenal gland, and the virus has been identified in the glands themselves pointing to the likelihood that cortisol dynamics are altered in sars patients. the hypothalamic-pituitary-adrenal (hpa) axis might also be affected by sars viruses on the ground of a reversible hypophysitis or direct hypothalamic damage. ace2 is expressed on both hypothalamic and pituitary tissues explaining a possible viral tropism. a prospective study (chictr20000301150) is currently evaluating serum cortisol and acth levels in covid-19 patients [147] [148] [149] . in animals, coronaviruses have been known to cause ocular manifestations including conjunctivitis, uveitis, retinitis and even optic neuritis [150] . in humans, the eye conjunctiva is considered to be a potential site for sars-cov-2 transmission [151] , but currently there is no direct evidence to support that viral replication can cause injury and inflammation of the conjunctiva or other eye parts. among 38 covid-19 infected patients, in the hubei province case report series, 12 had ocular manifestations (31.6%). these were more common among patients with more severe systemic disease presentation (respiratory mostly) and blood test abnormalities. they included conjunctival congestion, chemosis or epiphora [152] . a recent protocol used optical coherence tomography to evaluate the retina of patients with covid-19 infection in 12 adults. hyper-reflective lesions of the inner plexiform layers and the ganglion cells were seen in all patients, and cotton wool spots and microhemorrhages in the retinal arcade of 4 patients with no effect on visual acuity or pupillary reflexes [153] . increasingly emerging data will allow better understanding of the nature and the mechanisms underlying the ocular manifestations associated with sars-cov-2. covid-19 probably represents the greatest pandemic event in modern human history. the disease presents with a broad spectrum of clinical signs and symptoms with involvement of vital organs such as the lungs, the heart, the gastrointestinal tract, the liver, the central nervous system, the blood and the kidneys. commonly, multisystemic involvement is associated with severe disease and might predict worse clinical outcomes and increased mortality. the main mechanism described is the high binding affinity of the virus with the ace2 receptors that are widely expressed in most human cells. the exact role of ace2 receptors in covid-19 pathophysiology is part of ongoing investigations. furthermore, the role of the infection on dysregulation of ace2 receptors expression, whether treatment with arbs and aces modifies this expression and whether patients with comorbidities and chronic illnesses have higher expression of ace2 receptors and are therefore more vulnerable to infection are also questions that need to be addressed in the near future. the sars-cov-2 virus enters the body through the respiratory tract and infects the epithelial cells of the trachea, bronchi, bronchioles and finally the lungs. it then infects the host, and infiltrating and circulating immune cells transfer the virus to other organs. moreover, the blood-borne sars virus infects other organs as well. immunosuppressed patients, including the elderly and patients with chronic disease, experience more severe disease with increased mortality rates. the extent of immune cell damage, represented by the lymphocyte count, is considered a strong predictor of outcome and reflects the immune status of the patient. this multisystemic disease is 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jurisdictional claims in published maps and institutional affiliations conflict of interest the authors declare no relevant conflict of interest. key: cord-351651-6dbt99h0 authors: sun, zhong; thilakavathy, karuppiah; kumar, s. suresh; he, guozhong; liu, shi v. title: potential factors influencing repeated sars outbreaks in china date: 2020-03-03 journal: int j environ res public health doi: 10.3390/ijerph17051633 sha: doc_id: 351651 cord_uid: 6dbt99h0 within last 17 years two widespread epidemics of severe acute respiratory syndrome (sars) occurred in china, which were caused by related coronaviruses (covs): sars-cov and sars-cov-2. although the origin(s) of these viruses are still unknown and their occurrences in nature are mysterious, some general patterns of their pathogenesis and epidemics are noticeable. both viruses utilize the same receptor—angiotensin-converting enzyme 2 (ace2)—for invading human bodies. both epidemics occurred in cold dry winter seasons celebrated with major holidays, and started in regions where dietary consumption of wildlife is a fashion. thus, if bats were the natural hosts of sars-covs, cold temperature and low humidity in these times might provide conducive environmental conditions for prolonged viral survival in these regions concentrated with bats. the widespread existence of these bat-carried or -released viruses might have an easier time in breaking through human defenses when harsh winter makes human bodies more vulnerable. once succeeding in making some initial human infections, spreading of the disease was made convenient with increased social gathering and holiday travel. these natural and social factors influenced the general progression and trajectory of the sars epidemiology. however, some unique factors might also contribute to the origination of sars in wuhan. these factors are discussed in different scenarios in order to promote more research for achieving final validation. since 2002, two epidemics of severe acute respiratory syndrome (sars) have originated from china, one in late 2002 and the other in late 2019. the etiological agents of these epidemics have been confirmed as a new subset of coronaviruses (covs), namely, sars-cov and sars-cov-2 ( figure 1 ), respectively, for the 2002 and the 2019 sars epidemics [1] . covs are named for their crown-like spikes on the viral surface. they are classified into four main sub-groupings known as alpha, beta, gamma, and delta. before the emergence of sars-cov, four covs were known as human coronaviruses (hcovs), i.e., covs capable of infecting human beings. these four hcovs cause a "common cold" and include hcov-229e and hcov-nl63 of the alpha group and hcov-oc43 and hcov-hku1 of the beta group [2] . since the discovery of sars-cov causing sars in china in 2002 [2] , another hcov was identified in 2012 as mers-cov, causing middle east respiratory syndrome (mers) [3] . figure 1 . phylogenetic analysis of virus isolated from severe acute respiratory syndrome (sars)-2 patients. sequence of wuhan seafood market pneumonia virus isolate wuhan-hu-1 was used for comparing with whole genome sequence database from national center for biotechnology information (ncbi) by using basic local alignment search tool (blast). maff (aist) was used to align the first 100 matching sequences. phylogenetic trees were constructed by using mega x through neighbor-joining (nj) methods. according to the phylogenetic tree, sars-2, bat sars-like coronavirus isolate bat-sars-like coronavirus (sl-cov) zc45, and bat sars-like coronavirus isolate bat-sl-covzxc21 share a common ancestor. sars-cov differs from mers-cov because it uses angiotensin-converting enzyme 2 (ace2) as a receptor for binding to human cells [4] . in contrast, mers-cov uses dipeptidyl peptidase 4 (dpp4) as a receptor for infecting human cells [5] . phylogenetically, sars-cov and mers-cov are distinct and both are distant from other covs, including hcovs. the recent outbreak of "wuhan pneumonia" in late 2019 in central china has been linked with a new cov formally identified as sars-cov-2. sars-cov-2 is not only phylogenetically closely related with sars-cov, an etiological agent of sars, but also uses a same receptor, ace2, as sars-cov does. thus, even though "wuhan pneumonia" has been called with various other disease names such as "new coronavirus pneumonia (ncp)" and now as "coronavirus disease 2019 (covid-19)", we feel that it may be more appropriate to refer to "wuhan pneumonia" as "sars-2" and the previous sars as "sars-1" if necessary. the etiological agent for "wuhan pneumonia" has been changed from "2019-ncov" to "sars-cov-2". a further change of "covid-19" into "sars-2" is logical and reasonable for streamlining taxonomy between disease agent and disease. in this minireview, we evaluate natural and social factors influencing both 2002 and 2019 sarss in order to understand some common epidemiological features that may be beneficial for controlling the ongoing epidemic and also for preventing future outbreak. this comprehensive knowledge is also helpful for searching the origin(s) of the viruses and for elucidating their initial occurrence(s). patients. sequence of wuhan seafood market pneumonia virus isolate wuhan-hu-1 was used for comparing with whole genome sequence database from national center for biotechnology information (ncbi) by using basic local alignment search tool (blast). maff (aist) was used to align the first 100 matching sequences. phylogenetic trees were constructed by using mega x through neighbor-joining (nj) methods. according to the phylogenetic tree, sars-2, bat sars-like coronavirus isolate bat-sars-like coronavirus (sl-cov) zc45, and bat sars-like coronavirus isolate bat-sl-covzxc21 share a common ancestor. sars-cov differs from mers-cov because it uses angiotensin-converting enzyme 2 (ace2) as a receptor for binding to human cells [4] . in contrast, mers-cov uses dipeptidyl peptidase 4 (dpp4) as a receptor for infecting human cells [5] . phylogenetically, sars-cov and mers-cov are distinct and both are distant from other covs, including hcovs. the recent outbreak of "wuhan pneumonia" in late 2019 in central china has been linked with a new cov formally identified as sars-cov-2. sars-cov-2 is not only phylogenetically closely related with sars-cov, an etiological agent of sars, but also uses a same receptor, ace2, as sars-cov does. thus, even though "wuhan pneumonia" has been called with various other disease names such as "new coronavirus pneumonia (ncp)" and now as "coronavirus disease 2019 (covid-19)", we feel that it may be more appropriate to refer to "wuhan pneumonia" as "sars-2" and the previous sars as "sars-1" if necessary. the etiological agent for "wuhan pneumonia" has been changed from "2019-ncov" to "sars-cov-2". a further change of "covid-19" into "sars-2" is logical and reasonable for streamlining taxonomy between disease agent and disease. in this mini-review, we evaluate natural and social factors influencing both 2002 and 2019 sarss in order to understand some common epidemiological features that may be beneficial for controlling the ongoing epidemic and also for preventing future outbreak. this comprehensive knowledge is also helpful for searching the origin(s) of the viruses and for elucidating their initial occurrence(s). it is amazing that, within a short time span of less than 17 years, two similar epidemic outbreaks occurred in china: sars-1 in 2002 and sars-2 in 2019. although identification of viral origin(s) is very critical for understanding these epidemics, a study comparing a wide variety of natural and social factors potentially influencing the progression and the trajectory of these epidemics is also important. through a comparative analysis of environmental factors and human activities in these two serious public health events, we wish to find some common ground for the occurrence of sars-1 and sars-2. sars-1 broke out in foshan, guangdong province, in november 2002 [6] . sars-2 started in wuhan in hubei province no later than early december 2019 [7] . in china, november and december are winter months, and are the coldest months of the year in these two locations [8, 9] . cold temperature usually provides a conducive environmental condition for virus survival. in addition to this, we also noticed that severe drought occurred in both locations at the times of the outbreaks. the annual rainfall in foshan in december 2002 nearly reached 0 mm [10] . in fact, drought occurred in the whole of guangdong province that year, causing more than 1300 reservoirs drying up and 286,000 hectares of farmland suffering drought [11] . coincidentally, wuhan also suffered its worst drought in nearly 40 years, with precipitation of only 5.5 mm in december 2019 [12, 13] . these drought conditions were rare for both locations as their average annual precipitations are greater than 1100 mm [8, 9] , which are higher than the global average annual rainfall of 990 mm, of which 715 mm is over land [14] . cold, dry conditions are more conducive than cold conditions alone for virus survival [15, 16] . during the cold winter, air-dried virus particles are a dangerous form of virus, which survives for a long period of time in airflows [17] . besides providing conducive conditions for virus survival and spreading, winter cold conditions also damper humans' innate immunity. cold temperatures cause reduced blood supply and thus the decreased provision of immune cells to the nasal mucosa. low humidity can reduce the capacity of cilia cells in the airway to remove virus particles and secrete mucus as well as repair airway cells. in addition, human cells release signal proteins after viral infection to alert neighboring cells to consider the danger of virus invasion. however, in low-humidity environments, this innate immune defense system is impaired [18] . more seriously, low humidity can cause nasal mucus to become dry; nasal cavity lining to become fragile, or even ruptured; and make the entire upper respiratory tract vulnerable to virus invasion [19] . the environmental situation of another coronavirus outbreak also seems to support the above-mentioned theory. mers-cov was first detected in a patient living in jeddah, saudi arabia, in june of 2012 [20] . the annual rainfall in jeddah is low at 61mm, and there was no rain at all in june of that year in jeddah [21] . therefore, relative to temperature, low humidity seems to be a more critical environmental factor influencing outbreak of human coronavirus disease. for both sars outbreaks, bat was suspected as a natural host for sars-covs. it was claimed that sars-cov virus originated from horseshoe bats in a cave of yunnan province [22] . in 2005, sars-like covs (sl-covs) were found in wild chinese horseshoe bats (rhinolophus sinicus) collected from a cave in yunnan province of china [22] . in 2013, live sl-cov was isolated from vero e6 cells incubated in bat feces [23] . the isolated virus showed more than 95% genome sequence identity with human and civet sars-covs. sl-cov possesses the ability to infiltrate cells using its s protein to combine with ace2 receptors [24] . this observation indicated that sars-cov originated from chinese horseshoe bats and that sl-cov isolated from bats poses a potential threat to humans without the involvement of any intermediate hosts. between 2015 and 2017, 334 bats were collected from zhoushan city, zhejiang province, china. a total of 26.65% of those bats were detected as having a conserved coronaviral protein rna-dependent rna polymerase (rdrp). full genomic analyses of two sl-covs (bat-sl-cov zc45 and bat-sl-cov zxc21) showed 81% nucleotide identity with human/civet sars covs. these viruses reproduced and caused disease in suckling rats, with virus-like particles being observed in the brains of suckling rats by electron microscopy [25] . thus, prior to 2018, bats collected in some areas of china have been shown to carry covs capable of directly infecting humans. a recent study showed that sars-cov-2 has 96% homology at the whole genome level with bat coronavirus. pairwise protein sequence analysis of seven conserved non-structural proteins showed that this virus belongs to the species of sars-cov [26] . in phylogenetic analysis, sars-cov and sars-cov-2 not only share a common ancestor, but also have an amino acid identity of 82.3% [27] [28] [29] . viruses often require intermediate hosts before transmitting from bats to humans. for example, the intermediate host of nipah virus is pig, and the intermediate host of mers-cov is camel [30, 31] . during sars-1 outbreak, civet was initially considered as a natural host for sars-cov [31] . later it was redefined as an intermediate host after bats were claimed as the natural hosts for sars-cov. in addition to civet, researchers also found sars-cov from domestic cat, red fox, lesser rice field rat, goose, chinese ferret-badger, and wild boar in guangdong's seafood market. it was believed that the virus was transmitted to civet from yunnan horseshoe bats, and civet cats carrying the virus were transported to guangdong, which led to sars-cov infection on humans and sars outbreak in guangdong [32] . currently, some intermediate hosts have been suspected for sars-cov-2. a study showed that sars-cov-2 has the same codon usage bias as shown for snakes. therefore, snake may be the intermediate host for sars-cov-2 [33] . however, david robertson, a virologist from the university of glasgow, united kingdom, stated, "nothing supports the invasion of snakes." at the same time, paulo eduardo brandão, a virologist from the university of st. paul, also said, "there is no evidence that snakes can be infected by this new coronavirus and act as hosts" [34] . a study on the genome sequence of diseased pangolins smuggled from malaysia to china found that pangolins carry coronavirus, suggesting that pangolins may be intermediate hosts for sars-cov-2 [35] . pangolins seized in anti-smuggling operations in guangxi and guangdong of southern china were detected with multiple cov linages with 85.5-92.4% genome sequence similarity to those of sars-cov-2 [36] . more interestingly, covs collected from caged pangolin obtained from an unspecified research organization showed over 99% genome sequence identity to those of sars-cov-2 [37] . meanwhile, nanshan zhong, the leader of the sars-cov-2 virus treatment expert group, predicted the intermediate host of sars-cov-2 to be bamboo rat [38] on the basis of the animal distribution in zhoushan, which is not only the natural habitat of bat-sl-covzc45-carrying bats, but also the natural habitat of cobra, bamboo rat, and pangolin [39] [40] [41] . before viruses in wildlife make a jump to infect human beings, they usually accumulate a series of mutations in their viral genomes [42] and invade human beings as a result of human occupation of their normal ecosystem, as exemplified with a story of initial human infection by hiv carried by chimpanzees in rainforests of west africa [43, 44] . at the outset, sars-covs might have a species barrier before it can be transmitted to humans. however, due to human activities, the virus has expanded its host of infection. it was found that the sars-cov responsible for sars-1 in 2002 existed in civet [32] . viruses phylogenetically similar to sars-cov-2 in genome sequence have now being detected in wild bats [26] , snakes [33] , and pangolins [35] [36] [37] 45] . thus, humans might become unfortunate hosts for sars-covs as a result of some inappropriate interactions with wildlife and thus exposure to unfriendly viruses ( figure 2 having identified some relevant natural and social factors common for affecting both sars epidemics, it is also necessary to discuss if variations in these factors contributed to the unique outbreak of sars-2 in wuhan. because many factors confounding the sars-2 epidemic are still unknown, we herein discuss sars-2 outbreak in wuhan (figure 3 ) under different scenarios. having identified some relevant natural and social factors common for affecting both sars epidemics, it is also necessary to discuss if variations in these factors contributed to the unique outbreak of sars-2 in wuhan. because many factors confounding the sars-2 epidemic are still unknown, we herein discuss sars-2 outbreak in wuhan (figure 3 ) under different scenarios. an early guess and also a dominant view expressed in published reports assumes that sars-2 outbreak started from a single site in wuhan, namely, huanan seafood market [46] . however, the only source of bats that have been publicly identified as carrying virus phylogenetically close to sars-cov-2 is far away from wuhan in zhoushan, zhejiang. zhoushan is also one of the largest breeding bases in zhejiang for bamboo rat, which is suspected as one of the intermediate hosts for sars-cov [38, 47] . thus, in order for these bats and/or rats to pass the virus to humans, they must have first been able to migrate or be moved to wuhan and also must have carried viruses that actually achieved mutations for affording the capability of infecting human beings. bats have an ability to migrate more than 1000 kilometers and tend to fly to insect-rich areas [48] . abundant insects are often found in wildlife market areas due to their selling of various animals. animal carcasses also make these places suitable habitats for bats. bats are also attracted to artificial green lights and tend to gather around green light areas [49] . in agreement with these natural characteristics, bats have been found to inhabit locations near yangtze river bridge, which has rows of green lights that are tuned on for all of the night-time. incidentally, huanan seafood market is only 20 minutes away from this bridge. bats gathered near the yangtze river bridge might have released the virus and even infected intermediate hosts for some time. the cold and dry winter helped viruses to survive in the environment and eventually found some ways to cross the species barrier, a phenomenon known as "viral chatter" [50] . the increased vulnerability of human beings in winter time and the increased human exposure to wild animals during holidays made infection to sars-cov-2 more likely. at present, there is no evidence to prove the source of bamboo rats in huanan seafood market. therefore, there are two possible places for bamboo rat be infected with sars-cov-2. the first site might be the bat habitat in zhoushan. due to the promotion of bamboo rat breeding by huanong brothers in 2018, the amount of bamboo rat breeding and market demand increased significantly [51] . since the market demand increases, the new bamboo rat breeding base may not be far from the local habitat of sars-cov-2-carrying bats. the model of sars-cov-2 transmission, similar to nipah virus, is that farms are built around bat habitats, causing bats to pass the virus to animals through saliva, urine, and feces [30] . at the same time, because zhejiang is a natural habitat for bamboo rats, it is possible that some farms directly introduced wild bamboo rats, which were already infected with sars-cov-2 virus. for the above reasons, the bamboo rats carrying sars-cov-2 virus were transported from the infected place to the incident site in the same way that civets spread sars-cov [32] . the second site is wuhan, the place of the sars-cov-2 outbreak, and it is also the end point for some bat migration. zhengli shi's team from wuhan institute of virology, chinese academy of sciences, isolated a live sars-like strain in the feces of horseshoe bats [23] . this suggests that the way the bats spread the virus is not only via direct contact, but also through feces. therefore, when bats carrying sars-cov-2 virus forage at huanan seafood market, they may pass the virus directly or indirectly to intermediate hosts. however, to confirm this scenario, it is necessary to find wild bats in wuhan and its neighboring areas that carry covs identical to those isolated from various sars-2 patients. it is also necessary to find a mechanism for the very quick outbreak in such a wide area by a natural source of sars-cov-2. epidemiological investigations showed that 13 of the first 41 patients diagnosed with sars-cov-2 had nothing to do with huanan seafood market [45] . another survey of sars-2 found that no bats were on sale in huanan seafood market [52] . with so many bats concentrated into a local area, the spreading of viruses by bats might be much wider than just being restricted to one wildlife trading place such as the huanan seafood market. the viruses might have lived in this big "incubation bed" for some time and achieved some mutations before jumping on to the final hosts-human beings. a study on horseshoe bats in hong kong and guangdong showed that the viruses carried by horseshoe bats in these two places are different. however, some horseshoe bats were found to carry two viruses after mating and foraging activity. this indicates that horseshoe bats not only have the ability to migrate, but also the ability to promote the spread of virus within the same roost and from roost to roost. in addition, sequencing the entire genome of virus carried by bats in multiple regions revealed frequent recombination among different strains. for example, civet sarsr-cov sz3 recombination was detected between sarsr-rh-batcov rp3 from guangxi, china, and rf1 from hubei, china [53] . therefore, there is a possibility that sars-cov-2 spread from zhoushan to wuhan due to bat migration. it turned out that bats are not only attracted by green lights but also red lights [54] . along the yangtze river there are also huge bridges decorated with a massive number of red lights. thus, bats migrating along the yangtze river might be attracted by these red lights and be relocated nearby. wuhan might be a new habitation site for a massive number of bats. these bats, coming from different locations, might carry different virus strains. the separate evolution and the recombination of these viruses might lead to the creation of various sars-covs capable of cross-species transmission and ultimate infection of human beings. many observations have shown the outbreak of sars-2 actually started from multiple sites, instead of just a single site, as originally reported [27, 52, 53, 55] . in evaluating the epidemiological patterns of sars-2 within wuhan, surrounding wuhan, and remote from wuhan, it appears that the incidences of sars-2 have some distinct patterns. although the remotely occurring sars-2 usually have a human-human linkage and can be traced to a single source of infection, some wuhan cases and the surrounding cases in hubei province still lack reliable sources of infection. amazingly, most of the sars-2 patients can be traced to a single unique etiological agent, sars-cov-2. how could this likely single source of virus quickly infect so many people in such large geographic area? this is a question that is difficult to answer now, but must be answered in future. although the origins and the occurrences of sars-cov-2 are both unclear, the control measures for the current epidemic should focus on immediate cut-off of transmission of the disease and through disinfection of infected locations. quarantine of patients (both confirmed and suspected), isolation of susceptible population, and protection of high-risk professions are necessary measures for reducing exposure to the viruses and eliminating the risk of getting infected by the viruses. at the same time, infected locations must be adequately disinfected. areas that will be open to the public should be carefully surveilled for the existence of sars-cov-2 and be cleaned of the virus if it is found. modern communication methods should be effectively used for passing reliable information on the epidemic status, the treatment measures, and the self-protection skills, among others. as a matter of fact, if fine-tuned and highly-effective internet control for "public opinions" can be turned into beneficial use of monitoring the "epidemic situation", fighting against an even larger outbreak of any infection would be much easier and cost-effective. sars-cov-2 has entered human communities, and eliminating virus from human bodies does not means its eradication in nature. the risk of sars-cov-2 infection will remain for a long time. thus, adequate cautions must be taken for safe-guarding against future outbreaks of sars. the prevention can be achieved by implementing a multi-facet system that considers both natural and social aspects of the sars epidemiology discussed earlier. for example, regular surveillance of viral status in nature should be carried out to monitor the variation/evolution and abundance/localization of the virus. this information may be served as an early warning and used for preparation of potential vaccines. the government should issue laws and policies to tighten protection of wildlife and prohibit consumption of wild animals. a grass-roots and transparent reporting system should be established and put into public use for reporting any case of confirmed or suspected human infection. the disease-reporting system should be organically synchronized with the meteorological system so that adverse environmental conditions conducive for viral infection on human beings can be forecasted and macro-scale preparations can be made in case an emergency occurs. finally, but not lastly, in developing human society including building massive constructions for residence and transportation, potential ecological impact on wildlife and possible consequences of breaking natural balance of the ecosystems should be carefully evaluated. this mini-review evaluated the common epidemiological patterns of both sars epidemics in china and identified cold, dry winter as a common environmental condition conducive for sars virus infection to human beings. thus, meteorological information should be integrated into future forecast of potential outbreak of new sars. the identification of bats as very likely natural hosts for sars-covs and consideration of some other wild animals as potential intermediate hosts leads to a prevention requirement of protecting natural ecosystem and prohibiting consumption of wildlife. the presentation of different scenarios of sars outbreaks points to some urgency in identifying the true origin(s) of sars-covs and establishing more comprehensive anti-infection measures that will resist any kind of viral assault. author contributions: all authors have made a contribution to this manuscript. z.s. designed, drafted, and edited the initial manuscript. k.t. reviewed and edited the initial manuscript. s.s.k. edited the initial manuscript. g.h. conceptualized and designed the framework of the manuscript. s.v.l. wrote the revision of the manuscript and brought many of his independently originated ideas into the revised manuscript. all authors have read and agreed to the published version of the manuscript. funding: this work is supported in part by the national natural science foundation of china under grant no. 71964020. the proximal origin of sars-cov-2. artic network an overview of their replication and pathogenesis angiotensin-converting enzyme 2 is a functional receptor for the sars coronavirus host species restriction of middle east respiratory syndrome coronavirus through its receptor, dipeptidyl peptidase 4 epidemiologic clues to sars origin in china outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle nbsc. national bureau of statistics prc: china statistical yearbook characteristics and influences of precipitation tendency in foshan under environmental varia heavy drought in the middle and lower reaches of yangtze river the average rainfall in wuhan in december was 26 millimeters, and there were only scattered light rain on the 3rd. wuhan weather news gpcc's new land surface precipitation climatology based on quality-controlled in situ data and its role in quantifying the global water cycle effects of air temperature and relative humidity on coronavirus survival on surfaces the effects of temperature and relative humidity on the viability of the sars coronavirus decline in temperature and humidity increases the occurrence of influenza in cold climate low ambient humidity impairs barrier function and innate resistance against influenza infection isolation of a novel coronavirus from a man with pneumonia in saudi arabia monthly weather forecast and climate jeddah, saudi arabia discovery of a rich gene pool of bat sars-related coronaviruses provides new insights into the origin of sars coronavirus isolation and characterization of a bat sars-like coronavirus that uses the ace2 receptor isolation and characterization of a novel bat coronavirus closely related to the direct progenitor of severe acute respiratory syndrome coronavirus genomic characterization and infectivity of a novel sars-like coronavirus in chinese bats discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding a new coronavirus associated with human respiratory disease in china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster nipah virus infection: current scenario host determinants of mers-cov transmission and pathogenesis tracing the sars-coronavirus homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human why snakes probably aren't spreading the new china virus viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (manis javanica). viruses sequence similarity between pangolin and infected human strain is 99%. sohu. available online the new coronavirus is likely to come from game products such as bamboo rats and tadpoles. netease news analysis of the mammal diversity and fauna in zhejiang province mammalian fauna and distribution of putuoshan island in zhoushan adaptive evolution of mers-cov to species variation in dpp4 vanishing borders: protecting the planet in the age of globalization origins of hiv and the aids pandemic. cold spring harb clinical features of patients infected with 2019 novel coronavirus in a novel coronavirus genome identified in a cluster of pneumonia cases-wuhan the largest bamboo rat chinese silver star bamboo rat breeding base in zhoushan. shanghang.net determinants of spring migration departure decision in a bat migratory bats respond to artificial green light with positive phototaxis mapping disease transmission risk of nipah virus in south and southeast asia adventures of huanong brothers: shooting bamboo rat videos became popular, fans exceeded 5 million and annual income exceeded 300,000. tencent us from coronavirus: live updates on covid-19. live science ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related rhinolophus bat coronavirus in china reveal bats as a reservoir for acute, self-limiting infection that allows recombination events migratory bats are attracted by red light but not by warm-white light: implications for the protection of nocturnal migrants evolution and variation of 2019-novel coronavirus acknowledgments: thanks to the alumni of tongji medical college, huazhong university of science and technology for their selfless help and miss tao's suggestions for manuscript. the authors declare no conflict of interest. key: cord-277430-x02u7oh0 authors: zhang, hongyan; wang, linwei; chen, yuanyuan; wu, qiuji; chen, gaili; shen, xiaokun; wang, qun; yan, youqin; yu, yi; zhong, yahua; wang, xinghuan; chua, melvin l. k.; xie, conghua title: outcomes of novel coronavirus disease 2019 (covid‐19) infection in 107 patients with cancer from wuhan, china date: 2020-06-23 journal: cancer doi: 10.1002/cncr.33042 sha: doc_id: 277430 cord_uid: x02u7oh0 background: patients with cancer have a higher risk of coronavirus disease 2019 (covid‐19) than noncancer patients. the authors conducted a multicenter retrospective study to investigate the clinical manifestations and outcomes of patients with cancer who are diagnosed with covid‐19. methods: the authors reviewed the medical records of hospitalized patients who were treated at 5 hospitals in wuhan city, china, between january 5 and march 18, 2020. clinical parameters relating to cancer history (type and treatment) and covid‐19 were collected. the primary outcome was overall survival (os). secondary analyses were the association between clinical factors and severe covid‐19 and os. results: a total of 107 patients with cancer were diagnosed with covid‐19, with a median age of 66 years (range, 37‐98 years). lung (21 patients; 19.6%), gastrointestinal (20 patients; 18.7%), and genitourinary (20 patients; 18.7%) cancers were the most common cancer diagnoses. a total of 37 patients (34.6%) were receiving active anticancer treatment when diagnosed with covid‐19, whereas 70 patients (65.4%) were on follow‐up. overall, 52.3% of patients (56 patients) developed severe covid‐19; this rate was found to be higher among patients receiving anticancer treatment than those on follow‐up (64.9% vs 45.7%), which corresponded to an inferior os in the former subgroup of patients (hazard ratio, 3.365; 95% ci, 1.455‐7.782 [p = .005]). the detrimental effect of anticancer treatment on os was found to be independent of exposure to systemic therapy (case fatality rate of 33.3% [systemic therapy] vs 43.8% [nonsystemic therapy]). conclusions: the results of the current study demonstrated that >50.0% of infected patients with cancer are susceptible to severe covid‐19. this risk is aggravated by simultaneous anticancer treatment and portends for a worse survival, despite treatment for covid‐19. there is an unprecedented outbreak of the novel coronavirus disease 2019 (covid19) worldwide, which is caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2). [1] [2] [3] [4] this illness is characterized by fever, dyspnea, cough, and gastrointestinal symptoms of diarrhea, nausea, and vomiting. 5 as of april 22, 2020, the latest numbers indicated that there were >2,000,000 covid-19 cases worldwide, and >100,000 deaths had occurred. 6 we previously have shown that patients with cancer have a higher risk of contracting covid-19. 7 compared with the community, the estimated incidence of covid-19 is approximately 2.3-fold higher in this susceptible group of patients, and the risk is attributable to both active anticancer treatment and recurrent visits to the hospital without appropriate infection control measures in place. in addition, in our small case series, we observed that the median age cancer month 0, 2020 of infected patients with cancer was older (>60 years) compared within the community, and these patients had a tendency to develop more severe illness. it also was suggested that among the different cancer types, patients with lung cancer who are aged >60 years are particularly at risk of covid-19. 7 although it may appear to be intuitive that patients with an abnormal respiratory epithelium are likely to be more prone to rapid virus entry into the lungs, more data are needed to clarify some of these associations. currently, several guidelines regarding the management of patients with cancer also have been proposed, but arguably, these are mostly consensus agreements, with little guidance derived from data regarding the outcomes of patients with cancer who are diagnosed with covid-19. [8] [9] [10] [11] examples of some pertinent questions include possible differences in the severity of covid-19 between patients with different cancer types and the implications of active anticancer treatment on the clinical presentation, severity, and treatment outcomes of covid-19 pneumonia. to fill these gaps in knowledge, we conducted a multicenter retrospective study regarding the outcomes of patients with cancer who were diagnosed with covid19 . the primary aim of the current study was overall survival (os). secondary analyses included the reporting of clinical presentation and outcomes based on the different cancer types, and the association between mortality due to covid-19 and whether the patient was receiving ongoing active anticancer treatment (systemic therapy, local therapy, or a combination). the current study was a multicenter, retrospective, observational study of 5 hospitals (zhongnan hospital of wuhan university, leishenshan hospital, the fifth hospital of wuhan, the seventh hospital of wuhan, and wuhan hankou hospital) in wuhan city, china. we reviewed the medical records of 3559 hospitalized patients with covid-19 who were treated at these institutions from january 5 to march 18, 2020. it is interesting to note that wuhan leishenshan hospital was 1 of 2 emergency makeshift hospitals that were constructed in the city to isolate and treat patients with covid-19 during the peak of the outbreak. inclusion criteria included: 1) confirmation of a diagnosis of covid-19 based on the fifth edition criteria (see supporting information a 5 ); 2) a prior confirmed histological and/or clinical diagnosis of cancer; and 3) available information regarding current and prior cancer treatments. there were no exclusion criteria. th current study was approved by the ethics committee of the zhongnan hospital of wuhan university (no. 2020041). because anonymized, aggregated data were analyzed, a waiver of informed consent was approved by the institutional review board. the diagnosis of covid-19 was made based on the fifth edition criteria, which were developed in response to the outbreak by the national health commission of china during the study period (supporting information a, section supplementary methods). briefly, a diagnosis of covid-19 could be made if patients had a positive real-time reverse transcriptase-polymerase chain reaction (rt-pcr) test for sars-cov-2 and/or demonstrated characteristic findings of atypical pneumonia on computed tomography scan of the chest. 12, 13 typical computed tomography chest findings included bilateral pulmonary parenchymal ground-glass and consolidative pulmonary opacities that were distributed in the peripheral zones of the lungs. 5, 14 we further categorized patients into those with mild and those with severe covid-19. patients were diagnosed as having severe covid-19 if they manifested any of the following clinical conditions: 1) tachypnea of ≥30 respiratory rate per minute; 2) oxygen saturation of ≤93% at room air; 3) arterial partial pressure of oxygen (pao2) per fraction of inspired oxygen (fio2) of ≤300 mm hg; 4) respiratory failure requiring mechanical ventilation; 5) septic shock; and 6) multiorgan failure requiring care in the intensive care unit. 15 all samples were processed at designated laboratories in compliance with the world health organization guidance. all samples were tested for sars-cov-2 by quantitative rt-pcr using the kit recommended by the centers for disease control and prevention. we adhered to the strobe (strengthening the reporting of observational studies in epidemiology) standards of reporting for the current cohort study. frequencies and percentages were reported for categorical variables, whereas means (with standard deviations) and medians (with interquartile ranges [iqrs]) were used to describe quantitative data. the primary outcome was os, which was defined as the time from the onset of symptoms to death from any cause. secondary analyses included the percentage of patients with severe covid-19 and the association between cancer month 0, 2020 clinical (cancer type, patient age, and comorbidities) and treatment parameters (status of anticancer treatment) and severe covid-19 and os. survival curves were illustrated using the kaplan-meier method and compared using the log-rank test. hazard ratios (hrs) with 95% confidence intervals (95% cis) were calculated using the cox proportional hazards model, and the proportional hazards assumption was tested with schoenfeld residuals. os was updated as of april 17, 2020. detailed information regarding demographics, smoking history (former vs current smokers), comorbidities (hypertension, diabetes, and cardiorespiratory conditions), signs and symptoms at onset, laboratory results (complete blood count, renal and liver panels, and inflammatory markers), and covid-19 treatment were collected. patients also were classified based on whether they were receiving active anticancer treatment (including surgery, radiotherapy, chemotherapy, immunotherapy, targeted therapy, endocrine therapy, and best supportive treatment) or were taking part in posttreatment follow-up (defined as >1 month from the completion of treatment) at the time of diagnosis with covid-19. all statistical analyses were performed using spss statistical software (version 23.0; ibm corporation, armonk, new york). a 2-sided p value <.05 was considered to be statistically significant. no correction for multiple testing was performed. of 3559 patients, 107 patients were diagnosed with covid-19 and had a diagnosis of cancer (supporting information b); the breakdown of cases across the 5 institutions is summarized in supporting table 1 in supporting information a. the clinical characteristics of these patients were summarized in table 1 . the median age of the patients was 66 years (range, 36-98 years). approximately 56.1% of the patients (60 patients) were male and 43.9% (47 patients) were female. a total of 72 patients (67.3%) had a history of comorbidities, which included hypertension (52 patients; 48.6%), diabetes (22 patients; 20.6%), cardiac conditions (14 patients; 13.1%), and chronic obstructive pulmonary disease (5 patients; 4.7%); 9 patients had a positive smoking history. lung cancer was the most common diagnosis (21 patients; 19.6%), followed by gastrointestinal (20 patients; 18.7%), genitourinary (20 patients; 18.7%), and head and neck (17 patients; 15.9%) cancers (table 1) . a total of 84 patients (78.5%) had early-stage cancers (stages i-iii, based on the eighth edition of cancer staging manual by american joint committee on cancer), and 23 patients (21.5%) had stage iv disease. of these, only 37 patients (34.6%) were receiving active anticancer treatment at the time of their covid-19 diagnosis. five patients had received or were continuing to receive local treatment (surgery and/or radiotherapy), and 21 patients were receiving systemic therapy either as monotherapy or in combination with local treatment. a total of 11 patients were receiving best supportive treatment alone (table 1 ). only 4 of 37 patients continued with their anticancer treatment (table 2) . table 3 shows the baseline hematological and biochemical parameters of the current study cohort. lymphocytopenia (55 patients; 51.4%), elevated c-reactive protein (62 patients; 57.9%), and procalcitonin (n = 52 patients; 48.6%) were the most common abnormalities among our patients with cancer. next, we observed that patients receiving active anticancer treatment experienced more pronounced lymphopenia (median, 0.55×10 9 /l [iqr, 0.29-1.12×10 9 /l] vs 1. covid-19 treatments that were administered are summarized in table 2 in terms of the frequencies of severe covid-19 complications in the current study cohort, 21 patients (19.6%) developed acute respiratory distress syndrome, 13 patients (12.1%) developed heart failure, and 3 patients (2.8%) developed acute renal injury ( table 2) . as of the time of last follow-up on april 17, 2020, we recorded 23 (21.5%) covid-19-related deaths, whereas 84 patients (78.5%) had been discharged. the case fatality rates for the overall study cohort, patients who were receiving active anticancer treatment, and those on follow-up were 21.5% (23 of 107 patients), 37.8% (14 of 37 patients), and 12.9% (9 of 70 patients), respectively. we observed that patients receiving active (fig. 1a) . the disparity in os also was observed between the 2 groups when patients receiving only best supportive treatment were excluded (hr, 3.117; 95% ci, 1.236-7.859 [p = .016]) (fig. 1b) . the median duration from the onset of symptoms to recovery and death was 31 days (range, 8-53 days) and 20 days (range, 6-45 days), respectively. we further investigated potential associations between clinical and treatment parameters and the likelihood of severe covid-19 and death. we observed that patients with gastrointestinal cancers were most likely to experience severe illness ( fig. 2a) , and this corresponded to 35% of deaths (7 of 20 patients) for this cancer type (fig. 2b) table 3 in supporting information a). this is a crucial observation, especially when the oncology community remains uncertain regarding the implications of initiating or continuing anticancer treatment for patients with cancer who are diagnosed with covid-19 during this pandemic, given the scarcity of evidence. prior to this study, a smaller case series by zhang et al among 28 patients with cancer also demonstrated an interaction between recent exposure to anticancer treatment within 14 days of a covid-19 diagnosis and severity of the illness. 17 taken together, the current study data support the belief that anticancer treatment should be best avoided, if possible, in patients with cancer who unfortunately contract sars-cov-2 infection. in addition, for asymptomatic or noninfected individuals who are undergoing anticancer treatment, the results from the current study strengthen the argument for tight infection control measures to prevent virus transmission to patients within the hospital or ambulatory treatment facility. cancer month 0, 2020 we made several interesting observations in the current study cohort. foremost, we previously had reported a preliminary observation demonstrating that older patients (ie, those aged >60 years) who are diagnosed with lung cancer are at a higher risk of covid-19. 7 in this larger study, we again observed that patients with lung cancer constituted a high percentage of covid-19 cases (19.6%) among patients with different cancer types, although the percentages were comparable to those of patients with gastrointestinal, genitourinary, and head and neck cancers. although these patients may be at risk of contracting covid-19, we did not observe that they necessarily had a higher incidence of severe illness compared with patients without lung cancer ( fig. 2a) , which would suggest that synchronous or metachronous lung cancers do not influence the pathogenetic mechanisms underpinning severe covid-19. 18, 19 next, although patients with cancer were likely to experience severe covid-19, their clinical presentation and laboratory parameters were comparable to the trends that were reported in the general community. 5, 16 rather, in the current study cohort of 107 patients, we observed that active anticancer treatment within 1 month of a diagnosis of covid-19 was associated with profound lymphopenia (median of 0.55 vs 1.05 for those on follow-up) and markedly elevated inflammatory markers of c-reactive protein (36.00 vs 27.40) and procalcitonin (0.17 vs 0.06). among the constellation of covid-19 symptoms, myalgia and dyspnea were more frequent among patients receiving anticancer treatment compared with those who were on surveillance. it is interesting to note that we found that fewer of these patients in the former subgroup of patients received covid-19 therapies; approximately 21.6% received steroid therapy and 13.5% received ivig compared with 44.3% and 24.3%, respectively, in the latter patient subgroup. although we could not determine the potential reasons underpinning such a trend, it must be rationalized that the efficacy of these therapies in the treatment of patients with covid-19 remains questionable. thus, we judged that this observation may not have biased the association between cancer treatment status and os. we next explored the interactions between the different types of anticancer therapies and the likelihood of death from covid-19 in the current study cohort. it is interesting to note that we observed that patients who were receiving systemic therapy (including chemotherapy, targeted therapy, immunotherapy, and endocrine therapy) were not more susceptible to severe illness and death than those who received local therapy or best supportive treatment (fig. 2c,d) . in addition, we questioned whether anticancer agents such as immune checkpoint blockade inhibitors potentially could worsen the trajectory of covid-19 pneumonia. 20, 21 nonetheless, we did not observe any disparate effects on the severity and case fatality rate between patients receiving conventional systemic agents and immunotherapy (see supporting table 2 in supporting information a), although the current analysis was limited by the smaller numbers in each treatment cancer month 0, 2020 group. on this note, larger cohort studies with the aggregation of multiple data sets will help to provide more granular insights in this regard, as well as examine the interactions of all the potential clinical confounders such as comorbidities, cancer types, and their specific treatments, and covid-19 treatment on the outcomes of patients with cancer. the results of the current study demonstrated the clinical characteristics and outcomes of covid-19 in a large cohort of 107 patients with different cancer types, and suggested a high incidence of severe illness and case fatality rates compared with the community population. these adverse outcomes were observed among patients cancer month 0, 2020 who either were receiving anticancer treatment or were on surveillance, but the risk of death was significantly worse in the former patient subgroup. based on this and other studies, it therefore is imperative to consider the deferment of anticancer treatment, if possible, in patients with cancer who unfortunately are diagnosed with covid-19. in the same vein, we reiterate that tight infection control measures are crucial to prevent the risk of virus transmission to patients who are receiving ongoing anticancer treatment. the funders had no role in the design and conduct of the study; the collection, management, analysis, and interpretation of the data; the preparation, review, or approval of the article; and the decision to submit the article for publication. a novel coronavirus from patients with pneumonia in china clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) 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(covid-19) pandemic: an international collaborative group clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records information for laboratories about coronavirus (covid-19) ct imaging features of 2019 novel coronavirus (2019-ncov) the central people's government of the people's republic of china china medical treatment expert group for covid-19. comorbidity and its impact on 1590 patients with covid-19 in china: a nationwide analysis clinical characteristics of covid-19-infected cancer patients: a retrospective case study in three hospitals within wuhan, china. ann oncol the pathogenesis and treatment of the 'cytokine storm' in covid-19 clinical features of patients infected with 2019 novel coronavirus in wuhan do checkpoint inhibitors compromise the cancer patients' immunity and increase the vulnerability to covid-19 infection? controversies about covid-19 and anticancer treatment with immune checkpoint inhibitors the data regarding the baseline patient information, survival outcomes, and detailed treatment information will be deposited in the research data deposit public platform (www.resea rchda ta.org.cn). the other data supporting the findings of the current study are available within the article and its supporting information files and from the corresponding authors upon request. key: cord-328787-r0i3zo6t authors: xue, ling; jing, shuanglin; miller, joel c.; sun, wei; li, huafeng; estrada-franco, josé guillermo; hyman, james m.; zhu, huaiping title: a data-driven network model for the emerging covid-19 epidemics in wuhan, toronto and italy date: 2020-06-01 journal: math biosci doi: 10.1016/j.mbs.2020.108391 sha: doc_id: 328787 cord_uid: r0i3zo6t the ongoing coronavirus disease 2019 (covid-19) pandemic threatens the health of humans and causes great economic losses. predictive modelling and forecasting the epidemic trends are essential for developing countermeasures to mitigate this pandemic. we develop a network model, where each node represents an individual and the edges represent contacts between individuals where the infection can spread. the individuals are classified based on the number of contacts they have each day (their node degrees) and their infection status. the transmission network model was respectively fitted to the reported data for the covid-19 epidemic in wuhan (china), toronto (canada), and the italian republic using a markov chain monte carlo (mcmc) optimization algorithm. our model fits all three regions well with narrow confidence intervals and could be adapted to simulate other megacities or regions. the model projections on the role of containment strategies can help inform public health authorities to plan control measures. the ongoing coronavirus disease 2019 (covid-19) pandemic threatens the health of humans and causes great economic losses. predictive modelling and forecasting the epidemic trends are essential for developing countermeasures to mitigate this pandemic. we develop a network model, where each node represents an individual and the edges represent contacts between individuals where the infection can spread. the individuals are classified based on the number of contacts they have each day (their node degrees) and their infection status. the transmission network model was respectively fitted to the reported data for the covid-19 epidemic in wuhan (china), toronto (canada), and the italian republic using a markov chain monte carlo (m-cmc) optimization algorithm. our model fits all three regions well with narrow confidence intervals and could be adapted to simulate other megacities or regions. the model projections on the role of containment strategies can help inform public health authorities to plan control measures. the development of international trade and tourism has accelerated the spatial spread of infectious diseases. the limited data available on emerging epidemics adds to the challenge of mitigating the spread of emerging infections [1] . the unprecedented coronavirus disease 2019 outbreak began at the end of 2019. the number of reported cases keeps rising worldwide and thousands of lives have been claimed. this pandemic is having an enormous impact on world health, disturbing the stability of the societies, and triggers great economic losses. predicting the future of the pandemic, assessing the impacts of current interventions, and evaluating the effectiveness of alternate mitigation strategies are of utmost importance for saving lives. mathematical models can be used to understand the dynamics of epidemics and help inform control strategies. a numerous number of models are being used to project the current covid-19 pandemic. ziff and ziff analyzed the number of reported cases for wuhan (china) and showed that the growth of the daily number of confirmed new cases indicates an underlying fractal or small-world network of connections between susceptible and infected individuals [2]. wang et al. developed an seir model to estimate the epidemic trends in wuhan, assuming the prevention and control measures were either sufficient or insufficient to control the epidemic [3] . kucharski et al. combined a stochastic transmission model with data on cases of covid-19 in wuhan and international cases to estimate how the transmission had varied over time between january and february in 2020 [4] . kraemer et al. analyzed the impact of interventions on the spread of covid-19 in china using transportation data [5] . chinazzi et al. used a global meta-population disease transmission model to project the impact of travel limitations on the national and international spread of the epidemic. they showed that the travel restriction of wuhan, china had a more marked effect on the international scale than that on mainland china [6] . ferguson et al. found that optimal mitigation policies (combining home isolation of suspected cases, home quarantine of those living in the same household as suspected cases, and social distancing of the elderly and others in the greater toronto area (gta, canada) and the italian republic are continuing to grow. we fit the parameters of our network model to the confirmed cases in each of these regions. although wuhan, toronto, and italy differ in some ways, the way that sars-cov-2 is transmitted from one person to another is quite similar. individuals may acquire infection from other infectious individuals, even if they do not contact each other directly. the watts-strogatz model supplies an ideal tool to study the spread of epidemics among individuals even if their locations are not considered. we used the watts-strogatz model to generate random networks with the small world properties appropriate for infectious disease transmission in these cities [16, 17] . the epidemic curves are all fitted very well using the small-world network structure models, indicating that the typical small-world property is able to capture the contact patterns during covid-19 epidemics. the differences in these fitted parameters and starting times reflect the differences in the underlying transmission mechanisms and potential spread in the regions. the model then projected the trends of covid-19 spread by simulating epidemics in the wuhan, toronto, and italy networks. our findings can guide public health authorities to implement effective mitigation strategies and be prepared for potential future outbreaks. we develop a network-based model by extending the network sir model [18] by incorporating the characteristics of covid-19 transmission to assess the spread of the disease in heterogeneous populations. we derive the explicit expression of the epidemic threshold and discuss the final epidemic size for the network model. and d k = d k /n k represent the fractions of susceptible, exposed, asymptomatically infected, symptomatically infected, hospitalized, recovered, and dead individuals with degree k, respectively. here, n k is the total number of individuals with degree k, and n k = s k +e k +a k + i k +h k + r k +d k , and s k +e k +a k + i k +h k + r k +d k = 1. p (k |k) represents the probability that an edge from a node with degree k connects to a node with degree k . for uncorrelated networks, p (k |k) = k p (k )/ k [19] . since the node with degree k shares an edge with the node degree k, and only has (k − 1) free edges, a fraction k −1 k of nodes may acquire the infection. we assume that the transmission rates of symptomatically infected individuals and asymptomatically infected individuals are β and σβ, respectively. the factor σ accounts for the different transmission rates between asymptomatically infected individuals and symptomatically infected individuals. βks k k k −1 k p (k |k)i k represents the fraction of nodes with degree k infected by symptomatically infected nodes, and σβks k k k −1 k p (k |k)a k = βks k k k −1 k p (k |k)σa k represents the fraction of nodes with degree k infected by asymptomatically infected nodes. here, k −1 k p (k |k)i k represents the probability that an edge from a degree k node connects to a symptomatically infected node with degree k , and k −1 k p (k |k)σa k represents the probability that an edge from a degree k node connects to an asymptomatically infected node with degree k . in model (2.1), the term (1 − k −1 k p (k |k)i k ) represents the probability of not being infected by a symptomatically infected node with degree k , and (1 − k −1 k p (k |k)σa k ) represents the probability of not being infected by an asymptomatically infected node with degree k . thus, is the probability that a node will neither be infected by a 5 j o u r n a l p r e -p r o o f symptomatically infected nor be infected by an asymptomatically infected neighbor with degree k , and 1 − ( is the probability of being infected by a symptomatically infected or an asymptomatically infected neighbor with degree k . therefore, the susceptible individuals are infected at rate and enter the exposed state. after incubation period with a mean time of 1/ days, exposed individuals become symptomatically infected and asymptomatically infected with probabilities δ and 1−δ, respectively. symptomatically infected individuals are hospitalized at rate ξ, and die at rate µ. asymptomatically infected individuals, symptomatically infected individuals, and hospitalized individuals recover at rates γ a , γ, and γ h , respectively. both the hospitalized individuals and symptomatically infected individuals die at rate µ. we derive the epidemic threshold to predict whether the epidemic will spread or die out and derive final epidemic size to quantify the total number of infected individuals. to estimate the transmission potential of the epidemic, we derive the important epidemic threshold, r 0 , defined as the average number of secondary cases produced by an infected individual in a completely susceptible population [20] . there exists a disease-free equilibrium, (s 1 , · · · , s n , e 1 , · · · , e n , a 1 , · · · , a n , i 1 , · · · , i n , h 1 , · · · , h n , r 1 , · · · , r n , d 1 , · · · , d n ) t = (1, · · · , 1, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0, 0, · · · , 0) t =: e 0 . we compute r 0 following the next generation matrix approach presented by van den driessche and watmough [21] . for simplicity, we only consider the compartments related to infection, namely, e k , a k and i k , and rewrite the equations as the difference between vectors f k and v k following the notations in [21] [ here, f ik represents the rate at which new infections are produced and v ik represents the rate at which individuals transfer between compartments, i = 1, 2, 3 and k = 1, · · · , n for model (2.1). the jacobian matrix f is where z = (z j ) = (e 1 , · · · , e n , a 1 , · · · , a n , i 1 , · · · , i n ) and 0 p (2) · · · (n − 1)p (n) 0 2p (2) · · · 2(n − 1)p (n) . . . . . . . . . . . . 0 np (2) · · · n(n − 1)p (n) the matrices v and v −1 are where i n is the n × n identity matrix, and the next generation matrix is since the rank of matrix f is 1, the spectral radius of f is its trace, i.e., it follows from (2.2) that the basic reproduction number r 0 becomes where β 1−δ γa σ and β δ γ+µ+ξ represent the average numbers of secondary cases produced by an asymptomatically infected individual and a symptomatically infected individual in a homogeneously mixed population, respectively. the term k 2 − k k represents the average excess degree of nodes in the network [22] . we shall derive the final size following the approach in [23] . the nonlinear term in the first and second equations of model (2.1) can be rewritten as when i k 1 and a k 1, i k a k ≈ 0. hence, hence, model (2.1) can be simplified as for a homogeneous network where all nodes have identical degree k, model (2.3) can be reduced to the following model by model (2.4) and a direct calculation, we have where s(+∞) = lim t→∞ s(t). to determine the final size of susceptible individuals, s(+∞), we set where y 0 = s 0 + e 0 . by (2.5), (2.6) and the definition of f (x), we have it is clear that f (x) is a positive, increasing, strictly convex function, and f (s 0 ) < s 0 . thus, f has a unique fixed point s + in the interval (0, s 0 ), which can be calculated numerically by using the iteration method and where f m denotes composition of f for m times. then, the final size of susceptible individuals for a homogeneous network, s(+∞), can be determined by s + . we now derive the final size for heterogeneous networks. integrating the first equation in model (2.3) from 0 to t, we have (2.7) by summing and integrating the equations in model (2.3), by equations (2.7),(2.8) and (2.9), we have where g k (0) ≥ 0, ∀k. therefore, for all k = 1, ..., n, the final size of susceptible individuals satisfies we define a map g : to analyze the properties of g(x), we shall introduce some notations. for the above definition defines a partial order in r n . for later use, we could extend this partial order to n × n matrices as follows. for any n × n matrices a, b, we have when 0 . . , w n (0)] t , by the definition of g(x) and partial order defined in (2.10), we have where g m is the composition function of g for m times. by the monotone criterion, we obtain due to the continuity of g, g(s) = s and g(s) = s. therefore, we have the following property [23] . due to the continuous differentiability of g, for any x ∈ r n and 1 ≤ i, j ≤ n. moreover, we shall simply write (2.11) in terms of the matrix form by . by the monotony of g, dg is also monotonous, i.e., dg(x) ≤ dg(y) for any 0 ≤ x ≤ y ≤ s(0). by utilizing the properties of w(x) and g(x), we can obtain the following theorem. (2) when w(0) > 0, g has a unique fixed point s ++ satisfying 0 s ++ < s(0). the proof of theorem 2.1 directly follows the proof in [23] . hence, the final size of susceptible individuals for a heterogeneous network, s(+∞), can be determined by s ++ to quantify the number of susceptible individuals left theoretically. we parameterized the model with reported data on covid-19 cases and presented forecasts of the epidemic trends for the three areas. we simulated the spread of covid-19 in wuhan, toronto, and italy on the watts-strogatz network with degree k min = 1 and k max = 10. the study period for wuhan starts from january 11, 2020, after the confirmed cases were reported, the public becomes aware of the infection and most people are trying to avoid gathering. the study period starts from january 26 for toronto and from january 31 for italy. in toronto and italy, usually people do not gather, especially after lockdown on wuhan city, the awareness of avoiding exposure to the virus is increasing. most people stay home during the study period, and the family sizes in wuhan, toronto, and italy on average are all around 3. therefore, the range of the node degrees is assumed to be between 1 and 10. the watts-strogatz model starts with a ring of n vertices in which each vertex is connected to its 2m nearest neighbors (m vertices clockwise and m counterclockwise). each edge is connected to a clockwise neighbor with probability p and preserved with probability 1 − p [19] , where the degree distribution is j o u r n a l p r e -p r o o f when p → 1, the expression reduces to a poisson distribution as follows in the simulations, we used this degree distribution. the total number of nodes for wuhan, toronto, and italy are 11081000, 5928000, and 59430000 as shown in table 1, table 3 , and table 6 , respectively. we parameterized the model using the mcmc approach [24] the rate at which the fraction of the cumulative number of cases changes is dc k /dt = ξi k , where c k (t) represents the fraction of the cumulative number of infected individuals with degree k. the number of newly infected can be expressed as where p k represents the number of new cases with degree k, and n k represents the total number of individuals with degree k. we run the mcmc simulation for 20000 iterations to fit the value of p k . zhou et al. showed that the median time from illness onset (i.e., before admission) to discharge was 22 days (iqr 18-25), whereas the median time to death was 18.5 days with iqr between 15 and 22 days [27] . we assume an exponential distribution for the time to recovery for asymptomatically infected individuals, symptomatically infected individuals, and hospitalized individuals. this results in the recovery rates γ a = γ = γ h = 1/22 per day, and the mortality rate, µ is 1/18.5 per day. the incubation period of covid-19 is around 7 days [4] , resulting in the progression rate = 1/7. qiu et al. reported that around 30% − 60% of people infected with covid-19 are asymptomatic or only have mild symptoms, and their transmissibility is lower, but still significant [28] . thus, we assume that the probability that an infected individual is asymptomatic is 1 − δ = 0.6, and σ = 1 for simulations. we divided the wuhan epidemic into four phases according to the reported data [3] . the first phase is before lockdown on jan 23, 2020. the second phase is between jan 24, 2020 and feb 1, 2020 when the hospitals were short of beds. the third phase is between feb 2, 2020 and feb 6, 2020 when the thunder god mountain hospital (tgmh) and fire god mountain hospital (fgmh) were put into use. the fourth phase began when door-to-door screening was implemented on feb 7, 2020 and tgmh, fgmh, and mobile cabin hospitals (mch) were put into use. the study period for toronto (canada) was decomposed into two phases, namely, the period before mar 18 and the period after mar 18 when the city announced the emergence and schools and universities in toronto were closed on mar 18. the study period for italy was divided into two phases. the early epidemic phase was between jan 31, 2020 and mar 8, 2020 when the infection was spreading through the northern provinces. the second period begins on mar 9, 2020 when the national lockdown started. the parameters and initial conditions of simulations for wuhan on the ws network are shown in table 1 . the probability of transmission through adequate contact is estimated by mcmc. the 5000 realizations of the basic reproduction numbers derived for wuhan using the parameter values listed in table 1 are shown in table 2 . from jan 11 to mar 31, we estimate that the mean reproduction number on the ws network decreases from 3.41 in the first phase to 5.34 × 10 −3 in the fourth phase. the epidemic on the ws network is shown in figure 1 . up to jan 23, 2020 when wuhan lockdown started, the estimated epidemic size is 3.96 × 10 6 . during the second stage, after the lockdown of wuhan and before the tgmh and fgmh were put into use, the predicted final size is 2.17 × 10 6 . thus, the lockdown of wuhan reduced the expected final size by 45.22%. during the third stage, after tgmh and fmgh were put into use, the final size is 1.02 × 10 5 . hence, the city lockdown and the usage of tgmh and fgmh reduced the final size by 97.42%. during the fourth stage, after mch was put into use, the predicted final size is 51269, and the expected final size of infection is reduced by 98.70% due to the increase of healthcare capacity. the variability of the numbers of confirmed new cases is consistent with the variability of the reproduction numbers listed in table 2 . in the first two phases, the epidemic spread rapidly with larger reproduction numbers that are larger than 1, and the numbers of infected cases increase. in the last two phases, the spread of disease is controlled, and the reproduction numbers are smaller than 1. in the third phase, because a large number of cases are confirmed by door-to-door screening and expanded healthcare capacity, the cumulative number of confirmed cases increased. on the other hand, the epidemic will die out because the reproduction number is less than one. in the fourth phase, the spread of the disease has been under control with the reproduction number being less than one. hence, the number of new cases decreases. the parameters and initial conditions of simulations for the gta are shown in table 3 . the 5000 realizations of the basic reproduction numbers derived for toronto using the parameter values listed in table 3 are shown in table 2 . the reproduction numbers are much smaller due to social distancing policy, school closure, as well as behavior changes. the summary of the simulations is shown in table 4 and table 5 . simulation results are shown in figure 2 . the peak size is 60.19 (95%ci: 47.42-72.97), the peak time is apr 2 (95%ci: mar 29-apr 7), and the final size is 2712 (95%ci: 1603-3820). the parameters and initial condition of simulations for italy is shown in table 6 . the 5000 realizations of the basic reproduction numbers derived for italy using the parameter values listed in table 6 are shown in table 2 . the reproduction numbers in the second phase are much smaller than that in the first phase due to the awareness of the severity of the epidemic. the summary of the simulation results is shown in table 7 and table 8 . figure 3 shows that the peak number of new cases is 5492 (95%ci: 5277-5708) on mar 26 (95%ci: mar 24-mar 27), and the final size is 2.59 × 10 5 (95%ci: 2.10 × 10 5 − 3.08 × 10 5 ). the close contacts identified by contact tracing will be quarantined due to exposure to covid-19 to see if they become sick. to evaluate the impact of mitigation strategies on the spread of covid-19, model (2.1) is rewritten as follows j o u r n a l p r e -p r o o f journal pre-proof where sq k = sq k /n k represents the fraction of quarantined individuals with degree k. the parameter q represents the rate at which susceptible individuals are quarantined, and λ represents the rate at which the quarantined and uninfected close contacts transfer to the susceptible compartment again. in the simulations, we let λ = 1/14 to approximate a mean time of 14 days in the exposed state. for wuhan, the cumulative number of infected individuals after lockdown and tgmh, fgmh, as well as mch were put into use are shown in figure 4 . the results show that the lockdown and the increase in healthcare capacity are effective in controlling the numbers of confirmed cases. for toronto, the number of newly infected individuals and the cumulative number of infected individuals produced on the ws network after implementing additional containment strategies besides school closure are shown in figure 5 . we simulated the scenarios of implementing various containment strategies for toronto. simulation results showed that personal protection, reducing the node degrees of symptomatically infected individuals, and quarantine of close contacts are effective in reducing the peak epidemic size and final epidemic size. reducing the transmission rate β, by x% also reduces r 0 by x%. when β is reduced by 20% by personal protection or social distancing, the peak occurs one day earlier, and the final epidemic size is reduced by around 18%. when β is reduced by 40%, the peak occurs two days earlier, and the final epidemic size is reduced by around 33.3%. when q = 1/8, the peak occurs four days earlier, and the final epidemic size is reduced by 45.21%. when q = 1/4, the peak appears five days earlier, and the final epidemic size is reduced by 58.22%. when the node degrees of symptomatically infected individuals are reduced by 1, 2, and 3, the number of new cases j o u r n a l p r e -p r o o f produced per day at the peak is reduced by 13.74%, 26.93%, and 39.18%. the final epidemic size is reduced by 15.15%, 29.65%, and 43.55% when the node degrees of symptomatically infected individuals are reduced by 1, 2, and 3, respectively. for italy, the number of newly infected individuals and the cumulative number of infected individuals simulated on the ws network after implementing hypothetical containment strategies are shown in figure 6 . various scenarios of implementing mitigation strategies showed that the peak epidemic size and final epidemic size in italy are greatly reduced by personal protection, social distancing, behavior change of symptomatically infected individuals, and quarantine. the simulations show that the peak would have arrived earlier if the containment had been intensified. when the probability of contact transmission coefficient β, is reduced by 20% by personal protection or social distancing, the peak occurs one day earlier, and the final epidemic size is reduced by 21.56%. when β is reduced by 41.44%, the peak occurs one day earlier, and the final epidemic size is reduced by around 40%. when q = 1/8, the peak occurs six days earlier, and the final epidemic size is reduced by 52.87%. yet, when q = 1/4, the peak occurs eight days earlier, and the final epidemic size is reduced by 67.12%. when the node degree of symptomatically infected individuals is reduced by 1, 2, and 3, the number of new cases produced per day at the peak is reduced by 16.50%, 32.93%, and 49.11%, respectively. the final epidemic size is reduced by 17.90%, 34.70%, and 50.51% when the node degrees of symptomatically infected individuals are reduced by 1, 2, and 3, respectively. modelling the dynamics of covid-19 epidemics and assessment of mitigation strategies could be instrumental to public health agencies for surveillance and healthcare planning. for the models to be reliable, the simulated epidemic must account for the stochastic and heterogeneous contact among individuals. hence, we developed a network model that captured the contact heterogeneity among individuals. we applied the model to analyze the transmission potential, and mitigation strategies for curbing the spread of covid-19 epidemics in the cities of wuhan, china and toronto, canada, and in the italian republic. the epidemic threshold derived from our network model can be used to predict the risks of spreading scenarios. we also 18 j o u r n a l p r e -p r o o f provided an explicit expression of the final epidemic size, which facilitates estimating the scale of an outbreak for any region of interest. our results provide insights in defining a mathematical framework for the analysis and containment of epidemic transmission in the real world. the flexible network model framework can simulate a wide range of mitigation strategies can be examined by the flexible model framework. it can be extended to quantify the effectiveness of personal protection, social distancing, reducing the node degree of infected individuals, and quarantine on the dynamics of epidemics in different regions. when the mitigation strategy is intensified, the model predicts that the number of new cases peaks earlier and the final epidemic size is greatly reduced. the social contact network structure and parameter values determine the transmission and epidemic course of such an emerging infectious disease. we choose the watts-strogatz to approximate real social networks, when the exact contact tracing data is unavailable. we assumed that the range of the node degree is between one and ten for each network in the absence of real contact tracing data, that is, on average each day an infected person would have between one and ten contacts where they could transmit the infection to another person. in the real world, the range of the degree will depend on the distribution of the household sizes of the region and time being studied. moreover, the network structure can be altered by behavior change of individuals during epidemics. when this happens, the network structure can be adapted in our model to predict the impact of these changes on the epidemic threshold, epidemic peak value, peak time, stopping time, and final size of infected population. the epidemics for the three places under study were fitted very well by our model with a small confidence interval. hence, the forecasts by the model can be reliable. we did not provide the stopping time since too many uncertainties may affect the duration of the epidemics. as shown in the simulations, the transmission dynamics for four phases in wuhan are quite different due to the variability on the intensity of interventions, the availability of healthcare facilities, as well as the utilization of personal protective equipment (ppe). the dynamics in the first phase is quite different from that in the second phase for toronto. the same phenomenon is observed in italy. at the early stage, almost no interventions were implemented, and the public was not aware of or did not pay much attention to the severity of the highly contagious disease. with the increase of the number of reported confirmed cases and with the aid of social media, the public becomes aware of the severe consequence and has increased the level of personal protection and have avoided gathering, so that the reproduction number decreases and the estimated epidemic size declines by reducing the node degree of the network. similarly, after applying the mitigation measures in italy on march 8 and closing all schools in toronto on march 18, the epidemics tend to be under control. hence, social distancing, self-isolation, quarantine, the utilization of ppe, and other measures of avoiding exposure to the virus can greatly reduce the size of infection during the covid-19 outbreak. therefore, it is essential to raise the awareness of these countermeasures to avoid contact between individuals. the possibility of recurrent outbreaks of the disease cannot be overstated. even if the number of new cases is declining, it is still necessary to continue taking protective measures to prevent the occurrence of future outbreaks. the social media should warn the public not to relax their 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coronavirus infections could be seeding new outbreaks we declare that there is no conflict of interest associated with this work. all co-authors claim that there is no conflict of interest among the co-authors. on behalf of all co-authors j o u r n a l p r e -p r o o f key: cord-273064-c58nf9vb authors: hallowell, benjamin d.; carlson, christina m.; jacobs, jesica r.; pomeroy, mary; steinberg, jonathan; tenforde, mark w.; mcdonald, emily; foster, loretta; feldstein, leora r.; rolfes, melissa a.; haynes, amber; abedi, glen r.; odongo, george s.; saruwatari, kim; rider, errin c.; douville, gina; bhakta, neenaben; maniatis, panagiotis; lindstrom, stephen; thornburg, natalie j.; lu, xiaoyan; whitaker, brett l.; kamili, shifaq; sakthivel, senthilkumar k.; wang, lijuan; malapati, lakshmi; murray, janna r.; lynch, brian; cetron, martin; brown, clive; roohi, shahrokh; rotz, lisa; borntrager, denise; ishii, kenta; moser, kathleen; rasheed, mohammad; freeman, brandi; lester, sandra; corbett, kizzmekia s.; abiona, olubukola m.; hutchinson, geoffrey b.; graham, barney s.; pesik, nicki; mahon, barbara; braden, christopher; behravesh, casey barton; stewart, rebekah; knight, nancy; hall, aron j.; killerby, marie e. title: severe acute respiratory syndrome coronavirus 2 prevalence, seroprevalence, and exposure among evacuees from wuhan, china, 2020 date: 2020-09-17 journal: emerg infect dis doi: 10.3201/eid2609.201590 sha: doc_id: 273064 cord_uid: c58nf9vb to determine prevalence of, seroprevalence of, and potential exposure to severe acute respiratory syndrome coronavirus 2 (sars-cov-2) among a cohort of evacuees returning to the united states from wuhan, china, in january 2020, we conducted a cross-sectional study of quarantined evacuees from 1 repatriation flight. overall, 193 of 195 evacuees completed exposure surveys and submitted upper respiratory or serum specimens or both at arrival in the united states. nearly all evacuees had taken preventive measures to limit potential exposure while in wuhan, and none had detectable sars-cov-2 in upper respiratory tract specimens, suggesting the absence of asymptomatic respiratory shedding among this group at the time of testing. evidence of antibodies to sars-cov-2 was detected in 1 evacuee, who reported experiencing no symptoms or high-risk exposures in the previous 2 months. these findings demonstrated that this group of evacuees posed a low risk of introducing sars-cov-2 to the united states. to determine prevalence of, seroprevalence of, and potential exposure to severe acute respiratory syndrome coronavirus 2 (sars-cov-2) among a cohort of evacuees returning to the united states from wuhan, china, in january 2020, we conducted a cross-sectional study of quarantined evacuees from 1 repatriation flight. overall, 193 of 195 evacuees completed exposure surveys and submitted upper respiratory or serum specimens or both at arrival in the united states. nearly all evacuees had taken preventive measures to limit potential exposure while in wuhan, and none had detectable sars-cov-2 in upper respiratory tract specimens, suggesting the absence of asymptomatic respiratory shedding among this group at the time of testing. evidence of antibodies to sars-cov-2 was detected in 1 evacuee, who reported experiencing no symptoms or high-risk exposures in the previous 2 months. these findings demonstrated that this group of evacuees posed a low risk of introducing sars-cov-2 to the united states. suspending operation of buses, subways, and ferries within the city (7) . as of january 23, a total of 571 confirmed covid-19 cases had been reported in china (8) . after china enacted the travel ban, the us department of state planned evacuation flights for us citizens and other third country nationals in wuhan. we describe the demographic and clinical characteristics, potential exposures to sars-cov-2, personal protective measures implemented, and sars-cov-2 real-time reverse transcription pcr (rrt-pcr) and serologic test results for evacuees from 1 repatriation flight from wuhan. these data can be used to better determine sars-cov-2 epidemiology, including assessing the point prevalence of past and current sars-cov-2 infections in this cohort and identifying factors associated with infection in this cohort. these findings can also be used to help estimate the initial risk for transmission to contacts in the united states posed by evacuees from wuhan and are relevant to current and future implementation of public health control measures, such as isolation and quarantine. we investigated quarantined evacuees from a january 28, 2020, repatriation flight from wuhan to the united states. before the flight departed wuhan, evacuees were evaluated to ensure that they had no fever or respiratory signs/symptoms. at arrival in the united states and again at the quarantine facility, evacuees were asked to complete a us traveler's health declaration form disclosing any symptoms; they were also screened for illness and fever, asked about symptoms in the past 72 hours, and asked about any high-risk exposures (including working in or visiting healthcare settings; caring for or visiting persons with fever, respiratory illness, or a confirmed covid-19 diagnosis; or visiting any live animal markets) in wuhan in the past 14 days. those who reported symptoms or high-risk exposures were evaluated by a cdc quarantine medical officer, who determined if they required further evaluation and isolation from the quarantined cohort. nasopharyngeal and oropharyngeal swab samples and serum specimens were obtained from participating evacuees when they arrived at the quarantine station in the united states. as part of quarantine procedures, evacuees were actively monitored for fever and respiratory signs/symptoms for 14 days after departure from wuhan; any evacuee in whom either fever or respiratory signs/symptoms developed during this time was evaluated for covid-19 (9) , and additional nasopharyngeal and oropharyngeal specimens were collected (10,11). all specimens were collected, processed, and shipped to cdc for testing (10,11). presence of sars-cov-2 in nasopharyngeal and oropharyngeal swab samples was confirmed by rrt-pcr detection of viral rna in respiratory specimens (12). serum specimens were initially tested for sars-cov-2 antibodies by sars-cov-2 elisa (appendix 1, https://wwwnc.cdc.gov/eid/ article/26/9/20-1590-app1.pdf). we asked evacuees to complete a detailed, selfadministered survey during the flight from wuhan (appendix 2, https://wwwnc.cdc.gov/eid/ article/26/9/20-1590-app2.pdf). the survey captured information on demographics, clinical signs/ symptoms, travel outside of hubei province, face mask use, limitation of time spent in public, and past high-risk exposures (including contact with confirmed covid-19 case-patients; persons with fever, acute respiratory illness, or both; healthcare and laboratory facilities; and animals and live animal markets). we assessed high-risk exposures over the past 2 weeks and the past 2 months. we compared high-risk exposures over the past 2 weeks with rrt-pcr results for persons who provided an upper respiratory specimen (because 14 days was the upper end of the estimated incubation period for covid-19 [13, 14] ). we also compared high-risk exposures over the past 2 months with the serologic test results for evacuees who provided a serum sample (because sars-cov-2 had probably been circulating for the 2 months before their departure [15] ). we entered survey responses into redcap electronic data capture tools hosted at cdc (16) , and all entries were verified by a second reviewer for accuracy and completeness. data were analyzed by using sas software version 9.4 (sas institute, inc., https://www.sas.com). cdc determined that this investigation was public health surveillance (us department of health and human services, title 45 code of federal regulations 46, protection of human subjects). evacuees' participation in the collection of biological specimens and the survey was voluntary. at the time of arrival in the united states, no evacuee had a measured fever or reported any signs or symptoms that required further evaluation. of the 195 evacuees, 193 completed surveys; 99% (191/193) of respondents provided a nasopharyngeal sample, an oropharyngeal sample, or 1 of each for sars-cov-2 rrt-pcr testing, and 96% (186/193) provided a serum sample for testing. the median age of all 193 evacuees was 42 (range 0-74) years, and 53% (100/189) were male (table 1) . most were either asian (49%, 94/192) or white (35%, 68/192). one evacuee reported having had close contact with a person with laboratory-confirmed co-vid-19 in the previous 2 weeks. specifically, reported exposures included direct physical contact, being within 6 feet of the person while that person was coughing or sneezing, taking an object handed from or handled by the person, and traveling in the same vehicle as the person (table 2) . no other evacuees reported exposure to a person with laboratory-confirmed covid-19 in the previous 2 months. however, 6% (12/191) reported having had close contact with a person with fever, acute respiratory illness, or both in the previous 2 weeks and 16% (30/186) in the previous 2 months (table 2) . one evacuee had visited a live animal market in the previous 2 weeks and 5% (9/186) in the previous 2 months. three percent (6/191) of evacuees had visited settings with nondomesticated live animals in the previous 2 weeks and 5% (10/186) in the previous 2 months. one percent (2/191) of evacuees had had direct physical contact with a nondomesticated live animal (both instances with stray dogs) in the previous 2 weeks. no additional evacuees had had direct physical contact with a nondomesticated live animal in the previous 2 months. during the previous month, after hearing about covid-19 cases in wuhan, 95% (178/188) of evacuees reported having limited their time in public in wuhan, including avoiding public gatherings (87%), public transportation (84%), and all public settings (e.g., grocery stores or restaurants; 70%) ( table 3 ). in addition, in the previous month, after hearing about covid-19 cases in wuhan, 76% of evacuees reported having worn a face mask while in public spaces. this finding represented a significant increase from the 34% of evacuees who reported having worn a face mask while in public spaces in the previous 2 months (mcnemar test statistic 74.05; p<0.0001). five percent (9/193) of evacuees reported having experienced signs or symptoms associated with covid-19 (measured or subjective fever, cough, shortness of breath) in the previous 2 weeks, and 12% (24/193) reported signs/symptoms associated with covid-19 in the previous 2 months. one evacuee who reported signs/symptoms associated with covid-19 in the previous 2 weeks sought medical care, and no evacuee required hospitalization while in wuhan (table 4) . sars-cov-2 was not detected by rrt-pcr in any of the 190 nasopharyngeal or 190 oropharyngeal swab specimens collected from 191 unique evacuees (189 provided nasopharyngeal and oropharyngeal samples, 1 nasopharyngeal sample only, and 1 oropharyngeal sample only). during the 14-day quarantine period, fever developed in 2 evacuees; additional nasopharyngeal and oropharyngeal swab specimens were collected and tested, and sars-cov-2 was not detected in either specimen type. one evacuee showed serologic evidence of a past sars-cov-2 infection. serum from that person had antibodies against sars-cov-2 at titers of 400 determined by elisa and 320 determined by microneutralization test. this person was male, was in the 19-44-year age group, was traveling without any family members, and reported no signs/symptoms associated with covid-19 in the past 2 months. he reported no high-risk exposures (including exposure to or contact with live animals, live animal markets, persons known to be ill with covid-19, or persons with fever or acute respiratory signs/symptoms). he reported that since early january he had spent limited time out in public, including avoiding public transport, avoiding public gatherings, and not attending school/university. elisa results for the remaining 185 serum specimens measured sars-cov-2 antibody titers at <400, and the samples were therefore considered seronegative. our report on sars-cov-2 prevalence, seroprevalence, and potential exposures among evacuees returning from wuhan is part of the public health response enacted to slow transmission of sars-cov-2 in the united states. although this population of evacuees is probably not representative of all wuhan residents in terms of risk of acquiring sars-cov-2 infection, our results indicate limited exposure to sars-cov-2 among this group of early evacuees from wuhan. compared with previously reported covid-19 case-patients in wuhan, our population was younger (median 42 vs. 59 years of age) and their reported frequency of potential sars-cov-2 exposures was lower, including exposure to persons with respiratory signs/symptoms, work-associated healthcare exposures, and exposure to live animal markets (15) . of note, although our questionnaire covered exposure to animals and animal markets, most transmission within wuhan during the evacuees' relevant exposure period before the repatriation flight to the united states was probably human-to-human (15, 17) . our study population, which consisted predominantly of us expatriates, probably had other factors that reduced their risk for exposure and were not documented as part of our investigation. for example, it is possible that the expatriates' households in wuhan were smaller than other households in wuhan, which has been associated with a lower risk for transmission (18) (19) (20) (21) ; however, because we did not document household size in our investigation, we cannot show such an association. nearly all evacuees took preventive measures to limit potential exposure to sars-cov-2 while in wuhan. however, 16% of evacuees did have direct contact with persons who had fever or acute respiratory illness. previous investigations among evacuees traveling from wuhan to germany and japan detected sars-cov-2 rna in 7 asymptomatic persons (22, 23) , suggesting that symptom-based screening alone may not be effective for detecting sars-cov-2 infection. evacuees in our study underwent intensive screening such that no evacuee had signs/symptoms at the time of evacuation and none had detectable sars-cov-2 in upper respiratory tract specimens, suggesting the absence of asymptomatic respiratory shedding among this group at the time of testing. in addition, no sars-cov-2 was detected in respiratory specimens from the 2 evacuees in whom fever developed during quarantine. the lack of sars-cov-2 detection in asymptomatic travelers at the time of testing and in the 2 travelers in whom fever developed could result from a lower risk for exposure among this group compared with wuhan residents or other reported evacuees (22, 23) . the elisa and microneutralization tests used in this investigation have produced robust responses to serum from confirmed sars-cov-2 patients (b. freeman et al., unpub data, https://www.biorxiv. org/content/10.1101/2020.04.24.057323v2 28). although 24 evacuees reported signs/symptoms associated with covid-19 (subjective fever, cough, or shortness of breath) in the previous 2 months, none were seropositive for sars-cov-2. in contrast, an antibody response was detected in 1 person who did not report illness in the previous 2 months, indicating past sars-cov-2 infection, suggestive of past asymptomatic or mildly symptomatic infection. the overall seroprevalence of 1% suggests a low level of exposure to sars-cov-2 over the preceding 2 months in wuhan. however, a lack of antibody response may not mean an absence of past infection; serologic responses were not always found in persons with mild middle east respiratory syndrome coronavirus illness and positive rrt-pcr results for that virus (24) . future serologic testing among co-vid-19 case-patients may be useful for determining whether persons with asymptomatic or mild cov-id-19 disease become seropositive. efforts by this cohort to limit their exposure by limiting their time in public may have helped prevent infection, even in a city with extensive ongoing community transmission. because sars-cov-2 seems to be transmitted primarily through respiratory droplets, limiting time in public may have helped prevent infection because proximity to infected persons is needed for virus transmission (25) . before the evacuees in our study departed wuhan, china was implementing measures to control sars-cov-2 by suspending public transport and vehicle traffic and canceling lunar new year gatherings (7) . cdc currently recommends that all persons wear cloth face coverings in public; the purpose is to help protect others from potential droplet exposure, not to protect the persons wearing the face coverings (26) . thus, although 76% of evacuees reported mask use after hearing about covid-19 in wuhan, individual mask use probably had minimal effect on their individual risk of acquiring infection. information about virus prevalence, seroprevalence, and possible sars-cov-2 exposures in this population of evacuees has the potential to inform current and future quarantine and isolation policies. in this population, who underwent intensive screening and monitoring, we detected no evidence of current infection with sars-cov-2 and very limited evidence of past infection. other than the 193 evacuees included in our study, 3 cases of covid-19 were detected in the united states during quarantine of later cohorts of evacuees after signs/symptoms developed and the evacuees underwent testing, demonstrating the value of quarantine and active monitoring of evacuees to detect covid-19 cases (27) . emerging infectious diseases â�¢ www.cdc.gov/eid â�¢ vol. 26, no. 9, september 2020 limited to persons who submitted serum specimen. â¶limited to persons who reported an occupation (other than student, stay-at-home parent, or retired). #limited to persons 2-18 years of age and those reporting student as occupation. our investigation has limitations. first, the survey was self-administered and based on self-report; therefore, questions were open to interpretation and subject to reporting bias. because respiratory specimens from asymptomatic persons were collected at a single point in time, we are unable to show whether asymptomatic shedding might have occurred later during quarantine. also, rrt-pcr assays and serologic tests are inherently limited by their individual sensitivity and specificity; however, we believe that the limitations of test specificity and sensitivity across this population of evacuees were minimal. in addition, because only 1 serum specimen was taken at the time of us arrival, we were unable to detect antibodies that may have developed later. as of may 1, a total of 1,062,446 covid-19 cases had been confirmed in the united states, including 39 in repatriated persons (3 cases in 808 returned evacuees across 5 flights from hubei province and 36 cases from the diamond princess cruise ship) (28) . initial efforts to slow introduction of sars-cov-2 to the united states began in january 2020 and included quarantine of persons with high-risk exposures, screening of travelers at airports, and isolation and contact tracing of confirmed case-patients (28) . our investigation demonstrated that this group of evacuees posed a low risk of introducing sars-cov-2 to the united states, and their exposure to sars-cov-2 in wuhan was probably limited. these results should help inform public health guidance on quarantine and isolation measures for travelers arriving from high-risk areas and further characterize the epidemiology of this emerging virus. table 4 . signs/symptoms, clinical course, and past medical history for evacuees reporting illness who were on a repatriation flight from wuhan, china, to the united states in early 2020* no./total no. (%) â�  self-reported illness in past 2 mo, n = 39 *all persons who self-reported illness submitted serum and a nasopharyngeal or oropharyngeal swab specimen. covid-19, coronavirus disease. â� persons for whom responses were missing were excluded from the numerator and denominator. â�¡measured fever or subjective fever, cough, or shortness of breath. â§measured or subjective fever and shortness of breath or cough. world health organization. pneumonia of unknown cause-china world health organization. novel coronavirus (2019-ncov) situation report-1: 21 coronaviridae study group of the international committee on taxonomy of viruses. the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 world health organization. novel coronavirus (2019-ncov) situation report-102 washington state 2019-ncov case investigation team. first case of 2019 novel coronavirus in the united states the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak world health organization. novel coronavirus (2019-ncov) situation report-3: 23 centers for disease control and prevention. interim guidelines for collecting, handling, and testing clinical specimens from persons under investigation (puis) for centers for disease control and prevention. interim laboratory biosafety guidelines for handling and processing specimens associated with 2019 novel coronavirus (2019-ncov) 2019-ncov cdc response team. initial public health response and interim clinical guidance for the 2019 novel coronavirus outbreak-united states incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia research electronic data capture (redcap)-a metadata-driven methodology and workflow process for providing translational research informatics support the continuing 2019-ncov epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in wuhan, china only strict quarantine measures can curb the coronavirus disease (covid-19) outbreak in italy impact of contact tracing on sars-cov-2 transmission the characteristics of household transmission of covid-19 epidemiology and transmission of covid-19 in 391 cases and 1286 of their close contacts in shenzhen, china: a retrospective cohort study evidence of sars-cov-2 infection in returning travelers from wuhan, china the rate of underascertainment of novel coronavirus (2019-ncov) infection: estimation using japanese passengers data on evacuation flights scope and extent of healthcare-associated middle east respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in riyadh, saudi arabia isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-ncov) outbreak how to protect yourself & others covid-19): cases in the u.s update: public health response to the coronavirus disease 2019 outbreak-united states we thank the following members of the riverside university system: josephine cortez, anthony martinez, brianna anderson, hanh nguyen, kim clifton, vanessa arreola, jarrett herbst, jide adeyeye, stephanie loe, geoffrey leung, mike mesisca, gregory harriman. we also thank the cdc covid-19 patient under investigation team. at the time of the study, dr. hallowell was an epidemic intelligence service officer in the division of viral diseases, national center for immunization and respiratory diseases, cdc. his research interests include epidemiology of infectious diseases, vaccines, and public health. key: cord-275835-z38cgov9 authors: mogharab, vahid; pasha, anahita manafi khajeh; javdani, frashid; hatami, naser title: the first case of covid-19 infection in a 75-day-old infant in jahrom city, south of iran date: 2020-04-13 journal: j formos med assoc doi: 10.1016/j.jfma.2020.03.015 sha: doc_id: 275835 cord_uid: z38cgov9 nan the first case of covid-19 infection in a 75day-old infant in jahrom city, south of iran in late december of 2019, a new coronavirus was discovered in china. on 11 february 2020, the world health organization named the disease caused by this virus covid-19. the disease quickly spread to chinese cities and other parts of the world, including thailand, japan, taiwan and iran. 1 the number of infected patients increased daily until the world health organization in june declared the outbreak a serious and urgent threat to public health. most people infected with the virus recover well, but some also may experience fatal complications, such as acute organ failure, septic shock, acute pulmonary edema, acute pneumonia, and acute respiratory distress syndrome. 1 as infection has been transmitted from individual to individual, 2 the first cases of the disease in areas outside of wuhan, occurred in travelers from wuhan; as the first case of covid-19 was confirmed to be a 35-year-old woman living in wuhan who traveled to korea. 3 on january 20, 2020, a 55-year-old woman working in wuhan, arrived at taiwan and was referred to quarantine authorities with symptoms of sore throat, dry cough, fatigue, and feeling low-grade fever on january 11. 4 while covid-19 infection seems to be more prevalent in adults than in children, rare cases of children infection are being reported, mainly seen in family clusters. 5 the presented case is a 75-day-old infant that was referred to the pediatric emergency department, with a history of severe dry cough and abnormal noisy breathing sound (heard without a stethoscope) during the last 11 days. the patient had been suffering from fever since about 7 days ago; the fever was having a good response to antipyretic. but mother had not been using a thermometer for screening the fever. about three days ago coughs got more severe, along with an increased breathing sound and dyspnea appeared. on arrival, the infant had a respiratory rate of 50 per minute, a temperature of 37.6 centigrade, pulse rate of 172 and o2 saturation of 85%. in physical examination, an intercostal retraction was seen and lung auscultation revealed diminished wheeze and ralse in both sides. after taking oxygen with the hood, the o2 saturation got increased to 97% and intercostal retraction disappeared. therefore, respiratory rate reduced to 35 times per minute. a normal complete blood count and levels of na þ and k þ were reported upon the patient's arrival. the high-resolution computed tomography (hrct) of the patient after two hours of patient arrival is shown in fig. 1 , which shows bilateral peripheral consolidation with a ground glass view. while, as reviewed in cao et al. study, most studies have reported the infection to be more severe in adults rather than the child, the dissemination of covid-19 in children implies that it has high transmitting potential in a specific transmission dynamics. 5 pediatricians have to know more about the epidemiological and clinical aspects of the disease to diagnose and control covid-19. world health organization declares global emergency: a review of the 2019 novel coronavirus (covid-19) incubation period of 2019 novel coronavirus (2019-ncov) infections among travelers from wuhan, china the first case of 2019 novel coronavirus pneumonia imported into korea from wuhan, china: implication for infection prevention and control measures first case of coronavirus disease 2019 (covid-19) pneumonia in taiwan sars-cov-2 infection in children: transmission dynamics and clinical characteristics the authors have no conflicts of interest relevant to this article. key: cord-273209-ou80n3p3 authors: zheng, fang; liao, chun; fan, qi-hong; chen, hong-bo; zhao, xue-gong; xie, zhong-guo; li, xi-lin; chen, chun-xi; lu, xiao-xia; liu, zhi-sheng; lu, wei; chen, chun-bao; jiao, rong; zhang, ai-ming; wang, jin-tang; ding, xi-wei; zeng, yao-guang; cheng, li-ping; huang, qing-feng; wu, jiang; luo, xi-chang; wang, zhu-jun; zhong, yan-yan; bai, yan; wu, xiao-yan; jin, run-ming title: clinical characteristics of children with coronavirus disease 2019 in hubei, china date: 2020-03-24 journal: curr med sci doi: 10.1007/s11596-020-2172-6 sha: doc_id: 273209 cord_uid: ou80n3p3 since december 2019, covid-19 has occurred unexpectedly and emerged as a health problem worldwide. despite the rapidly increasing number of cases in subsequent weeks, the clinical characteristics of pediatric cases are rarely described. a cross-sectional multicenter study was carried out in 10 hospitals across hubei province. a total of 25 confirmed pediatric cases of covid-19 were collected. the demographic data, epidemiological history, underlying diseases, clinical manifestations, laboratory and radiological data, treatments, and outcomes were analyzed. of 25 hospitalized patients with covid-19, the boy to girl ratio was 1.27:1. the median age was 3 years. covid-19 cases in children aged <3 years, 3.6 years, and ≥6-years patients were 10 (40%), 6 (24%), and 9 (36%), respectively. the most common symptoms at onset of illness were fever (13 [52%]), and dry cough (11 [44%]). chest ct images showed essential normal in 8 cases (33.3%), unilateral involvement of lungs in 5 cases (20.8%), and bilateral involvement in 11 cases (45.8%). clinical diagnoses included upper respiratory tract infection (n=8), mild pneumonia (n=15), and critical cases (n=2). two critical cases (8%) were given invasive mechanical ventilation, corticosteroids, and immunoglobulin. the symptoms in 24 (96%) of 25 patients were alleviated and one patient had been discharged. it was concluded that children were susceptible to covid-19 like adults, while the clinical presentations and outcomes were more favorable in children. however, children less than 3 years old accounted for majority cases and critical cases lied in this age group, which demanded extra attentions during home caring and hospitalization treatment. since december 2019, an epidemic caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection has occurred unexpectedly in wuhan, hubei province, china, and it had quickly spread from wuhan to the other areas in china and abroad [1] [2] [3] [4] . the world health organization named this novel coronavirus disease, covid-19, which was known as the novel conoravirus pneumonia (ncp) in china. full-genome sequencing analysis indicated that sars-cov-2 has 89% nucleotide identity with bat sars-like-covzxc21 and 82% with that of human sars-cov [5] . according to the updated information from national health commission of the people's republic china, by february 15, 2020, the current epidemic status has shown a total of 69 110 confirmed cases in the worldwide, and 68 584 confirmed cases, 8228 suspected cases with 1666 deaths reported around 31 provinces and cities in china [6] . in recent weeks, emerging studies have reported that most patients with covid-19 had an epidemiological history including a travel or residence history in wuhan city and neighboring areas, and contacting with confirmed or suspected cases [7] . the main clinical features of adult patients included fever, dry cough, dyspnea, myalgia, fatigue, normal leukocyte counts or leukopenia, and radiographic evidence of pneumonia [8] . covid-19 was more likely to affect older men with comorbidities and could result in acute respiratory distress syndrome (ards) [9] . wang et al [10] elaborated hospital-related transmission of covid-19 was suspected in 41% of patients, 26% of patients received icu care, and mortality was 4.3%. compared to adults, the number of reported pediatric patients is limited [11, 12] , and the clinical characteristics of pediatric covid-19 was rarely reported. the objective of this study is to describe the clinical characteristics of 25 hospitalized pediatric covid-19. we did a retrospective study including data from an established network of 10 purposely selected public hospitals situated in wuhan urban and peri-urban areas of wuhan. this case series was approved by the institutional ethics board of tongji medical college, huazhong university of science and technology. inpatient records included all children aged 1 month-14 years admitted to hospital with covid-19 between february 1, 2020, and february 10, 2020. diagnostic criteria for covid-19 were determined according to the recommendation for the diagnosis and treatment of novel coronavirus infection in children in hubei (trial version 1) [13] . oral consent was obtained from patients' parents. the medical records of patients were analyzed by a trained team of physicians from the department of pediatrics in ten hospitals. all patients were confirmed by the test positive for sars-cov-2. demographic data, medical history, epidemiological history, underlying diseases, clinical symptoms, signs, laboratory data, radiological characteristics, treatments and outcomes were obtained with collection forms from electronic medical records. epidemiological history was confirmed if they met any one of the following criteria: (1) children with travel or residence history in wuhan city and neighboring areas, or other areas with persistent local transmission within 14 days prior to disease onset; (2) children with a history of contact with patients with fever or respiratory symptoms who had travel or residence history in wuhan city and neighboring areas, or in other areas with persistent local transmission within 14 days prior to disease onset; (3) children with a history of contact with confirmed or suspected cases of covid-19 within 14 days prior to disease onset; and (4) children who were related with a cluster outbreak. throat swab and/or nasal-pharyngeal swab samples were collected for extracting rna from suspected patients with sars-cov-2 infection. after collection, the samples were placed into a collection tube with 150 μl of virus preservation solution, and total rna was extracted within 2 h using the respiratory sample rna isolation kit (zhongzhi, wuhan, china). the detailed procedures had been described by huang et al [7] . these diagnostic criteria were determined according to the recommendation by the national institute for viral disease control and prevention, china. lab investigations included a complete blood count and serum biochemical tests for liver function, lactate dehydrogenase, electrolytes, coagulation, and c-reactive protein (crp). nasal and pharyngeal throat swabs were tested for common pathogens, including influenza a and b virus, respiratory syncytial virus, adenovirus, parainfluenza virus, mycoplasma pneumoniae, and chlamydia pneumoniae using realtime rt-pcr assays approved by the china food and drug administration. routine bacterial examinations were also performed. patients were performed on chest computer tomography (ct) scans. radiological diagnosis was reviewed by two experienced chest radiologists. continuous variables were described using mean, median, and interquartile range (iqr) values. categorical variables were described as percentages and compared using the χ 2 test, although the fisher exact test was used when data were limited. continuous variables were compared using independent group t tests when the data were normally distributed. otherwise, the mann-whitney test was used. all statistical analyses were analyzed using graph pad prism 6.0 software (usa). a two-sided p of less than 0.05 was considered statistically significant. a total of 25 patients with covid-19 were included in this study. there were 14 (56%) males and 11 (44%) females with the boy to girl ratio being 1.27:1. the median age was 3 years (iqr, 2-9 years; range, 3 months-14 years). children aged <3 years, 3-6 years, and ≥6 years were 10 (40%), 6 (24%), and 9 (36%) respectively. most patients were previously healthy and only 2 had underlying disease. one patient had congenital heart diseases, malnutrition, and suspected hereditary metabolic diseases. the other one had congenital heart disease. both of them had already undergone operations. twenty-one (84%) had epidemiological contact history and only 4 patients didn't have any epidemiological history (table 1) . clinical diagnoses included upper respiratory tract infection (uri) (n=8), mild pneumonia (n=15), and critical cases (n=2). 14 of 25 patients (56%) aged less than 6 years had mild illness. patients had an uneven age distribution. the high incidence of infection was noted to be aged <3 years (40%) ( fig. 1) the blood counts of children on admission showed that the median level of white blood cell count was 6.2 × 10 9 /l (iqr 4.30-9.85). the median level of lymphocyte count was 2.19 × 10 9 /l (iqr 1.15-3.31), and 10 of 25 patients showed lymphopenia (less than age-related reference values). the median values of crp were 14.5 mg/l (iqr 0.93-25.04). liver function test and myocardial enzyme assay had been done in 12 children. these tests revealed median alanine aminotransferase level of 12 u/l (10-13) and median creatine kinase isoenzyme level of 19 u/l (13-36) (table 2). except for the 2 critical cases, patients had normal renal function and coagulation function. both 2 critical cases had high levels of serum lactic dehydrogenase. one critical patient was complicated with hyponatremia (table 3) . all cases were confirmed as sars-cov-2 infection by virus nucleic acid test. other identified pathogens included mycoplasma pneumoniae (3/25, 12%), influenza virus type b (2/25, 8%), and enterobacter aerogenes (1/25, 8%). on admission, 24 patients were subjected to chest ct scans. chest ct images showed essential normal in 8 cases (33.3%), unilateral involvement in 5 cases (20.8%) and bilateral involvement in 11 cases (45.8%) (table 2). the typical findings of chest ct images were bilateral patchy shadows or lung consolidations. an analysis of the age distribution of chest ct images showed that bilateral lung involvement was present in about 70% of children with aged <3 years, which was the highest percentage among the different age groups. the percentage of unilateral lesion and normal lungs were higher in children with aged ≥6 years than other age groups ( fig. 2 ). radiographic images of the 2 critical cases on admission revealed bilateral lung consolidations ( fig. 3 ). patients were quarantined in the designated hospitals. 12 patients (48%) received antiviral therapy (interferon, arbidol, oseltamivir, lopinavir/litonavir). for antiviral therapy, interferon was the most widely used in 12 (48%) of patients. 13 patients (56%) were treated with empirical antibiotics, and one patient showed bacteriological efficacy following treatment. 2 critical cases (8%) were additionally given invasive (table 3) . as of february 15, 2020, one patient completely recovered and had been discharged. the symptoms on admission were alleviated in 24 (96%). here, we report a cohort of 25 patients with confirmed covid-19. most children were previously healthy and had epidemiological contact history. the majority of pediatric patients had mild symptoms. common symptoms at admission were fever and dry cough. however, a proportion of patients presented initially with digestive symptoms, such as abdominal pain, vomiting, and diarrhea. only 2 patients with severe illness developed ards and required pediatric intensive care unit (picu) admission, invasive mechanical ventilation therapy, and blood purification. all of them had gradually recovered and one patient had been discharged. in our study, most patients had mild diseases including upper respiratory tract infection and mild pneumonia, which were less severe than symptoms reported in adult patients [9, 10] . wang et al [10] demonstrated that 26% of hospitalized adult patients with confirmed covid-19 received icu care, and mortality was 4.3%. however, we only found 2 cases of children who received picu care, and none of the patients in this study died from the disease. the occurrence of mild illness in pediatric patients has no clear explanation. possible explanations may be related to the published data from other outbreaks of coronavirus infection, such as sars and middle east respiratory syndrome (mers). it has been reported that children had a much milder and shorter course of sars infection than adults, and only 3.3% of confirmed patients with mers-cov infection were aged less than 10 years [14] [15] [16] [17] . therefore, children with covid-19 had fewer infections and much milder illness than adults, which may be a feature of sars-cov-2 infection. however, these findings need to be confirmed by large, well-designed studies. however, there were 2 critical cases aged about 1 year in our study. it is known that secondary bacterial pneumonia caused the majority of the deaths in pandemic influenza [18] . in our study, one case had relatively high level of crp with negative blood culture, and another one had the normal level of crp with positive sputum culture. it has been established that several factors contributed to the low prevalence of positive blood or sputum culture results in pediatric pneumonia [19] . furthermore, radiographic images of the 2 critical cases revealed bilateral lung consolidations. thus, both of these 2 cases could be partly attributed to secondary bacterial infection. in addition, patients who were hospitalized with covid-19 had an uneven age distribution. the highest incidence of infection occurred in children was noted aged <3 years. this may be related to special respiratory tract structure infection, or immature immune system at this age, as well as a low compliance of wearing face masks in this age group. chen et al [9] reported that covid-19 clustered within groups of humans in close contact. children aged <3 years need constant care, which would increase the contact and the risk of exposure to sars-cov-2. in fact, a recent study reported nine infant cases and all infections occurred after the family members' infection with sars-cov-2 [12] . our study has several limitations. first, majority of our cases were still hospitalized for medical care, and we cannot therefore describe the full spectrum of this illness. second, our study was limited by unified laboratory examinations. in some mild cases, serum electrolyte, cytokines, coagulation and renal function parameters were not evaluated. third, we have included data for most but not all patients with laboratory-confirmed covid-19 pediatric patients in hubei, which resulted in a limited case size. in conclusion, the present data reveal that children were susceptible to covid-19 like adults, while the clinical presentations and outcomes were more favorable in children. however, children less than 3 years old accounted for majority cases and critical cases lied in this age group, which demanded extra attentions during home caring and hospitalization treatment. pneumonia of unknown etiology in wuhan, china: potential for international spread via commercial air travel outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle coronavirus infections-more than just the common cold the continuing 2019-ncov epidemic threat of novel coronaviruses to global health --the latest 2019 novel coronavirus outbreak in wuhan, china genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan national health commission of the people's republic china clinical features of patients infected with 2019 novel coronavirus in wuhan a novel coronavirus from patients with pneumonia in china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china frist case of severe childhood novel coronavirus pneumonia in china novel coronavirus infection in hospitalized infants under 1 year of age in china pediatric branch of hubei medical association pbow. recommendation for the diagnosis and treatment of novel coronavirus infection in children in hubei (trial version 1) lessons from the past: perspectives on severe acute respiratory syndrome clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (sars) in children severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection case characteristics among middle east respiratory syndrome coronavirus outbreak and non-outbreak cases in saudi arabia from predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness risk factors, and outcomes of bacteremic pneumonia in children all authors declare no conflict of interest. key: cord-316990-kz9782rj authors: han, xuehua; wang, juanle; zhang, min; wang, xiaojie title: using social media to mine and analyze public opinion related to covid-19 in china date: 2020-04-17 journal: int j environ res public health doi: 10.3390/ijerph17082788 sha: doc_id: 316990 cord_uid: kz9782rj the outbreak of corona virus disease 2019 (covid-19) is a grave global public health emergency. nowadays, social media has become the main channel through which the public can obtain information and express their opinions and feelings. this study explored public opinion in the early stages of covid-19 in china by analyzing sina-weibo (a twitter-like microblogging system in china) texts in terms of space, time, and content. temporal changes within one-hour intervals and the spatial distribution of covid-19-related weibo texts were analyzed. based on the latent dirichlet allocation model and the random forest algorithm, a topic extraction and classification model was developed to hierarchically identify seven covid-19-relevant topics and 13 sub-topics from weibo texts. the results indicate that the number of weibo texts varied over time for different topics and sub-topics corresponding with the different developmental stages of the event. the spatial distribution of covid-19-relevant weibo was mainly concentrated in wuhan, beijing-tianjin-hebei, the yangtze river delta, the pearl river delta, and the chengdu-chongqing urban agglomeration. there is a synchronization between frequent daily discussions on weibo and the trend of the covid-19 outbreak in the real world. public response is very sensitive to the epidemic and significant social events, especially in urban agglomerations with convenient transportation and a large population. the timely dissemination and updating of epidemic-related information and the popularization of such information by the government can contribute to stabilizing public sentiments. however, the surge of public demand and the hysteresis of social support demonstrated that the allocation of medical resources was under enormous pressure in the early stage of the epidemic. it is suggested that the government should strengthen the response in terms of public opinion and epidemic prevention and exert control in key epidemic areas, urban agglomerations, and transboundary areas at the province level. in controlling the crisis, accurate response countermeasures should be formulated following public help demands. the findings can help government and emergency agencies to better understand the public opinion and sentiments towards covid-19, to accelerate emergency responses, and to support post-disaster management. as of march 7 2020, the global number of confirmed cases of corona virus disease 2019 (covid19) surpassed 100,000, covering more than 100 countries [1] . covid-19 is a respiratory disease caused by sina-weibo (http://us.weibo.com), often referred to as weibo, is one of the most popular social media platforms in china. weibo had over 516 million active users each month in 2019. this study acquired weibo texts related to covid-19. using weibo application programming interfaces (apis), weibo messages related to covid-19 were collected with "pneumonia" and "coronavirus" as the keyword with timestamps between 00:00 on january 9, 2020 and 24:00 on february 10, 2020. the following information was extracted: user id, timestamp (i.e., the time at which the message was posted), text (i.e., the text message posted by a user), and location information. the original weibo texts contain interfering information such as http hyperlinks, spaces, punctuation marks, hashtags, and @users. text filtering was thus necessary to eliminate noise and improve the efficiency of word segmentation. these types of interfering information were removed by regular expression operations ("re" module) in python (python software foundation, beaverton, or, usa). very short weibo texts (less than four words) and duplicated weibo texts were deleted. that left 1,413,297 weibo messages, including 105,330 texts with geographical location information. a time series analysis of weibo texts was used to investigate the temporal diversification of the number of weibo texts during covid-19. the original time series of social media data fluctuated in cycles of days [20] . to explore further the temporal trend of weibo texts, the original time series was decomposed using the seasonal-trend decomposition procedure based on loess (stl), using statistical product and service solutions (spss inc., chicago, il, usa) software. as expressed in equation (1), the time series can be considered the sum of three components: a trend component, a seasonal component, and a remainder in stl: x t = t t + s t + r t . (1) where x t is the original time series of interest. t t is the trend component. s t is the seasonal component. r t is the residual component. a topic extraction and classification model combining the lda model and the random forest (rf) algorithm was used to hierarchically process covid-19-related weibo texts. existing research has already proved that the lda model has obvious superiority in identifying semantic topic information from massive text automatically [16, 18] . due to their high computational efficiency in both training and evaluation, in addition to their ability to achieve state-of-the-art results, random forests (rf) are frequently used in text classification [21] . the first step was to mine and generalize the topics from the covid-19-related weibo sample using the lda model. then, topic extraction results were utilized as training samples for the rf algorithm to classify the weibo data. as shown in figure 1 , the covid-19-related weibo texts were generalized into seven topics: "events notification", "popularization of prevention and treatment", "government response", "personal response", "opinion and sentiments", "seeking help", and "making donations". a secondary classification was implemented to divide "personal response", "opinion and sentiments", and "seeking help" into 13 more detailed sub-topics, including "fear and worry", "questioning the government and media", "condemning bad habits", "objective comment", "taking scientific protective measures", "blessing and praying", "appealing for aiding patients", "willing to return work", "staying at home and taking necessary precautions", "popularizing anti-epidemic knowledge in family", "seeking medical help", "seeking relief materials", and "other". the processes of topic extraction and classification are shown in figure 2 , including the steps of word segmentation and topic extraction using the lda and rf models. the processes of topic extraction and classification are shown in figure 2 , including the steps of word segmentation and topic extraction using the lda and rf models. the processes of topic extraction and classification are shown in figure 2 , including the steps of word segmentation and topic extraction using the lda and rf models. chinese word segmentation was necessary because there are no obvious separators between chinese words. a python package for chinese text segmentation called "jieba" was utilized. by building a user dictionary including keywords related to covid-19, the package segmented words efficiently. after this process, the most common stop words that lacked valuable information were removed. lda is a bayesian probability model that has three layers-"document-topic-word" [22] , with which to identify semantic topic information in large-scale document sets or corpora. in lda, documents are represented as random mixtures of latent topics, each of which is characterized by a distribution of words [23] . this unsupervised machine learning technique has recently emerged as a preferred method for working with large collections of text documents. the "gensim" package in python was used to implement the lda model. through repeated experiments, the optimal number of initial topics was set as 20. the topic-terminology lists obtained from the lda model contain the vocabularies of each initial topic and the frequency with which those vocabularies occur. the document-topic lists show the probability that each weibo text is associated with each of the initial 20 topics. we assigned each weibo text to the topic that it most closely resembled according to the probabilities in the document-topic lists. based on the topic-terminology lists, 20 topics were generalized into seven ("thirteen" in the secondary classification) by merging similar topics and discarding irrelevant topics. the rf classifier is considered a top-notch supervised algorithm in a wide variety of automatic classification tasks [24] . random forests are a combination of tree predictors, wherein each tree depends on the values of a random vector sampled independently and all trees in the forest have the same distribution [25] . the rf algorithm was used to classify the weibo texts into different topics. this was implemented using a machine learning package called "scikit-learn" in python. based on the document-topic lists, 7000 annotated weibo texts were used as training samples and 1400 annotated weibo texts were used as test sets. the number of classification trees (n estimators) was an important parameter for classification accuracy [23] . we used the out-of-bag (oob) outputs to determine the optimized values of the parameters at 200. kernel density estimation is generally used to detect the intensity of events by generating a smooth surface using a quadratic kernel function [26] . let (s 1 , . . . , s i , . . . ,s n ) be a series of event samples distributed with an unknown densityλ(s), which can be estimated by equation (2): where k is the kernel function, τ is a smoothing parameter called the bandwidth, that is, the search radius within which to calculate density, and s − s i is the distance between s and s i . to identify the hot spots of weibo texts, kernel density estimation was performed using arcgis software. there are two parameters: the kernel search radius (bandwidth) for calculating the density and cell size for the output raster data. a kernel search radius (100-500 km) was used to analyze spatial characteristics at different scales. a cell size of 5 km was used to show the output raster map. spearman's rank correlation coefficient or spearman correlation is a nonparametric measure of rank correlation (statistical dependence between the rankings of two variables). it assesses how well the relationship between two variables can be described using a monotonic function. the spearman correlation coefficient is defined as the pearson correlation coefficient between the rank variables [27] . for a sample of size n, the n raw scores x i ,y i are converted to ranks rgx i , rgy i , and spearman correlation (r s ) is computed as equation (3): where ρ denotes the usual pearson correlation coefficient, but applied to the rank variables. cov(rgx, rgy) is the covariance of the rank variables. σ rgx and σ rgy are the standard deviations of the rank variables. precision, recall, and the f1-measure were used to evaluate the accuracy of the classification. precision is the fraction of correctly classified positive items among the total. recall measures the proportion of actual positives that are correctly identified. the f1-measure is a weighted harmonic mean of precision and recall. higher values of the f1-measure indicate that the classification method is more effective [28] . precision (p), recall (r), and f1-measure (f1) are defined as equations (4)-(6): where t p is the number of correctly classified positive items. f p is the number of incorrectly classified positive items. f n is the number of incorrectly classified negatives. the results of the time series analysis of covid-19-related weibo texts are shown in figure 3 . figure 3a shows the original time series of the number of weibo texts. split by day, it shows that the lowest point of the weibo number on the curve for each day appeared at 06:00, after which the curve began to rise sharply. figure 3b shows part of the cyclical change in the number of covid-19-related weibo posts. the lowest point of cyclical change occurred at 06:00 every day, with two daily peaks around 11:00 and 23:00. figure 3c shows the seasonally adjusted time series, which shows the trend of the number of covid-19-related weibo texts after eliminating the seasonal factor. figure 3d shows the trend component reflecting the trends of the number of covid-19 related weibo. after covid-19 occurred, a slight increase appeared for a short time, then the amount increased sharply on 20 january. the fluctuation reached a peak on 21 january, and then began to decrease but fluctuated until 29 january. the curve rose obviously on 31 january and reached a peak on 1 february. it then steadily fluctuated from 2 february to 5, started to climb on 6 february, and then steadily declined after reaching the highest peak on 7 february. as can be seen from figure 4 , the rising trend of daily weibo numbers and that of the confirmed cases of epidemics is very similar in this early stage. they both rapidly rose around january 19. however, the overall weibo response was quick and higher than the number of confirmed cases. since then, the number of confirmed cases continued to rise, but due to the chinese new year holiday, weibo data remained stable (or even slightly decreased) and continued to rise steadily after 29 january in line with the trend of confirmed cases. as can be seen from figure 4 , the rising trend of daily weibo numbers and that of the confirmed cases of epidemics is very similar in this early stage. they both rapidly rose around january 19. however, the overall weibo response was quick and higher than the number of confirmed cases. since then, the number of confirmed cases continued to rise, but due to the chinese new year holiday, weibo data remained stable (or even slightly decreased) and continued to rise steadily after 29 january in line with the trend of confirmed cases. the spatial distribution of weibo related to covid-19 is shown in figure 5 . the weibo numbers were mainly concentrated in the east-central parts of china, as shown in figure 5a . there were more than 5000 weibo texts in shandong province (the capital of jinan), hubei province (capital of wuhan), henan (capital of zhengzhou), guangdong (capital of guangzhou), sichuan (the capital of chengdu), and jiangsu (capital of nanjing), anhui province (capital of hefei), hebei province (capital of shijiazhuang), beijing, shaanxi (capital of xi'an), liaoning (capital of shenyang), hunan (capital of changsha), and shanxi (capital of taiyuan). figure 5b shows the spatial distribution of the kernel density with a search radius of 200 km, indicating that the high-density areas of weibo related to covid-19 were in wuhan, beijing, shanghai, guangzhou, chengdu, xi'an, and zhengzhou, and presents a continuous trend among the hot points of wuhan, beijing, and shanghai. in order to explore the correlation between public opinion and the epidemic situation, this study used statistical product and service solutions (spss inc., chicago, il, usa) software to perform spearman correlation analysis on the number of relevant weibo texts and confirmed cases in provincial level (number is 34). the descriptive statistics of two variables (the number of weibo texts the spatial distribution of weibo related to covid-19 is shown in figure 5 . the weibo numbers were mainly concentrated in the east-central parts of china, as shown in figure 5a . there were more than 5000 weibo texts in shandong province (the capital of jinan), hubei province (capital of wuhan), henan (capital of zhengzhou), guangdong (capital of guangzhou), sichuan (the capital of chengdu), and jiangsu (capital of nanjing), anhui province (capital of hefei), hebei province (capital of shijiazhuang), beijing, shaanxi (capital of xi'an), liaoning (capital of shenyang), hunan (capital of changsha), and shanxi (capital of taiyuan). figure 5b shows the spatial distribution of the kernel density with a search radius of 200 km, indicating that the high-density areas of weibo related to covid-19 were in wuhan, beijing, shanghai, guangzhou, chengdu, xi'an, and zhengzhou, and presents a continuous trend among the hot points of wuhan, beijing, and shanghai. the spatial distribution of weibo related to covid-19 is shown in figure 5 . the weibo numbers were mainly concentrated in the east-central parts of china, as shown in figure 5a . there were more than 5000 weibo texts in shandong province (the capital of jinan), hubei province (capital of wuhan), henan (capital of zhengzhou), guangdong (capital of guangzhou), sichuan (the capital of chengdu), and jiangsu (capital of nanjing), anhui province (capital of hefei), hebei province (capital of shijiazhuang), beijing, shaanxi (capital of xi'an), liaoning (capital of shenyang), hunan (capital of changsha), and shanxi (capital of taiyuan). figure 5b shows the spatial distribution of the kernel density with a search radius of 200 km, indicating that the high-density areas of weibo related to covid-19 were in wuhan in order to explore the correlation between public opinion and the epidemic situation, this study used statistical product and service solutions (spss inc., chicago, il, usa) software to perform spearman correlation analysis on the number of relevant weibo texts and confirmed cases in provincial level (number is 34). the descriptive statistics of two variables (the number of weibo texts in order to explore the correlation between public opinion and the epidemic situation, this study used statistical product and service solutions (spss inc., chicago, il, usa) software to perform spearman correlation analysis on the number of relevant weibo texts and confirmed cases in provincial level (number is 34). the descriptive statistics of two variables (the number of weibo texts and confirmed cases in provinces) is shown in table 1 . figure 6 shows that the spearman correlation coefficient is 0.84 and significant statistical significance (p = 0.00 < 0.01), so public opinion and epidemic situation have a significant positive correlation with a confidence degree of 0.01. and confirmed cases in provinces) is shown in table 1 . figure 6 shows that the spearman correlation coefficient is 0.84 and significant statistical significance (p = 0.00 < 0.01), so public opinion and epidemic situation have a significant positive correlation with a confidence degree of 0.01. the spatial kernel density characteristics of weibo texts at different scales can be shown by setting different search radii (figure 7) . the result with a search radius of 100 km shows that wuhan was the focus center, surrounded by beijing, shanghai, guangzhou, chengdu, and xi'an, which were star-shaped and supplemented by prominent weibo high-value areas of provincial capitals. the result with a search radius of 200 km reflects that wuhan, beijing, shanghai, and guangzhou are the core, chengdu, xi'an, zhengzhou, jinan, and shijiazhuang are prominent, and the triangular region of wuhan, beijing, and shanghai is in a continuous trend. the result with a search radius of 300 km shows a contiguous regional pattern with core nodes of the beijing-tianjin-hebei junction region, the whole area of the east hubei province and adjacent province region, and the cross-border region of jiangsu, zhejiang, and anhui as well as two independent core regions of guangzhou and chengdu. the result with a search radius of 400 km highlights the contiguous areas in which the cross-border area of hebei-shandong, hubei-hebei, and the jiangsu-zhejiang-shanghai-anhui border area are core nodes, and guangzhou and chengdu are two independent core areas. the result with a search radius of 500 km shows the core area as a triangular region, with beijing, hebei, shandong, henan, hubei, anhui, jiangsu, zhejiang, and anhui connected, and gradually connected with guangdong and sichuan. the spatial kernel density characteristics of weibo texts at different scales can be shown by setting different search radii (figure 7) . the result with a search radius of 100 km shows that wuhan was the focus center, surrounded by beijing, shanghai, guangzhou, chengdu, and xi'an, which were star-shaped and supplemented by prominent weibo high-value areas of provincial capitals. the result with a search radius of 200 km reflects that wuhan, beijing, shanghai, and guangzhou are the core, chengdu, xi'an, zhengzhou, jinan, and shijiazhuang are prominent, and the triangular region of wuhan, beijing, and shanghai is in a continuous trend. the result with a search radius of 300 km shows a contiguous regional pattern with core nodes of the beijing-tianjin-hebei junction region, the whole area of the east hubei province and adjacent province region, and the cross-border region of jiangsu, zhejiang, and anhui as well as two independent core regions of guangzhou and chengdu. the result with a search radius of 400 km highlights the contiguous areas in which the cross-border area of hebei-shandong, hubei-hebei, and the jiangsu-zhejiang-shanghai-anhui border area are core nodes, and guangzhou and chengdu are two independent core areas. the result with a search radius of 500 km shows the core area as a triangular region, with beijing, hebei, shandong, henan, hubei, anhui, jiangsu, zhejiang, and anhui connected, and gradually connected with guangdong and sichuan. figure 8 illustrates the statistical results of the percentage of first-level topics of covid-19. "opinion and sentiments" accounted for 34.42% of all topics. "popularization of prevention and treatment" and "government response" were the second and third most frequent, at 18.97% and 16.29%, respectively. the proportion of "events notification" and "personal response" comprised 13.94% and 12.82%, respectively. "seeking help" and "making donations" then accounted for 2.01% and 1.55%, respectively. figure 8 illustrates the statistical results of the percentage of first-level topics of covid-19. "opinion and sentiments" accounted for 34.42% of all topics. "popularization of prevention and treatment" and "government response" were the second and third most frequent, at 18.97% and 16.29%, respectively. the proportion of "events notification" and "personal response" comprised 13.94% and 12.82%, respectively. "seeking help" and "making donations" then accounted for 2.01% and 1.55%, respectively. a more in-depth analysis of the proportions of sub-topics is presented in figure 9 . "staying at home and taking necessary precautions", "blessing and praying", and "objective comment" were the three most widespread sub-topics, accounting for 23.26%, 20.89%, and 14.99% of texts. the proportion of "taking scientific protective measures" and "fear and worry" comprised 12.48% and 10.47%, respectively. this was followed by "condemning bad habits" and "seeking medical help", which accounted for 6.02% and 4.14%. the proportion of other sub-topics was less than 3%. after computing precision, recall, and f1-measure values, the classification accuracy of the topics and sentiments is presented in table 2 . for the seven topics, the precision was found to be 83% and f1 was 82%. for the 13 sub-topics, the precision and f1 values were 78% and 76%, respectively. a more in-depth analysis of the proportions of sub-topics is presented in figure 9 . "staying at home and taking necessary precautions", "blessing and praying", and "objective comment" were the three most widespread sub-topics, accounting for 23.26%, 20.89%, and 14.99% of texts. the proportion of "taking scientific protective measures" and "fear and worry" comprised 12.48% and 10.47%, respectively. this was followed by "condemning bad habits" and "seeking medical help", which accounted for 6.02% and 4.14%. the proportion of other sub-topics was less than 3%. a more in-depth analysis of the proportions of sub-topics is presented in figure 9 . "staying at home and taking necessary precautions", "blessing and praying", and "objective comment" were the three most widespread sub-topics, accounting for 23.26%, 20.89%, and 14.99% of texts. the proportion of "taking scientific protective measures" and "fear and worry" comprised 12.48% and 10.47%, respectively. this was followed by "condemning bad habits" and "seeking medical help", which accounted for 6.02% and 4.14%. the proportion of other sub-topics was less than 3%. after computing precision, recall, and f1-measure values, the classification accuracy of the topics and sentiments is presented in table 2 . for the seven topics, the precision was found to be 83% and f1 was 82%. for the 13 sub-topics, the precision and f1 values were 78% and 76%, respectively. after computing precision, recall, and f1-measure values, the classification accuracy of the topics and sentiments is presented in table 2 . for the seven topics, the precision was found to be 83% and f1 was 82%. for the 13 sub-topics, the precision and f1 values were 78% and 76%, respectively. to display accurate temporal changes in the different topics, the number of weibo texts for each topic was counted using one-hour time intervals as shown in figure 10 . the topics of "events notification", "popularization of prevention and treatment", "personal response", and "opinion and sentiments" all climbed from 19 january reaching a peak on the 21st. the curve then steadily declined towards the 29th and rose slowly to 1 february. there was a small peak on february 1, then it stabilized and reached a peak again on 5 february. the topics of "government response" and "making donations" started to rise steadily from 20 january, then declined after showing a small peak around 26 january, after which it started to climb on 4 february and reached a peak on 5 february. "seeking help" started to rise suddenly on 22 january showing a small peak before and after wuhan was placed under lockdown on the 23rd, then climbing on 4 february reaching a peak on 6 february and then levelling off. figure 11 presents the time series of all sub-topics except "other". from the perspective of the general trends, the three sub-topics, "questioning the government and media", "staying at home and taking necessary precautions", and "taking scientific protective measures" showed a similar variation tendency over time. the numbers of texts on those three sub-topics improved quickly on 20 january and peaked on the 21st, then gradually decreased but fluctuated towards 29 january, rose obviously on 31 january, and reached a peak on 1 february. since then, the curve has been steadily fluctuating, beginning to rise on 5 february. "fear and worry", "objective comment", and "blessing and praying" climbed from 20 january, reached their peak on 21, fell steadily, then rose again on 5 february and figure 11 presents the time series of all sub-topics except "other". from the perspective of the general trends, the three sub-topics, "questioning the government and media", "staying at home and taking necessary precautions", and "taking scientific protective measures" showed a similar variation tendency over time. the numbers of texts on those three sub-topics improved quickly on 20 january and peaked on the 21st, then gradually decreased but fluctuated towards 29 january, rose obviously on 31 january, and reached a peak on 1 february. since then, the curve has been steadily fluctuating, beginning to rise on 5 february. "fear and worry", "objective comment", and "blessing and praying" climbed from 20 january, reached their peak on 21, fell steadily, then rose again on 5 february and stabilized. "appealing for aiding patients" and "seeking medical help" suddenly increased from 6 february and reached a peak around 8 february. after that, the "appealing for aiding patients" showed a downward trend, and the "seeking medical help" remained a high concern. "popularizing anti-epidemic knowledge in family" and "condemning bad habits" both started to climb on 20 january. after reaching a summit on the 21st, the decline since stabilized. "seeking relief materials" began to rise on 22 january, fell to a peak on 23, then stabilized after rising on 5 february. "willing to return work" had a slight increase and fluctuation since 20 january and has shown a significant upward trend since 4 february. kernel density analysis (radius of 200 km) was carried out on weibo with geographical locations in each topic, as shown in figure 12 . the spatial distribution of "events notification", "popularization of prevention and treatment", "government response", "personal response", and "opinion and sentiments" is similar to the general characteristics of figure 5b , forming hot spots in beijing-tianjin-hebei, shandong, henan, hubei, yangtze river delta, sichuan, and guangdong, but there are differences within the topics. "events notification" takes beijing, wuhan, shanghai, and sichuan as prominent high-value areas, and the areas of the beijing-tianjin-hebei cross border area, east hubei, and the jiangsu-zhejiang-shanghai cross border areas are the main nodes in a continuous pattern. "popularization of prevention and treatment" is presented with beijing, guangzhou, and shanghai as the prominent high values, supplemented by wuhan, chengdu, hefei, zhengzhou, and other high-value areas. "government response" has beijing, sichuan, and xi'an as high values, though zhengzhou, wuhan, changsha, shanghai, guangzhou, haikou, and other cities have responded significantly. "personal response" is prominently reflected by beijing, shanghai, guangzhou, and wuhan, with beijing, wuhan, and shanghai as the center and guangzhou and chengdu as relatively kernel density analysis (radius of 200 km) was carried out on weibo with geographical locations in each topic, as shown in figure 12 . the spatial distribution of "events notification", "popularization of prevention and treatment", "government response", "personal response", and "opinion and sentiments" is similar to the general characteristics of figure 5b , forming hot spots in beijing-tianjin-hebei, shandong, henan, hubei, yangtze river delta, sichuan, and guangdong, but there are differences within the topics. "events notification" takes beijing, wuhan, shanghai, and sichuan as prominent high-value areas, and the areas of the beijing-tianjin-hebei cross border area, east hubei, and the jiangsu-zhejiang-shanghai cross border areas are the main nodes in a continuous pattern. "popularization of prevention and treatment" is presented with beijing, guangzhou, and shanghai as the prominent high values, supplemented by wuhan, chengdu, hefei, zhengzhou, and other high-value areas. "government response" has beijing, sichuan, and xi'an as high values, though zhengzhou, wuhan, changsha, shanghai, guangzhou, haikou, and other cities have responded significantly. "personal response" is prominently reflected by beijing, shanghai, guangzhou, and wuhan, with beijing, wuhan, and shanghai as the center and guangzhou and chengdu as relatively independent high-value areas. "opinion and sentiments" was more prominent in high-value areas around wuhan, followed by the yangtze river delta, beijing-tianjin-hebei, and the pearl river delta urban agglomeration. "seeking help" and "making donations" show totally different characteristics. "seeking help" appears significantly around wuhan and shows a trend of diffusion to the surrounding areas, especially to the north. "making donations" has beijing and hainan as high values and spreads across the country, but is relatively concentrated in urban areas around wuhan, the yangtze river delta region, chengdu-chongqing region, guangzhou, zhengzhou, and even haikou in the south. the spatial distributions of the kernel density estimation of the 13 sub-topics are shown in figure 13 . except for "appealing for aiding patients", "seeking medical help", and "seeking relief materials", the spatial distribution of most topics is similar to the general characteristics of figure 5b . "fear and worry" formed high-value areas in wuhan, shanghai, suzhou, jiaxing, and other cities. "questioning the government and media" is mainly reflected in wuhan, supplemented by the beijing-tianjin-hebei transboundary area, east hubei, the jiangsu-zhejiang-shanghai neighborhood area, and guangzhou and chengdu, two relatively independent high-value areas. "condemning bad habits" is distributed in dots as a whole. beijing is a high-value region with prominent dots, and east hubei, the jiangsu-zhejiang-shanghai cross border area, guangzhou, and wuhan are independent high-value regions. "objective comment" takes wuhan as a prominent high-value area, supplemented by beijing, shanghai, guangzhou, and other high-value areas. "taking scientific protective measures" is a prominent spot-shaped high-value area in beijing, wuhan, and shanghai, and the areas within the beijing-tianjin-hebei neighborhood area, east hubei, the jiangsu-zhejiang-shanghai transboundary areas are the main nodes in a continuous pattern. "blessing and praying" is centered on the contiguous areas of beijing, wuhan, and shanghai, while guangzhou, chengdu, and zhengzhou are relatively independent high-value areas. "appeal for aiding patients" takes wuhan as the center of east hubei as the high-value area, and beijing, shanghai, and the neighborhood area as relatively high-value areas. "willing to return work" shows that beijing, guangzhou, and shanghai are prominent high-value areas, supplemented by wuhan, chengdu, hefei, jinan, and other relatively high-value areas. 'staying at home and taking necessary precautions' is led by wuhan, with beijing, wuhan, shanghai, and guangzhou as the highlighted high-value areas, and the beijing-tianjin-hebei cross border area, east hubei, the yangtze river delta, and the pearl river delta as the main nodes, showing a continuous trend. "popularizing anti-epidemic knowledge in family" is concentrated in wuhan and its surrounding cities, supplemented by relatively high-value areas such as beijing, shanghai, and guangzhou. "seeking medical help" and "seeking relief materials" are prominently concentrated in hubei. "seeking medical help" appears in wuhan and spreads to the surrounding area, especially to the east. the overall distribution of "seeking relief materials" and "seeking medical help" showed a similar distribution trend, with wuhan and its surrounding areas as high-value areas. "appealing for aiding patients" is mainly distributed in wuhan, beijing, shanghai, and other regions. in terms of the time series analysis, the number of relevant weibo texts under the covid-19 event shows a certain periodicity. there are two peaks at which weibo are sent every day. the peak in the morning usually appears around 11 o'clock, and the peak in the evening usually appears around 23 o'clock. in addition, the number of relevant weibo has a good correspondence with the development time node of the coronavirus event (shown in figure 4 ). since the characteristics of person-to-person infections for covid-19 were clarified on 20 january and the central government of china demanded high attention from the public, the number of weibo texts began to rise significantly, and the fluctuations dropped after reaching a peak on the 21st. by the early hours of 31 january, when the world health organization (who) announced the epidemic as a "public health emergency of international concern", the number of texts had risen markedly, and fell back after reaching its peak on 1 february. on 3 february huoshenshan hospital (wuhan) was officially put into use in response to the epidemic. on the afternoon of 5 february, the online help channel in people's daily was opened, and the number of weibo texts began to climb. when the "whistleblower" dr. wenliang li passed away on 7 february the number of weibo reached the highest level, exceeding 110,000 times a day. it then fluctuated, falling back but still at extremely high values. as shown in figure 4 , there were an increasing number of confirmed cases around january 19 which aroused substantial public concern, and weibo posts emerged in large numbers. then, the number of confirmed cases continued to increase while weibo texts maintained a stable and slightly downward trend, because of the chinese new year holiday. after january 29 weibo texts increased, with fluctuations. changing trends in public opinion, as expressed on weibo, reflect actual changes in confirmed cases. furthermore, other scholars obtained similar findings in different disaster events. in terms of the time series analysis, the number of relevant weibo texts under the covid-19 event shows a certain periodicity. there are two peaks at which weibo are sent every day. the peak in the morning usually appears around 11 o'clock, and the peak in the evening usually appears around 23 o'clock. in addition, the number of relevant weibo has a good correspondence with the development time node of the coronavirus event (shown in figure 4 ). since the characteristics of person-to-person infections for covid-19 were clarified on 20 january and the central government of china demanded high attention from the public, the number of weibo texts began to rise significantly, and the fluctuations dropped after reaching a peak on the 21st. by the early hours of 31 january, when the world health organization (who) announced the epidemic as a "public health emergency of international concern", the number of texts had risen markedly, and fell back after reaching its peak on 1 february. on 3 february huoshenshan hospital (wuhan) was officially put into use in response to the epidemic. on the afternoon of 5 february, the online help channel in people's daily was opened, and the number of weibo texts began to climb. when the "whistle-blower" dr. wenliang li passed away on 7 february the number of weibo reached the highest level, exceeding 110,000 times a day. it then fluctuated, falling back but still at extremely high values. as shown in figure 4 , there were an increasing number of confirmed cases around january 19 which aroused substantial public concern, and weibo posts emerged in large numbers. then, the number of confirmed cases continued to increase while weibo texts maintained a stable and slightly downward trend, because of the chinese new year holiday. after january 29 weibo texts increased, with fluctuations. changing trends in public opinion, as expressed on weibo, reflect actual changes in confirmed cases. furthermore, other scholars obtained similar findings in different disaster events. ye found that the developmental trend of dengue disease outbreak events and the trend of the number of weibo texts was highly correlated [11] . there is a synchronization between daily discussion frequencies on weibo and the real-world trend of the covid-19 outbreak. furthermore, the number of epidemic-related weibo texts is also influenced by social events, such as the spring festival holiday, the seal-off of wuhan, and the death of public personalities. time series analysis of various topics shows that the "events notification", "popularization of prevention and treatment", "personal response", "opinion and sentiments", and "government response" are similar to the overall trend of weibo. since 20 january, they have shown an upward trend during the shock. "making donations" and "seeking help" are relatively lagging behind. in the early stage of the covid-19 outbreak, a sudden increase in the confirmed cases caused a shortage of hospital beds. due to this, patients with suspected cases of covid-19 had to be in isolation at home. this demonstrated that the planning and allocation of medical resources was under enormous pressure in the early stage of the epidemic. then, with the establishment of the huoshenshan and leishenshan hospitals (wuhan) in early february, this situation was relieved but not resolved thoroughly. on 23 january wuhan was on lockdown, the "making donations" began to rise steadily and rose significantly after 4 february. "seeking help" started to significantly climb after 4 february and on 5 february, the curve reached its peak when an additional online help channel was opened. the above characteristics indicate that public expressing opinions in emergencies is not random but has periods of silence and noise that are highly volatile and vulnerable to external influences. these results are consistent with previous studies of public responses in emergency situations. the public sentiment in twitter was highly correlated with external factors, such as the impact from official mass media, important social events, extreme weather, and public holidays [29, 30] . the results of spatial kernel density analysis showed that epidemic-related weibo texts were mainly concentrated in hubei province, beijing-tianjin-hebei, the yangtze river delta, the pearl river delta, chengdu-chongqing, and shandong and henan. wuhan, hubei province, as the heart of the outbreak of covid-19, is undoubtedly a hot spot of public concern. most of the other regions mentioned above are densely populated areas and areas of economic development. in 2018, the proportion of the resident population in urban agglomerations such as beijing-tianjin-hebei, the pearl river delta, the yangtze river delta, and chengdu-chongqing reached 30.8%, and the gdp of these areas accounted for 53.7% of the country. high levels of economic development and population density do not only mean that these regions have a convenient transportation infrastructure network, as these factors may increase the possibility of the epidemic spreading among people more rapidly, which makes epidemic prevention and control more difficult. improving emergency management and social governance in urban areas during outbreak responses is an issue that should be emphasized. with regard to the spearman correlation coefficient, the epidemic situation has a high correlation with the spatial distribution of public opinion. thus, the spatial distribution of weibo texts could be related to the severity of the epidemic, the degree of population aggregation, and the level of economic development. these findings are similar to existing research outcomes. for example, the discussions of dengue fever in cyberspace have a strong degree of spatial correlation with real-world epidemic dengue activity [11] . areas with better socioeconomic conditions generally exhibit higher disaster-related twitter usage [29] . on a different spatial scale, the spatial kernel density analysis results ( figure 6 ) indicate that there should be different emergency response strategies at different administrative levels. when the search radius is less than 200 km, the hotspots of weibo texts are mainly at the city level. when the search radius is 300 and 400 km, there is a significant provincial transboundary area spatial agglomeration of weibo texts. thus, enhancing the emergency response at boundary zones among different provinces is the key governance point at the province level. the result with a search radius of 500 km shows a regional spatial hotspot. at the national level, the government should strengthen the response in key urban agglomerations. considering the differences in the risk levels of covid-19 among different spatial scales, establishing a hierarchical emergency response mechanism of "region-province-city" is expected to be of substantial significance. the spatial distribution of each topic is similar to the overall distribution of weibo, but the aggregation degree of each topic is different. the "events notification" and "popularization of prevention and treatment", respectively, show high-value areas with beijing as the core. as the capital and political center of china, beijing is also the headquarters of many public media. a report on the epidemic can play a role in stabilizing public sentiment. therefore, it is crucial for the government to take initiatives to make information transparent and to make an appeal for scientific prevention. the distribution of "government response" and "personal response" is similar, but the intensity and scope of the former is higher than that of the latter. in china, local governments responded very strongly and quickly to covid-19 by following the instructions of the central government. "seeking help" is concentrated around wuhan, and "making donations" is more plentiful than "seeking help" in quantity and is distributed globally, reflecting the emergency relief tradition of china: "when trouble occurs at one spot, help comes from all quarters". "seeking medical help", "seeking relief materials", "appealing for aiding patients", and "popularizing anti-epidemic knowledge in family" are mainly concentrated around wuhan, which is related to the severe epidemic situation and the lack of materials in wuhan. the spatial distribution of 'willing to return work' shows that there is a strong willingness to return to work in first-tier cities such as beijing, guangzhou, shanghai, and chengdu, which have more job opportunities or labor resources. in the early stage of covid-19 in china, the most expressed topic was 'opinion and sentiments', with a proportion of 34.42%. this shows that social media is an important channel through which the public carried out risk perception and shared opinions and emotions during the outbreak of covid-19. the proportion of "events notification", "popularization of prevention and treatment", and "government response" are more than 60%, suggesting that the public are mainly focused on fighting the epidemic, and the timely authoritative information released by the chinese government is targeted and effective. since 23 january over 30 provinces successively launched first-level responses to major public health emergencies within three days. as of 30 january, all provinces, including provinces with a few confirmed cases that were substantially distant from wuhan, had activated a first-level public health emergency response. in the meantime, china strengthened logistics and online platforms to facilitate the online ordering and shopping of goods via contactless delivery. many cities also issued notices regarding "closed management" to communities in their region, calling for avoiding unnecessary transportation and for working from home. these findings show that the government's timely release of targeted and effective authoritative information helped eliminate panic and promote the stability of public sentiment. meanwhile, less than 10% of "seeking help" and "making donations" indicate that more attention should be paid to information directly related to disaster relief: "seeking help" and "making donations" are extremely important, although in small quantities. paying more attention to vulnerable minority groups should also be considered a crucial aspect of social governance. in the sub-topics, "staying at home and taking necessary precautions", "blessing and praying", "taking scientific protective measures", and "popularizing anti-epidemic knowledge in family" accounted for more than 50%, indicating that the public opinion in the early stage of covid-19 was generally positive. in response to the government's requirements, most people stayed at home and actively took protective measures. many people paid tribute to medical staff and prayed for the epidemic to pass. some objective opinions about covid-19 were also expressed by weibo users, for example, "objective comment", "appealing for aiding patients", and "willing to return work". however, 19.17% of weibo texts concerned "fear and worry", "questioning the government and media", and "condemning bad habits", showing negative emotions during the epidemic. people expressed their fears about covid-19, condemned the consumption of wild animals, and expressed anger at the spread of rumors. when "whistle-blower" doctor li wenliang passed away, most people expressed their respect and condolences to him, but some expressed their dissatisfaction, considering that the government's response was too slow or that media reports were untrue. it can be inferred that the timely release and updating of epidemic-related information is an effective measure to avoid public panic and stop the spread of misinformation. this study comprehensively analyzed social media data in the early stage of covid-19 in china and proposed a topic extraction and classification model. the results of the evaluation show that the approach for topic extraction is accurate and viable for understanding public opinions. we obtained seven topics and 13 sub-topics related to covid-19 from weibo texts and analyzed their temporal-spatial distributions. (1) the topics with a proportion of more than 60% were "events notification", "popularization of prevention and treatment", and "government response". in the subtopics, "staying at home and taking necessary precautions", "blessing and praying", "taking scientific protective measures", and "popularizing anti-epidemic knowledge in family" was the most-expressed sub-topic. this finding indicates that timely release of information from the government was helpful in stabilizing public opinion in the early stage of covid-19. (2) the temporal changes in weibo texts are synchronous with the development of the covid-19 outbreak. public opinions during epidemic outbreaks are volatile and vulnerable to external influences. the spatial distribution of covid-19-related weibo texts shows a distribution pattern that beijing-tianjin-hebei, the yangtze river delta, the pearl river delta, and the chengdu-chongqing urban agglomeration were significant high-value areas besides wuhan. this means that the temporal-spatial distribution of opinions was related to the severity of the epidemic, the degree of population aggregation, and the level of economic development. (3) the spatial distribution of public opinions is regionally different and has a scale feature, exhibiting aggregation characteristics in cities, provincial border areas, and key urban agglomeration regions. though in small quantities, the "seeking help" and "making donations" topics can directly provide support for emergency response and post-disaster management. it is suggested that the government should strengthen the public opinion response and epidemic prevention and control in the key epidemic areas, urban agglomerations, and transboundary areas at the province level; in addition, it should formulate accurate response countermeasures following the public's demands in controlling the crisis. this study contributes to existing research on uncovering knowledge regarding emergencies from social media by presenting a reliable approach to mining people's detailed opinions about covid-19. the findings of this research could provide a rapid situational assessment, help decision makers to better understand public opinions toward covid-19, and support analysts in planning and executing appropriate resource allocation. nevertheless, this study has some limitations. first, the specific reasons for the temporal-spatial distribution of covid-19-related weibo texts need further exploration with more information. second, the paper only analyzed texts from social media, while other content, such as pictures and videos in blogs, may also be informative. third, there are manipulated opinions on social media (e.g., "fake news" and "troll opinions"). thus, the better quantification of the noise caused by manipulated opinions needs further investigation. in addition, reducing the noise caused by manipulated opinions in social media data needs to be explored further. with covid-19, which has been characterized as a pandemic by who [31] , we will continually acquire new data from weibo, train and improve the model, analyze the changes and driving mechanisms of public opinion, and provide active references for governmental responses. author contributions: x.h. drafted the manuscript and was responsible for data preparation, data processing, and analysis; j.w. was responsible for the research design, result analysis, and review of the manuscript; m.z. was responsible for spatial distribution analysis and mapping. x.w. was responsible for time series analysis and mapping. all authors have read and agreed to the published version of the manuscript. world health organization. who statement on cases of covid-19 surpassing 100,000 real-time estimation of the risk of death from novel coronavirus (covid-19) infection: inference using exported cases national health commission of the people's republic of china. announcement of the national health commission of the people's republic of china what is the reason for wuhan's "closing the city international opinion praises china's completion of huoshenshan hospital on the 10th two mountain hospitals": china construction three bureau undertakes the maintenance tasks of vulcan mountain and thunder mountain hospital national health commission of the people's republic of china. the latest situation of the new coronavirus pneumonia epidemic situation as of 24:00 on february 10 using social media to mine and analyze public sentiment during a disaster: a case study of the 2018 shouguang city flood in china social media analytics for natural disaster management study on disaster information management system compatible with vgi and crowdsourcing crowdsourcing geographic information for disaster response: a research frontier public behavior response analysis in disaster events utilizing visual analytics of microblog data exploration of spatiotemporal and semantic clusters of twitter data using unsupervised neural networks data-driven geography spatio-temporal distribution of negative emotions in new york city after a natural disaster as seen in social media topic modeling and sentiment analysis of global climate change tweets spatial, temporal, and content analysis of twitter for wildfire hazards use of social media for the detection and analysis of infectious diseases in china behavior of social media users in disaster area under the outburst disasters: a content analysis and longitudinal study of explosion in tianjin 12(th) using social media for emergency response and urban sustainability: a case study of the 2012 beijing rainstorm on-line random forests finding scientific topics latent dirichlet allocation improving random forests by neighborhood projection for effective text classification random forests a kernel density estimation method for networks, its computational method and a gis-based tool more about correlation information extraction: past, present and future. in multi-source, multilingual information extraction and summarization using twitter to better understand the spatiotemporal patterns of public sentiment: a case study in massachusetts, usa social and geographical disparities in twitter use during hurricane harvey world health organization. who characterizes covid-19 as a pandemic this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license acknowledgments: a special acknowledgement should be expressed to the china-pakistan joint research center on earth sciences. the authors declare no conflict of interest. key: cord-254538-vcf44w1k authors: rocha filho, c. r.; pinto, a. c. p. n.; rocha, a. p.; milby, k. m. m.; reis, f. s. d. a.; civile, v. t.; carvas junior, n.; santos, r. r. p.; ramalho, g. s.; trevisani, g. f. m.; ferla, l. j.; puga, m. e. s.; trevisani, v. f. m.; atallah, a. n. title: prognostic factors for clinical course of patients with covid-19: protocol for a rapid living systematic review date: 2020-05-09 journal: nan doi: 10.1101/2020.05.06.20087692 sha: doc_id: 254538 cord_uid: vcf44w1k context and objective: determining prognostic factors in a context of health crises such as the covid-19 scenario may provide the best possible care for patients and optimize the management and the resource utilization of the health system. thus, we aim to systematically review the prognostic factors for different outcomes of patients with covid-19. design and setting: protocol for a rapid living systematic review methodology following the recommendations proposed by the cochrane handbook. methods: we will include prospective and retrospective longitudinal cohorts. in view of the limited amount of information, we will also include case-control studies. we will search pubmed, embase, cochrane central register of controlled trials (central), lilacs, scopus and scielo to identify published, ongoing, and unpublished studies. no language restrictions will be applied. we will perform the critical appraisal of included studies with the quality in prognosis studies (quips) tool and the certainty of evidence will be evaluated using the grading of recommendations assessment, development and evaluation (grade). since the first report issued by the world health organization (who) in early december 2019, the coronavirus disease 2019 (covid-19) outbreak has escalated rapidly (1). up to april 29, 2020, more than 3 million cases of severe acute respiratory syndrome coronavirus-2 (sars-cov-2) infection had been reported from 210 countries and territories; more than 200 thousand people had died (2) . in the scenario of a public health emergency of international concern, the spectrum of illness presentation or its severity profile is one of the most important parameters for an effective decision-making (3) . it helps medical staff during the assessment of patients when the allocation of limited healthcare resources is a reality. it also helps within the effort to provide the best possible care for patients while ensuring the sustainability of the health system (1, 3) . prognostic factors are known as good indicators to predict disease progression and severity level (3) . currently, it is well established that the case fatality rate for sars-cov-2 infection increases with age and number of comorbidities (1). other factors, such as the decline of the immune function (4), proinflammatory profile (5) and alterations in the angiotensin i converting enzyme 2 (ace2) (4) are also being described by relevant clinical reports as predictors for covid-19 progression. despite the promising data, to the best of our knowledge the predictive capacity and reliability of these potential indicators has not been properly clarified yet. thus, the purpose of this rapid living systematic review is to identify the evidence about prognostic factors in patients with covid-19, considering the following research questions: the protocol of this systematic review was registred in the prospective register of systematic reviews (prospero) platform (crd42020183437). to conduct the rapid living systematic review, we will employ abbreviated systematic review methods. compared with the methods of a systematic review, the review team will apply the following methodological shortcuts (6): no specific searches of grey literature; no independent screen of abstracts. types of studies we will include prospective and retrospective longitudinal cohorts. in view of the limited amount of information, we will also include case control studies. we will not include cross sectional studies, as it is not possible to determine prognosis from this design. we will include studies that have evaluated patients with confirmed diagnosis of infection of sars-cov-2. we will include studies performed since november 2019. no language restrictions will be used in the selection. we will search medline via pubmed, embase via elsevier, cochrane library -cochrane central register of controlled trials (central), scopus, portal regional bvs -lilacs, and webof science, using relevant descriptors and synonyms, adapting the search to the requirements of each database. we will also search in the world health organization international clinical trials registry platform (who ictrp) and clinicaltrials.gov aiming to . cc-by-nc 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 9, 2020. . https://doi.org/10.1101/2020.05.06.20087692 doi: medrxiv preprint identify published, ongoing, and unpublished studies. finally, we will use the technique of snowballing, searching the lists of references of the included studies. we will use the terms related to the problem of interest and the filter for prognostic studies provided by wilczynski and haynes (8) . the search strategy in medline via pubmed is shown in table 1 . the search strategy above will be used in medline via pubmed and will be adapted to the specifications of each database. based on pre-specified eligibility criteria, two authors will select the studies for inclusion in the review (kmm and acpnp). when duplicated studies are found in more than one database (studies using the same participants and different outcome measurements or using different time points for the assessments), both reports will be included, but the two reports will be considered as parts of only one study. when duplicated reports are found, e.g. studies with the same participants, with the same outcome measurements and using the same time points for the assessments, the report with the smaller sample size will be excluded. after removing duplicate studies and reports, the authors will read the study titles and abstracts. studies that clearly do not match the inclusion criteria for the review will be excluded. the selected studies . cc-by-nc 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 9, 2020. . will then be fully read for further scrutiny. the reasons for exclusion of the studies that are fully read will be presented. disagreements between authors regarding study inclusion will be resolved by the third author (apr). to optimize the process of screening and selection of studies, we will use rayyan application (9) . two authors (acpnp and crrf) will independently extract data. discrepancies or disagreements will be solved by a third author (apr). a predefined form will be used to extract data from included studies. the form will include the following information: (i) the patients to assess the feasibility of performing a meta-analysis, we will also extract data for each primary and secondary outcome measure: (i) total number of patients (in each group); (ii) number of events in each group (for dichotomous outcomes);(iii) mean, standard deviation, standard error, median, interquartile range, minimum, maximum, 95% confidence interval (ci) (for continuous outcomes); (iv) p value; (v) hazard ratios with their respective standard errors or confidence intervals (95%). we will perform critical appraisal of included studies with quality in prognosis studies (quips) (10) scale as recommended by cochrane collaboration. we will evaluate the certainty of evidence using the grading of recommendations assessment, development and evaluation (grade) (11) . grade judgement is based on the overall risk of bias, consistency of the . cc-by-nc 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 9, 2020. . https://doi.org/10.1101/2020.05.06.20087692 doi: medrxiv preprint results, directness of the evidence, publication bias and precision of the results for each outcome. the grade profiler software, available online, will be used to summarize our findings on the quality of evidence (12) . assessment of risk of bias (acpnp and apr), and assessment of the quality of evidence (vtc and ncj) will be performed by two review authors. all the disagreements in the assessment of the risk of bias or quality of evidence will be solved through discussion or, if required, by consulting with a third author (ana). we will perform analyses according to the recommendations of cochrane, and the cochrane prognosis methods group, and we will use review manager 5 to perform meta-analysis when possible for hazard or odds ratios. we will pool hazard ratios (unadjusted (crude) or adjusted) or odds ratio with their standard errors for hospital admission, intensive care unit admission and/or respiratory support for adult inpatients with covid-19 and mortality, using generic inverse variance method with randomeffects model. we will also pool incidence results (for prognostic factors) with their respective confidence intervals (95%) by the inverse variance method with a random-effects model, using the dersimonian-laird estimator for τ 2. we will adjust data by freeman-tukey double arcosen transformation and confidence intervals will be calculate by the clopper-pearson method for individual studies. for these data, we will perform proportion meta-analysis using rstudio © software, with the "meta" package (version 4.9-6) and "metaprop" function. for studies that do not provide an hr and associated standard error (se), we will use information and results reported in the text, tables, and kaplan-meier (k-m) curves. we will contact the principal investigators of included studies asking for additional data, or to clarify issues regarding the studies. in the absence of a reply from the authors, we will expose the data in a descriptive manner avoiding imputation. . cc-by-nc 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 9, 2020. . https://doi.org/10.1101/2020.05.06.20087692 doi: medrxiv preprint we will employ the cochran's q test to assess the presence of heterogeneity considering a threshold of p value < 0.1 as an indicator of whether heterogeneity is present. in addition, we will assess statistical heterogeneity by examining the higgins i 2 statistic following these thresholds: this rapid living review will systematically evaluate the best available evidence to identify the risk and protective factors of covid-19, which we expect will help the front line on their decision making processes. while some data (13) have shown older adults are at higher risk for worse outcomes, other studies have raised additional questions on whether factors such as the decline in immune function (4), proinflammatory profile (5) and alterations on the angiotensin i converting enzyme 2 (ace2) (4) could also constitute risk factors for worse outcomes. at the same time, our review aims to clarify the uncertainty over which characteristics could constitute protective factors once a person has been exposed to sarsto ensure the quality of the results, we will follow the cochrane handbook of systematic reviews recommendations (7) . if possible, we plan to pool data into meta-analysis for reducing the probability of type 2 error within the comparisons. potential limitations for this study include the possibility of finding biased studies which can make them unsuitable for clustering or metaanalysis, or small sample studies that do not allow us to provide precise estimates. we believe that the strengths of this rapid systematic review include the transparency, the strict methods, the evaluation of the quality of evidence, and the extensive and more sensitive searches. this being said, we will be able to identify the current available evidence, differentiating the prognostic factors for each stage of the disease and to provide important . cc-by-nc 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 9, 2020. . https://doi.org/10.1101/2020.05.06.20087692 doi: medrxiv preprint information for clinical decision-making on coronavirus disease 2019 (covid-19) that has recently emerged and caused a deadly pandemic. this systematic review protocol was written as per the prisma-p guidelines (14). . cc-by-nc 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may 9, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may 9, 2020. . https://doi.org/10.1101/2020.05.06.20087692 doi: medrxiv preprint coronavirus disease 2019 (covid-19) bmj best practice world health organization. coronavirus disease 2019 (covid-19) estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china covid-19 and older adult the reality of getting old cochrane rapid reviews interim guidance from the cochrane rapid reviews methods group 2020 cochrane handbook for systematic reviews of interventions developing optimal search strategies for detecting clinically sound prognostic studies in medline: an analytic survey rayyan-a web and mobile app for systematic reviews assessing bias in studies of prognostic factors grading quality of evidence and strength of recommendations grade's software for summary of findings tables, health technology assessment and guidelines or (epidemia de pneumonia por coronavírus em wuhan) or (epidemia de pneumonia por coronavírus em wuhan de 2019-2020) or (epidemia de pneumonia por novo coronavírus de 2019-2020) or (epidemia pelo coronavírus de wuhan) or (epidemia pelo coronavírus em wuhan) or (epidemia pelo novo coronavírus (2019-ncov)) or (epidemia pelo novo coronavírus 2019) or (epidemia por 2019-ncov) or (epidemia por coronavírus de wuhan) or (epidemia por coronavírus em wuhan) or (epidemia por novo coronavírus (2019-ncov)) or (epidemia por novo coronavírus 2019) or (febre de pneumonia por coronavírus de wuhan) or (infecção pelo coronavírus 2019-ncov) or (infecção pelo coronavírus de wuhan) or (infecção por coronavirus 2019-ncov) or (infecção por coronavírus 2019-ncov) or (infecção por coronavírus de wuhan) or (infecções por coronavírus) or (pneumonia do mercado de frutos do mar de wuhan) or (pneumonia no mercado de frutos do mar de wuhan) or (pneumonia por coronavírus de wuhan) or (pneumonia por novo coronavírus de or (surto pelo novo coronavírus (2019-ncov)) or (surto pelo novo coronavírus 2019) or (surto por 2019-ncov) or (surto por coronavírus 2019-ncov) or (surto por coronavírus de wuhan) or (surto por coronavírus de wuhan de 2019-2020) or (surto por novo coronavírus (2019-ncov)) or (surto por novo coronavírus 2019) or (síndrome respiratória do oriente médio) or (síndrome respiratória do oriente médio (mers)) or (síndrome respiratória do oriente médio (mers-cov)) or (síndrome respiratória do oriente médio por coronavírus) or mh:c01 corona virus*) or (coronavirus (covid-19)) or (2019 novel coronavirus disease) or (covid-19 pandemic) or (covid-19 virus infection) or (coronavirus disease-19) or (2019 novel coronavirus infection) or (2019-ncov infection) or (coronavirus disease 2019) or (2019-ncov disease) or (covid-19 virus disease) or (severe acute respiratory syndrome coronavirus 2) or (wuhan coronavirus) or (wuhan seafood market pneumonia virus) or (covid19 virus) or (covid-19 virus) or (coronavirus disease 2019 virus) or corona virus*) or (coronavirus (covid-19)) or (2019 novel coronavirus disease) or (covid-19 pandemic) or (covid-19 virus infection) or (coronavirus disease-19) or (2019 novel coronavirus infection) or (2019-ncov infection) or (coronavirus disease 2019) or (2019-ncov disease) or (covid-19 virus disease) or (severe acute respiratory syndrome coronavirus 2) or (wuhan coronavirus) or (wuhan seafood market pneumonia virus) or (covid19 virus) or (covid-19 virus) or (coronavirus disease 2019 virus) or key: cord-355531-1cpli8kv authors: liang, jingbo; yuan, hsiang-yu title: the impacts of diagnostic capability and prevention measures on transmission dynamics of covid-19 in wuhan date: 2020-04-06 journal: nan doi: 10.1101/2020.03.31.20049387 sha: doc_id: 355531 cord_uid: 1cpli8kv background: although the rapidly rising transmission trend of covid-19 in wuhan has been controlled in late february 2020, the outbreak still caused a global pandemic afterward. understanding wuhan covid-19 transmission dynamics and the effects of prevention approaches is of significant importance for containing virus global transmission. however, most of the recent studies focused on the early outbreaks without considering improvements in diagnostic capability and effects of prevention measures together, thus the estimated results may only reflect the facts in a given period of time. methods: we constructed a stochastic susceptible-exposed-infected-quarantined-recovered (seiqr) model, embedding with latent periods under different prevention measures and proportions of documented infections to characterize the wuhan covid-19 transmission cross different stages of the outbreak. the epidemiological parameters were estimated using a particle filtering approach. results: our model successfully reproduced the dynamics of the wuhan local epidemic with two peaks on february 4 and february 12 separately. prevention measures determined the time of reaching the first peak and caused an 87% drop in the r_t from 3.09 (95% ci, 2.10 to 3.63) to 0.41 (95% ci, 0.18 to 0.66). an improved diagnostic capability created the second peak and increased the number of documented infections. the proportion of documented infections changed from 23% (95% ci, 20% to 26%) to 37% (95% ci, 33% to 41%) when the detection kits were released after january 26, and later up to 73% (95% ci, 64% to 80%) after the diagnostic criteria were improved. coronavirus disease 2019 (covid19) , identified originally in the city of wuhan, hubei province in china in 2019 december, has been causing concern of global pandemic 1 -2 . as the disease continues to grow, many studies have characterized disease transmission dynamics and estimated certain important epidemiological properties, including the basic reproductive number r0 and the number of actual infections [1] [2] [3] [4] [5] [6] [7] . the estimation of transmissibility r0 is important because the level of control measures required to contain the outbreak can thus be obtained 6 . although a wide range of the r0 was produced after the disease dynamics occurred in wuhan, most of the studies focused on early transmission dynamics 1, 4, 6, 8 . characterizing the transmissibility after initial periods when the control measures have been put in place and the covid-19 detection capability has been improved is important to understand the effect of those measures 4 . however, none of the studies has considered the changes in both prevention measures and detection capability. as of january 22, 2020, the virus has infected 571 individuals in china, including around 74.4 percent of cases within wuhan 9 10 . transportation restrictions were implemented in wuhan after january 23 11 . many studies have illustrated the effects of wuhan lockdown on disease spreading to other places 6 12 13 14 ; however, few studies investigated the contribution of transportation restriction in local transmission dynamics 15 . changes in detection capability can largely affect the proportion of documented infections. a recent study had shown that the number of cases was largely underestimated and more than 80% of infections were not documented during the initial periods when covid-19 was just discovered to be the causal agent 16 . after the introduction of new commercial kits to provide a higher diagnosis rate 17 and the improvements of diagnostic criteria 18 (figure 1 ), the capacity of diagnosis has been gradually increased. the proportion of documented infections raised as the capacity of diagnosis progressed. e.g., a higher diagnosis or healthcare capacity indicates that the proportion of documented infections can be higher given the same amount of infected persons; consequently, along with the epidemic growth, a higher number of cases can thus be documented. one of the benefits of using transmission models, such as sir or seir, to estimate r e is that many complex epidemiological factors and control measures can be naturally incorporated. the inclusion of the infectious incubation period, during which an infected individual has no symptoms, but can infect others, may affect transmissibility estimation. studies have shown the presence of the incubation infections of covid-19 19 . specifically, a recent study reported a 20-year-old woman from wuhan passed it to five of her family members but never got physically sick herself 20 . another study in germany reported that a case with mild symptoms infected two colleagues when they worked together 21 . given the transmission by asymptomatic and mildly symptomatic persons, it indicates that time from exposure to infection may be shorter than the incubation period. however, in most studies with seir models, an assumption was made that the incubation cases had weak . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org /10.1101 /10. /2020 or no infectious capacity 8 22 , which may not be able to reflect the incubation infectious of the covid-19. in this study, we have developed a stochastic susceptible-exposed-infected-quarantinedrecovered (seiqr) model, embedding with latent periods and the transportation restriction control under the different proportion of documented infections to describe the wuhan covid-19 transmission pattern after the initial outbreak stage. our model was an extension of the classic seir model by including quarantined status. we also demonstrated that transportation restriction and quarantine measures were able to contain the epidemic growth. we fitted our model using the daily number of newly infected covid-19 cases in wuhan, hubei province, china. the daily numbers of newly confirmed cases from january 11 to march 10 were collected from the bulletins of wuhan municipal health commission 9 . . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint description of the seiqr epidemic model. figure 2 : seiqr model structure. the population was divided into five compartments: s (susceptible), e (exposed and partly asymptomatically infectious), i (symptomatically infectious), q (quarantined), and r (recovered). a fraction of symptomatic infections were confirmed and documented by hospitals. we constructed a seiqr model to illustrate the spreading of covid-19 within the wuhan local population ( figure 2 ). s, e, i, q and r represented the number of individuals in susceptible, exposed (partly asymptomatically infectious), infectious (symptomatically infectious), quarantined, and recovered statuses with total population size n = s + e + i + q + r. here, the wuhan population was assumed to be fixed as 11 million. we made assumptions that exposed individuals became asymptomatically infectious after the latent period, and only symptomatically infectious individuals can be quarantined. the seiqr equations were derived as the following: cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint consistent with the assumption of most seir models, where δ e,t was defined as the number of individuals that were newly infected but not yet symptomatic from s to e status during time t to time t+1, δ i,t was the number of newly symptomatic infectious cases from e to i, δ q,t the newly quarantined cases from i to q, and δ r,t the newly recovered individuals from i to r. we assumed that δ e,t , δ i,t , δ q,t , and δ r,t followed poisson distributions: where σ was the incubation rate, determining the rate of exposed individuals becoming symptomatic cases. η was the latent time. q was the quarantine rate. γ was the recovery rate, which can be expressed as γ = 1/(tau − 1/σ), with assuming a fixed generation time tau equal to 10 days. β t was the transmission rate on day t. in this model we assumed wuhan transportation restriction policy modulated β t through an exponential relationship with a lag effect of lag1 = 6 days 4 : where pol t was an indicator for transportation restriction policy (e.g. pol t = 0 means there was no transportation restriction on that day (before january 23) 11 , otherwise pol t = 1 ), and α was the transportation restriction effect coefficient. β 0 was the basic transmission rate without transportation restriction. we included an observation model to link wuhan's incidence and hospital documented cases. the estimation of the number of hospital daily confirmed cases (hosp_confirm) t+lag2 given the simulated δ i,t was derived with a delay of lag2 = 6 days by equation (4), and the proportion of documented infections could be calculated by equation (5): . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint where p(m|i) represented the probability that a person with covid-19 seek medical attention, which was assumed as 0.8; p(hosp_diag|i) t was the hospital-diagnose rate, the probability that a person infected with covid-19 would be diagnosed as covid-19 case by the hospital; (proportion of documented infections) t , the probability that a person infected with covid-19 would be confirmed and documented by hospitals, could be estimated by the conduct of p(m|i) and p(hosp_diag|i) t . since the hospital diagnostic rate progressed by time, p(hosp_diag|i) t was assumed to have three different values: p(hosp_diag|i)_1 when the test kits were limited (before january 27), p(hosp_diag|i)_2 when the kits were enough but the diagnostic criteria were biased 7 (january 27 to february 11), and p(hosp_diag|i)_3 when the kits were enough and the diagnostic criteria were accurate 18 (after february 12) . the values of p(hosp_diag|i)_1,2,3 were estimated after fitting the model to the hospital's daily confirmed cases. the recorded cases on january 27, february 12, and february 13 were over-documented than the actual new infections due to the sudden change of detection capability happened on these days, we filled these points with smoothing values on the model fitting process. after obtaining the posterior simulation matrix of parameters and model hidden compartments, r t , the effective reproductive number at time t, was calculated using the next-generation matrix approach. following the same notation as in the study by diekmann et al. 23 , we obtained the transmission matrix t and the transition σ. each element in t represents the average newly infected cases in exposed (e) in a unit time transmitted by a single infected individual in exposed (e) or infectious group (i), which can be calculated as β t [( 1 σ −η 1 σ )] s t or β t s t . σ represents the transitions between cases in different groups. r t can be calculated as the first eigenvector using the following formula: where β t , s t , σ, q, γ, and n were defined as the same as the previous sections. the posterior distributions of epidemiological parameters were obtained using an smc algorithm implemented in the nimble r library. the priors for parameters in the modelfilter frameworks were drawn from the following distributions: for the incubation time,1/σ~u(1,10); for the latent time,η~u(1,7); 1/q~u(1,10), for the time from onset to quarantine; β 0~u (0,1) for transmission rate baseline; and α~n(0,1), for transportation control coefficient. . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint to assess convergence, we performed three independent runs of the smc algorithm set to 100,000 iterations of 1000 particle samples each. we then calculated the effective sample size (ess) and gelman-rubin convergence diagnostic statistic across the three independent chains. the spread of the wuhan local epidemic followed an exponential growth before february 4, and a short decreasing period. this decreasing period was followed by a second high peak occurring on february 12. our stochastic seiqr model successfully reproduced the dynamics with two peaks ( figure 3a) . specifically, the rise of the second peak was mainly caused by improved diagnostic criteria with delayed case ascertainment 18 . the predicted hospital cumulative numbers were higher than the documented cases until delayed cases being documented on february 12 ( figure 3b ). the time from illness onset to quarantine was estimated to have a mean of 5.65 days (95% ci, 1.91 to 9.76), the mean incubation time was estimated to be 5.57 days (95% ci, 2.67 to 7.95), and the mean latent time was estimated to be 2.92 days (95% ci, 1.09 to 5.28) (table1). . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint both transportation restriction and quarantine measures had a significant impact on the effective reproductive number r e . the value of r e was calculated using the disease transmission baseline with transportation restriction coefficient and time to quarantine from onset ( table 1 ). the initial r e was estimated to be 3.09 (95% ci, 2.10 to 3.63) during the early epidemic period ( figure 4) ; however, after the transportation restriction implemented, r e was dropped 87% to 0.41 (95% ci, 0.18 to 0.66). quarantine of symptomatic cases was a critical part of prevention efforts. without the quarantine effect, the estimated r e increased to 4.28 (95% ci, 3.72 to 6.63) based on equation (6). . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint a sharp rise in cumulative cases on february 12 can be explained by the improved diagnostic criteria with delayed case ascertainment. after the outbreak occurred, the detection capability of covid-19 in wuhan has been improved several times (figure 1 ). these improvements greatly affect the documented proportions of infected cases. e.g., from january 11 to january 26, the estimated proportion of documented infections was 0.23 (95% ci, 0.20 to 0.26), then increased to 0.37 (95% ci, 0.33 to 0.41) since the kits production enhanced after january 26, finally rose to 0.73 (95% ci, 0.64 to 0.80) as the diagnostic criteria became more accurate after february 12 ( figure 5a ). the simulated cumulative infectious with symptomatic onset were correlated but higher than the documented cases ( figure 5b ). care should be taken in interpreting the speed of growth in cases during the early outbreak, given an increase in the proportion of documented infections relating to the availability and use of testing kits has progressed. our results suggested a sharp rise in cumulative cases on february 12 can be explained by the delayed case being documented using new diagnostic criteria. this is the first study to demonstrate the effects of transportation restriction measures together with the improvement of diagnostic capacity on the transmission dynamics in wuhan. we found that the proportion of the documented infections increased as the availability of test kits and the accuracy of diagnostic progressed by time. our initial estimated proportion of documented infections was consistent with a recent study 16 . however, the estimated proportion increased up to around 73% after february 12. also, our results showed that transportation restrictions in wuhan successfully contained disease growth. these findings may provide some suggestions for further analyses. unlike most studies with the proportion of documented infections being fixed over time, our estimated proportion was close to the prediction in the study of ruiyun et al. (14%) 16 at the initial stage, but increased to around 70% by progress. diagnostic capability strongly influenced the proportion of documented infections. during the early outbreak in wuhan, a large proportion of cases were not able to be confirmed as the test kits were insufficient 16 . on january 26, the state food and drug administration (sfda) approved four new coronavirus detection kits from four companies 17 to increase the supply of detection kits, and our estimated proportion of documented infections increased to 37% after then. on february 12, the diagnostic criteria were enhanced by including clinically diagnosed cases 18 . the undocumented infections may be of mild illness and insufficiently serious about seeking treatment 16 . we found the estimated undocumented proportion of infections was less than 30% after february 12. this finding suggested that the proportion of mild symptomatic cases were likely to be around or less than 30%. our estimation of r t during the curve up period aligns with other recent studies 24 (3.11 by jonathan et al. 6 , 3.15 by tian et al. 8 , 1.4 to 3.9 by li et al. 1 ). furthermore, our results showed both transportation restriction and quarantine measures were able to limit virus transmission. transportation restrictions, including halting all forms of public transportation, trains, and air travel, sharply reduced social contacts and virus transmission rates. concurrent with the implementation of transportation measures, personal awareness of the virus and protective behavior (e.g., wearing facemasks, washing hands frequently, social distancing) also increased. although our study did not exclude the effects caused by changes in public response coming along with the transportation measures, we found r e dropped by 87% after the introduction of transportation restriction. these findings are in agreement with the results of kucharski et al. 7 and ruiyun et al. 16 . besides, quarantine of the symptomatic infections was also essential in curbing the epidemic 25 . under the actual condition in wuhan (with quarantine), the estimated time from symptom to quarantine was around 5.65 days at the initial stage, possibly due to a lack of sufficient resources during this period. our estimated incubation time was consistent with other recent studies 1 8 19 26 . given the estimated incubation period as 5.57 days but the latent period as 2.92 days, there can be a lot of transmissions that occurred during the asymptomatic infectious period. how to reduce possible contact during the asymptomatic infectious period is one of the major tasks to contain the virus spread. our results were in agreement with the advocation from the government that people who had close contact with confirmed cases need to be quarantined for at least 14 days 27 . overall, our studies suggested an improved capability with intensive transportation control and quarantine measures, can be able to contain covid outbreak in a city. . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint figure s1 . prediction of the number of newly symptomatic infectious (a), newly exposed individuals (b), newly quarantined cases(c), newly recovered cases (d) in wuhan. . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint figure s2 . prediction of the cumulative number of individuals in s (susceptible), e (exposed and partly asymptomatically infectious), i (symptomatically infectious), q (quarantined), and r (recovered) statuses separately. . cc-by-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.31.20049387 doi: medrxiv preprint early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia covid-19: towards controlling of a pandemic preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak pattern of early human-to-human transmission of wuhan early transmissibility assessment of a novel coronavirus in wuhan novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions articles early dynamics of transmission and control of covid-19: a mathematical modelling study early evaluation of the wuhan city travel restrictions in response to the 2019 novel coronavirus outbreak wuhan municipal health commission national health commission of the people's republic of china the state council_the people's republic of china the effect of human mobility and control measures on the covid-19 epidemic in china. science (80-. ) the impact of transmission control measures during the first 50 days of the covid-19 epidemic in china risk for transportation of 2019 novel coronavirus disease from wuhan to other cities in china the impact of traffic isolation in wuhan on the spread of substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2). science (80-. ) sfda approves new coronavirus nucleic acid detection reagent_chinese government website incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china presumed asymptomatic carrier transmission of covid-19 transmission of 2019-ncov infection from an asymptomatic contact in germany the serial interval of covid-19 from publicly reported confirmed cases the construction of nextgeneration matrices for compartmental epidemic models reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (sars-cov-2) outbreak feasibility of controlling covid-19 outbreaks by isolation of cases and contacts the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application is a 14-day quarantine period optimal for effectively controlling coronavirus disease key: cord-273692-jwqrfb6h authors: golinelli, d.; nuzzolese, a. g.; boetto, e.; rallo, f.; greco, m.; toscano, f.; fantini, m. p. title: the impact of early scientific literature in response to covid-19: a scientometric perspective date: 2020-04-18 journal: nan doi: 10.1101/2020.04.15.20066183 sha: doc_id: 273692 cord_uid: jwqrfb6h background. in the early phases of a new pandemic, identifying the most relevant evidence and quantifying which studies are shared the most can help researchers and policy makers. the aim of this study is to describe and quantify the impact of early scientific production in response to covid-19 pandemic. methods. the study consisted of: 1) review of the scientific literature produced in the first 30 days since the first covid-19 paper was published; 2) analysis of papers' metrics with the construction of a computed-impact-score (cis) that represents a unifying score over heterogeneous bibliometric indicators. in this study we use metrics and alternative metrics collected into five separate categories. on top of those categories we compute the cis. highest cis papers are further analyzed. results. 239 papers have been included in the study. the mean of citations, mentions and social media interactions resulted in 1.63, 10 and 1250, respectively. the paper with highest cis resulted "clinical features of patients[...]" by chaolin huang et al., which rated first also in citations and mentions. this is the first paper describing patients affected by the new disease and reporting data that are clearly of great interest to both the scientific community and the general population. conclusions. the early response of scientific literature during an epidemic does not follow a preestablished pattern. being able to monitor how communications spread from the scientific world toward the general population using both traditional and alternative metric measures is essential, especially in the early stages of a pandemic. worldwide, covid-19 is showing critical issues in the response of health systems, which are put to the test by this emergency. together with the fast spread of a new pathogen, we are witnessing a relatively new phenomenon, defined as "infodemic" by the who (who, 2020). an "infodemic" represents the uncontrolled spread of false or "exaggerated" information (i.e. misinformation) relating to the pathogen or epidemic, which might determine an unpredictable response by the population. this response can translate into an increase in the concern of the population towards the epidemics, and even outright panic. this can also lead to public unrest or other consequences that can be difficult to control. misinformation, like a virus itself, can be easily transmitted from person to person. the who has therefore highlighted that the spread of unconfirmed or incorrect information can be very dangerous for public health 1 . the information relating to infectious outbreaks have a complex dynamic and occur at various levels. on the one hand, the scientific community is quickly activated on producing evidence, studies and articles that describe the new pathogen, the first cases, the methods of transmission, etc. for example, the first scientific article related to covid-19 was indexed on pubmed on january 14th 2020 (bagoch 2020) . in it, authors reported that a cluster of pneumonia of unknown aetiology was published on promed-mail, possibly related to contact with the huanan seafood wholesale market in wuhan, china, and warned for the potential international spread via commercial air travel. on the other hand, the communication channels of the official sources (who, ministries of health, etc.) are committed to collecting, filtering and transmitting true and confirmed information, in order to provide a public service and to contain the population response. in turn, traditional media (newspapers, periodicals, etc.), both digital and printed, resume the news and disseminate it. at this level, misinformation can occur. that is, the creation -more or less fraudulent -of false news that can determine an emotional response in the population, creating false beliefs or panic. the last level of communication is on social media (e.g. twitter, facebook, instagram, etc.), where individual citizens can share news and messages, communicating their feelings and their point of view on the subject. these levels of communication are interconnected. for example, the sudden onset of a new virus forces the scientific community to describe the index-case, by publishing a paper in a scientific journal. subsequently, if it deems it necessary, the ministry of foreign affairs of one country can indicate the risk for people travelling to the area where the case occurred. a newspaper can later resume the news, which can be shared and commented by individual users on social media. in this framework, misinformation might be the most dangerous and contagious aspect, as underlined by the who. similarly to disease outbreak analysis, a viral content on the internet can also be seen as a chain reaction. therefore, as misinformation can be considered as a public health threat, in the early stages of a pandemic it is important to contain false information and to disseminate correct data that may come primarily from scientific studies. at the present, it is essential that methodologically solid information is disseminated, both to avoid misinformation and to spread only real world evidence, possibly through peer-reviewed articles. this despite the fact that the peer review at this stage is done less rigorously because of the emergency. it is important that the information gaps are filled, but it is also important to contrast the infodemic with solid information, news and data. summing up, in the early phases of a new pandemic, the scientific and academic community is quickly activated on producing evidence and scientific articles. however, traditional media and social networks resume and disseminate information in a proper or inappropriate way. identifying the most relevant evidence produced by the scientific community and quantifying which studies and which data are shared the most in the world can help researchers and policymakers in focusing on the most relevant ones and controlling the epidemic. this can be done by capturing and measuring traditional citations of scientific papers but also through the use of innovative and alternative scientometrics tools. scientometrics is the 1 field of study which measures and analyses scientific literature, including the measurement of the impact of research papers and the use of such measurements in policy and management contexts. alternative metrics (a.k.a. "altmetrics") are gaining increasing interest in the scientometrics community as they can capture both the volume and quality of attention that a research work receives online. altmetrics are nontraditional research impact measures that are based on web-based environments. altmetrics measurement derives from the social web and is increasingly used as an early indicator of research impact (p. wouters et al. 2015; j. ravenscroft et al. 2017; l. bornmann, r. haunschild 2018; nuzzolese et al. 2019) . the aim of this study is to describe and quantify the impact -in terms of dissemination of knowledge -of early scientific production in response to the covid-19 pandemic. we conducted a twofold study which includes a review of the early scientific literature and a scientometric analysis. specifically, the study consisted of the two following phases: 1) review of the scientific literature produced in the first 30 days since the first covid-19 paper was published on medline/pubmed; 2) identification of the digital object identifiers (doi) for each paper and analysis of citations and metrics measures to quantify their communicative impact (i.e. scientometric analysis). the initial search was implemented on february 20, 2020 in medline/pubmed. the search query consisted of terms considered by the authors to describe the new epidemic: [coronavirus* or pneumonia of unknown etiology or covid-19 or ncov]. although the virus name was updated to sars-cov-2 by the international committee on taxonomy of viruses on february 11th 2020 (gorbalenya 2020), we performed the search using the term "ncov" because it was presumed that no one, between february 11 and 13, would have used the term "sars-cov-2". to achieve the highest sensitivity, we decided to use only a combination of keywords avoiding mesh terms. asterisks are used to truncate words, so that every ending after the asterisks was searched. we placed a language restriction for english, without other limits. furthermore, we limited the search to the following time-span: from december 1, 2019 to february 13, 2020. due to the extraordinary rapidity with which scientific papers have been electronically published online (i.e. epub), it may happen that some of these have indicated a date later than february 13 2020 as publication date. a two-stage screening process was used to assess the relevance of identified studies. for the first level of screening, only the title and abstract were reviewed to preclude waste of resources in procuring articles that did not meet the minimum inclusion criteria. titles and abstracts of studies initially identified were checked by two independent investigators (e.b. and f.r.). all citations deemed relevant after title and abstract screening were procured for subsequent review of the full-text article. a form was developed to extract study characteristics such as publication date, publication type, aim of the study, and authors' nationality. in order to determine the impact of scientific papers and the attention received by the scientific community and the general public for each paper we traced altmetrics measures. altmetrics, meant as a subset of scientometrics, firstly first introduced by priem et al. (priem 2012) , is the study and use of all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april 18, 2020. . scholarly impact measures based on activity in online tools and environments. the term has also been used to describe the metrics themselves and includes also non-traditional research impact measures. altmetrics measurement derives from the social web and is increasingly used as an early indicator of research impact (cf. section 1). the sources used for altmetrics are heterogeneous and include -beside traditional citations in peer-reviewed papers -mentions and citations in blogs, wikipedia, twitter or facebook or reader counts on social reference managers and bookmarking platforms. in this study we use the altmetrics provided by plum analytics 2 (plumx) which is one of the leading platforms that provides altmetrics (nuzzolese 2019) . it is a provider of alternative metrics created in 2012 and covers more than 52.6m of artifacts, metrics and sources of metrics that are collected into five separate categories: (i) citations: contain both traditional citation indexes such as scopus, as well as citations that help indicate societal impact such as clinical or policy citations. (ii) mentions: measures activities such as news articles or blog posts about research. mentions is a way to tell that people are truly engaging with the research (examples are blog posts, comments, reviews, wikipedia links, and news media); (iii) social media interactions: includes tweets, facebook likes, etc. that reference the research. social media can help measure attention. social media can also be a good measure of how well a particular piece of research has been promoted; (iv) captures: indicate that someone wants to come back to the work. captures can be a leading indicator of future citations (examples are bookmarks, code forks, favorites, readers, and watchers); (v) usage: a signal if anyone is reading an article or otherwise using a research. all the papers selected in the first stage of this study (i.e. during scientific literature review) have been collected by using their corresponding dois as the key for querying plumx, as reported in boetto et al. 2020 . for each paper the citation count, the number of mentions on social media, the number of visits and clicks on online platforms, the number of readers on academic social networks (e.g. mendeley), and the mentions on blogs, wikis and traditional media/press were collected (table 1) . this allowed us to calculate, for each paper, the above reported five metric categories (citations, captures, mentions, social media, and usage). subsequently, given that the different categories have a different weight, as explained in boetto et al. 2020 , a comprehensive impact score (cis) was calculated. in fact, each paper has different numbers for each category considered and a standardized measure is needed to fairly quantify the communicative impact. cis represents a unifying score over heterogeneous bibliometric indicators and categories. after cis was computed for all the retrieved papers we used the zscore for obtaining standard values and the arithmetic mean for the average. intuitively, the z-score is a numerical measure that gives us an idea of how far from the mean a data point is. hence, a z-score is a scalar value that can be positive (i.e. the score is above the mean) or negative (i.e. is below the mean). finally, we computed the quantiles of the resulting cis values and identified a threshold t. we report descriptive statistics related to the different metric categories of the selected papers (mean, standard deviation -sd, median, and confidence interval -ci). we considered the papers in the upper quantile (95%) for each metric category (citations, capture, mentions, social media and usage). for each category we also reported the value (e.g. number of citations or mentions) associated with the 95% quantile. then, for papers above the identified cis threshold, we described the main study characteristics in terms of publication date, publication type, aim of the study, and authors' nationality. . all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april 18, 2020. . the search conducted yielded 442 potentially relevant papers. after deduplication and pertinence screening, 239 papers met the eligibility criteria for review and scientometric analysis (figure 1 ). 63.6% of the papers (152 out of 239) were editorials, commentaries or letters (mainly reported data). 10.5% of the papers (25 out of 239) were secondary papers, mainly narrative reviews, which collected the knowledge available up to that point on some specific topics (i.e. genomics of the virus, transmissibility, etc.). the remaining 25.9% (62 out of 239) were original primary studies: among these, case reports accounted for 42%, while in vitro or in vivo studies or genomic studies accounted for 21% of the total. the remaining primary studies were cohort studies, case control studies and surveys. as reported in table 2 , the mean of "citations" for each paper resulted in 1.63 (median: 0; max: 82). the mean of "mentions" per paper in blogs and news was 10 while the mean of "social media" interactions resulted in 1,250 per paper. on average each paper had 1.69 "captures" and 0.07 "usages", as defined in the methods section. the papers positioned in the upper quantile (95%) for each category considered are reported in table 1 in the supplementary materials. for citations, the papers in the 95% quantile are [supplementary materials, table 1 ids: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] . table 1 ids: 1, 2, 3, 8, 9, 12, 13, 14, 15, 16, 17] . for social media interactions, the papers in the 95% quantile are [supplementary materials, table 1 ids: 1, 2, 3, 7, 8, 9, 12, 14, 15, 16, 18] all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april 18, 2020 . . https://doi.org/10.1101 to obtain a unique and omni-comprehensive metric score we calculated the cis. the association of papers to their corresponding cis values is published in a spreadsheet, which is available online 3 . the following statistics provide a summary of the recorded cis values (figure 2 ): max=5.21, min=-0.21, mean=0.02, median=-0.19. the threshold identified is t=1.04. such a threshold is the value of the 95% quantile and allows us to record 8 out of 239 papers (figure 1, figure 2 ) as potentially more impactful. lower values for t are not significant for capturing relevant works (as explained in boetto et al. 2020 ). the resulting 8 most impactful studies' main features are described in table 3 . among those, 6 papers are case reports, 1 methodological study, 1 editorial. first authors come from china (n = 6), usa (n=1) and germany (n=1). the 8 papers' main topics are: case/s description (n=5), outbreak investigation (n=2) and 1 genomic study. in particular, the 3 articles with higher cis were "clinical features of patients infected with 2019 novel coronavirus in wuhan, china" (huang 2020) , "first case of 2019 novel coronavirus in the united states" (holshue 2020) , and "a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster" (chan 2020) , as reported in table 3 . the three papers -1 cohort study and 2 case studies -were all published in high impact journals (the lancet and the new england journal of medicine). the first paper, by chaolin huang et al. (huang 2020) , was published online on february 15th 2020 and reports a cohort of 41 patients with laboratory-confirmed sars-cov-2 infection. patients had serious, sometimes fatal, pneumonia and were admitted to the designated hospital in wuhan, china, by jan 2, 2020. the study shows that the time between hospital admission and ards (acute respiratory distress syndrome) was as short as 2 days and that at this stage the mortality rate was high (15%). also, the authors recommend that faecal and urine samples should be tested to exclude a potential alternative route of transmission. the second paper, by michelle l. holshue et al. (holshue 2020) , was published online on january 31th 2020 and reports the clinical features of the first reported patient with sars-cov-2 infection in the united states. the authors describe key aspects of the case including the decision made by the patient to seek medical attention after reading public health warnings about the outbreak, the identification of possible sars-cov-2 infection, which allowed for prompt isolation of the patient and subsequent laboratory confirmation of covid-19, as well as for admission of the patient for further evaluation and management. the third paper with the highest comprehensive impact score is the study by chan j. et al. (chan 2020) in which the authors report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to shenzhen, guangdong province, china, after a visit to wuhan, and an additional family member who did not travel to wuhan. the aim of this study was to describe and quantify the impact of early scientific production in response to the covid-19 pandemic. in an increasingly connected world, tracing the traditional and non-traditional metrics measures of scientific papers can help to understand and evaluate their communicative impact on the researchers' community and general population. the covid-19 pandemic is taking place in an historical period characterized by high rapidity of communications, through traditional media, internet, and social networks. at the present, the levels of digitalization and the speed of data and information exchange at a global level are incredibly higher than in any previous epidemics and pandemics (e.g. sars in 2003 (e.g. sars in , h1n1 in 2009 . it is therefore of primary importance to quickly identify the most relevant information, data and scientific evidence because this can be useful to guide policymakers, healthcare professionals and the general population in a time of crisis. when there is no consistent scientific data nor strong evidence, it is particularly relevant to identify which scientific information is capturing the attention. this can be done using several alternative bibliometric tools (i.e. altmetrics) that can be useful for tracing which scientific papers bounce more and have a greater impact, particularly in the early phases of an epidemic, when traditional metrics (e.g. citations) may not be as timely, relevant or exhaustive. from our analysis, the three papers with the highest number of citations are those with the greatest impact on the scientific community. in fact, all of them are original studies with data from "the field", describing the clinical characteristics, the clinical course and the transmission routes of covid-19 cases. "mentions" are the number of mentions retrieved in news or blog posts. except for one paper on the clinical characteristics of covid-19 patients in the first chinese outbreak (the same with the highest number of citations), it is interesting to note that the other two most mentioned papers describe the first cases of sars-cov-2 infection in europe (germany) and the united states. clearly those are interesting aspects for a wider audience than the scientific community alone. the "social media" interactions are consistent with the dynamics of traditional citations and mentions. the papers about the first cases outside china (especially in the united states) resonate the most, alongside the studies that describe the covid-19 clinical manifestations. "captures" is an alternative metric indicating that someone wants to go back to the paper or wants to deepen the topic. from our results and in our opinion, the most "captured" papers are those with appealing titles using evocative words, for example "the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china" (hui 2020) or "outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle" (lu 2020 ). the first two papers are commentaries, while the third one is a genomic study on the origin of sars-cov-2. with the cis we unify and identify what paper is showing more attention both from the scientific community and general public. this is because the cis in a standardized way, beside citations also catches the impact of other traditional media and social networks. again, the paper with highest cis resulted "clinical features of patients infected with 2019 novel coronavirus in wuhan, china" by chaolin huang et al. (huang 2020 ) and published on the lancet, which rated first also in citations and mentions. intuitively, this is the paper with the greatest impact because it is the first (january 24th 2020) describing a population of patients affected by the new disease, identifying its epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes. these data and information are clearly of great interest to both the scientific community and the general population. scientific citations, newspapers and blogs usually report more reliable information, whereas the most "sensational" things, with less technical details and a more appealing presentation -even within scientific works -bounce back on social media, as expected. as recently reported in this viewpoint (merchant 2020) , it is therefore mandatory for scientific communication to be effective not only for professionals but also for the general public. this is crucial for counteracting misinformation which is regarded as a real threat for public health and to promote information exchange that could facilitate any public health intervention. in fact, sharing the best possible scientific evidence is crucial for systems' preparedness, as well as it is also essential to monitor social media to avoid misinformation. in conclusion, being able to monitor how communications spread from the scientific world toward the general population, using both traditional and alternative metric measures, seems extremely important, especially in the early stages of a pandemic. traditional citation indexes such as scopus, and citations that help indicate societal impact such as clinical or policy citations. number of mentions retrieved in news articles or blog posts about research. the number of mentions included in tweets, facebook likes, etc. that reference a research work. an indication that someone wants to come back to the work. a signal that anyone is reading an article or otherwise using a research. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april 18, 2020 . . https://doi.org/10.1101 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april 18, 2020 . . https://doi.org/10.1101 the new york times (2020). 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'situation report -1 situation report -22 situation report -51 the metric tide: correlation analysis of ref2014 scores and metrics (supplementary report ii to the independent review of the role of metrics in research assessment and management)'. london: higher education funding council for england (hefce) clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study supplementary data are available at research evaluation journal online. key: cord-294385-6dlgv3tb authors: tong, xin; ning, mingzhe; huang, rui; jia, bei; yan, xiaomin; xiong, yali; wu, weihua; liu, jiacheng; chen, yuxin; wu, chao title: surveillance of sars‐cov‐2 infection among frontline health care workers in wuhan during covid‐19 outbreak date: 2020-08-20 journal: immun inflamm dis doi: 10.1002/iid3.340 sha: doc_id: 294385 cord_uid: 6dlgv3tb introduction: as an emerging infectious disease, coronavirus disease 2019 (covid‐19) has rapidly spread throughout worldwide. health care workers (hcws) on frontline directly participated in the diagnosis, treatment, and care of covid‐19 patients are at high risk of getting infected with the highly infectious severe acute respiratory syndrome coronavirus 2 (sars‐cov‐2), the novel coronavirus that causes covid‐19. in nanjing drum tower hospital, a total of 222 medical staff went to wuhan city for support. in this study, we aimed to determine any nosocomial infection among our cohort of hcws who worked in wuhan. methods: throat swab samples were obtained for rna testing on day 1 and 14 of their quarantine upon their return to nanjing. radiological assessments were performed by chest computed tomography (ct) on day 14 of their quarantine. the blood was collected from 191 hcws between may 12 and may 15. anti‐sars‐cov‐2 immunoglobulin m (igm) and igg antibody responses were determined by a chemiluminescence immunoassay. results: all the throat swab specimens were found negative for sars‐cov‐2. the radiological analysis revealed that there was no typical chest ct scan of covid‐19 among 222 hcws. consistently, anti‐sars‐cov‐2 igm or igg was also found to be negative among 191 hcws. conclusions: there was no nosocomial infection of sars‐cov‐2 among our cohort of the frontline hcws, suggesting that zero occupational infection is an achievable goal with appropriate training, strict compliance, and psychological support for the frontline hcws. severe acute respiratory syndrome coronavirus 2 (sars-cov-2) is an emerging infectious disease, first described in wuhan, china, has rapidly spread throughout worldwide. 1 because of efficient transmission of sars-cov-2, health care workers (hcws) on frontline directly involved in the diagnosis and treatment of coronavirus disease 2019 patients are at high risk of getting an infection of sars-cov-2. 2 the ever-increasing number of covid-19 cases, overwhelming workload, the depletion of personal protection equipment (ppe), physical fatigue, and psychological stress during the early outbreak has resulted in at least 22 073 cases of covid-19 among hcws. 3 a study from china center for disease control and prevention (cdc) showed that as of 17 february 2020, 3.8% confirmed covid-19 cases were among hcws. 4 a report from italy revealed 11% of covid-19 cases were hcws. 5 all the evidence suggested a high risk of occupational infection of sars-cov-2. in china, a large number of hcws from various provinces in china went to wuhan city for support. in nanjing drum tower hospital, a tertiary hospital in nanjing city of china, a total of 222 medical staff, including 63 doctors and 159 nurses stayed in three medical centers in wuhan city, respectively. four medical staffs worked in first people's hospital of jiangxia district from 26 january to 17 march, 56 medical staffs served in tongji hospital from 9 february to 31 march while 162 medical professionals first worked at wuhan no.1 hospital and later transferred to hubei general hospital from 13 february to 31 march. in this study, we aimed to determine any nosocomial infection among our cohort of hcws who worked in wuhan. prior to their departure from nanjing, hcws received a group training of sars-cov-2, including the transmission route, the diagnosis, the clinical manifestation, and treatment guidance of covid-19. upon their arrival to wuhan, they received an infection prevention and control training program held by the local hospitals, including detailed procedures of donning, doffing, and disposal of ppe as well as hand hygiene. the ppe includes n95 respirator, coverall gown, goggle/face shield, and glove. during their stay in wuhan, these hcws stayed in the contaminated area every 4 h/d, including performing aerosol-generating procedures, collecting or handling specimens, providing care for covid-19 patients, and sharing conversations with covid-19 patient within a one-meter reach. no hcws reported covid-19 clinical symptoms during their stay in wuhan. to further identify any possible infection of sars-cov-2, the seroprevalence, nucleic acid assay, and chest computed tomography (ct) of sars-cov-2 among 222 hcws were performed when they were back to nanjing. upon their return to nanjing, they started a 14-day quarantine. throat swab samples were obtained for rna testing on day 1 and 14 of their quarantine. viral rna was tested using real-time reverse transcriptional polymerase chain reaction kit (bgi genomics, beijing, china) as recommended by the chinese cdc following who guidelines. 1 radiological assessments were performed by chest ct on day 14 of their quarantine. the blood was collected from 191 hcws between 12 may and 15 may. anti-sars-cov-2 immunoglobulin m (igm) and igg antibody responses were determined by a chemiluminescence immunoassay-based test developed by yhlo biotech co, ltd, (shenzhen, china). this study was approved by the ethics committee of our hospital. written informed consent was waived by the ethics commission due to a public health outbreak investigation. the mean age of these hcws was 32 years (range: 24-58) and 57 (25.67%) were male. they worked 4 to 6 hour shifts for an average of 5.6 days a week. all the throat swabs collected on day 3 and 14 of the quarantine were found negative for sars-cov-2. the radiological analysis revealed that there was no typical chest ct scan of covid-19 among 222 hcws (table 1) . 6 consistently, anti-sars-cov-2 igm or igg were also found to be negative among 191 hcws, negative response to sars-cov-2 was detected in the 112 control hcws with no history of exposure to covid-19 patients. as positive controls, 21 serum samples from covid-19 patients had high titers of either sars-cov-2 igm or igg (figure 1 ). based on these results, there was no nosocomial infection of sars-cov-2 in our cohort. our results revealed that zero occupational infection is an achievable goal among our frontline hcws. this could be attributed by several reasons. first, comprehensive site training and an electronic reminder of infection prevention and control programs were carried out. second, our established infection prevention and control program was strictly adhered and constantly surveilled. third, our hcws were given substantial psychological and nutritional support during their stay in wuhan. our study also has several limitations. first, during their stay in wuhan, the throat swab samples were not collected routinely to determine any possible viral infection of sars-cov-2 among frontline hcws. second, blood samples were only collected at a one-time point when they were back in nanjing for the anti-sars-cov-2 igm and igg testing. to conclude, although covid-19 is a highly communicable disease, zero occupational infection of sars-cov-2 is an achievable goal with appropriate training, strict compliance, and psychological support for frontline hcws. this study was supported by the medical science and technology development foundation, nanjing department of health (ykk19056), nanjing medical science, and technique development foundation (qrx17141). early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia supporting the health care workforce during the covid-19 global epidemic novel coronavirus (covid-19) situation the novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19)-china serum samples from control hcws without covid-19 exposure were served as a negative control (n = 112). serum samples from covid-19 patients were used as positive controls (n = 21). reference specified by the manufacturer (<10 au/ml) hcw, health care worker integrated surveillance of covid-19 in italy clinical features of patients infected with 2019 novel coronavirus in wuhan surveillance of sars-cov-2 infection among frontline health care workers in wuhan during covid-19 outbreak the authors declare that there are no conflict of interests. xt, yc, and cw contributed to the study concept and design, xt, yc, rh, and bj contributed to the acquisition of data, analysis and interpretation of data, and critical revision of the manuscript. mn, jl, and ww contributed to investigation and methodology. xy and yx contributed to resources and software. the data that support the findings of this study are available from the corresponding author upon reasonable request. http://orcid.org/0000-0002-1657-010x key: cord-258113-mnou31j3 authors: wang, yaping; liao, baolin; guo, yan; li, feng; lei, chunliang; zhang, fuchun; cai, weiping; hong, wenxin; zeng, yu; qiu, shuang; wang, jian; li, yueping; deng, xilong; li, jianping; xiao, guangming; guo, fengxia; lai, xunxi; liang, zhiwei; wen, xueliang; li, pinghong; jiao, qian; xiang, fangfei; wang, yong; ma, chenghui; xie, zhiwei; lin, weiyin; wu, yanrong; tang, xiaoping; li, linghua; guan, yujuan title: clinical characteristics of patients infected with the novel 2019 coronavirus (sars-cov-2) in guangzhou, china date: 2020-05-19 journal: open forum infect dis doi: 10.1093/ofid/ofaa187 sha: doc_id: 258113 cord_uid: mnou31j3 background: the clinical manifestations and factors associated with the severity of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infections outside of wuhan are not clearly understood. methods: all laboratory-confirmed cases with sars-cov-2 infection who were hospitalized and monitored in guangzhou eighth people’s hospital were recruited from january 20 to february 10. results: a total of 275 patients were included in this study. the median patient age was 49 years, and 63.6% had exposure to wuhan. the median virus incubation period was 6 days. fever (70.5%) and dry cough (56.0%) were the most common symptoms. a decreased albumin level was found in 51.3% of patients, lymphopenia in 33.5%, and pneumonia based on chest computed tomography in 86%. approximately 16% of patients (n = 45) had severe disease, and there were no deaths. compared with patients with nonsevere disease, those with severe disease were older, had a higher frequency of coexisting conditions and pneumonia, and had a shorter incubation period (all p < .05). there were no differences between patients who likely contacted the virus in wuhan and those who had no exposure to wuhan. multivariate logistic regression analysis indicated that older age, male sex, and decreased albumin level were independently associated with disease severity. conclusions: most of the patients infected with sars-cov-2 in guangzhou, china are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. in december 2019, cases of unexplained pneumonia related to the huanan seafood market began appearing in wuhan, hubei province, china [1] . it was subsequently determined that the pathogen was a novel coronavirus, and the gene sequence was closely related (with 88% identity) to 2 bat-derived severe acute respiratory syndrome (sars)-like coronaviruses [2] . the virus is the seventh member of the known coronavirus family that is able to infect humans [3] . as the virus is similar to sars coronavirus (sars-cov), which is a member of the subgenus sarbecovirus (beta-cov lineage b) [4] , it was subsequently renamed sars-cov-2. the pneumonia caused by the virus was named coronavirus disease 2019 (covid19) . the outbreak of sars-cov-2 infection has become a global health concern. as of may 6, 2020, there were 82 885 documented cases in china and 4633 deaths due to the disease (http:// my-h5news.app.xinhuanet.com/h5activity/yiqingchaxun/ index.html). although the number of infected persons has increased rapidly, clinical investigations of patients, especially those outside of wuhan, are lacking. chen et al. [5] studied the clinical features of 99 patients with covid-19 and found that sars-cov-2 was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ards). several recent studies [6, 7] have indicated that the rapid spread of the virus is due to human-to-human transmission and have found evidence of familial cluster cases. wang et al. [8] studied 138 hospitalized patients with covid-19 in wuhan: 41% of the patients were suspected to have been infected by in-hospital transmission of sars-cov-2, 26% of the patients required treatment in the intensive care unit (icu), and the mortality rate was 4.3%. as of may 6, 2020, guangdong province, china, has the most confirmed cases outside of hubei (http://wsjkw.gd.gov.cn/ xxgzbdfk/content/post_2988153.html). guangzhou is the economic and health care center of guangdong province and is one of the most popular cities for migrant workers. the guangzhou eighth people's hospital is the major center for the care of patients with new emerging infectious disease in guangdong. thus, the purpose of this study was to examine the epidemiological, clinical, and laboratory characteristics of patients with sars-cov-2 infections in guangzhou. the records of patients with covid-19 diagnosed by the guangdong center for disease control (cdc) who were admitted to the guangzhou eighth people's hospital from january 20, 2020, to february 10, 2020, were retrospectively reviewed. the study was approved by guangzhou eighth people's hospital ethics committee, and written informed consent was obtained from patients involved before enrollment when data were collected retrospectively. for the analyses, patients were divided into those with severe disease and those with nonsevere disease based on world health organization (who) interim guidance [9] . patients were also divided into an "imported" group and a local group. imported group patients were those who had been to wuhan within 14 days or who were residents of wuhan before admission, and the local group included patients who had not left guangdong during the past month. the incubation period was defined as the duration of time from the contact with the source of transmission to the onset of symptoms. fitness for discharge was based on abatement of fever for at least 3 days, with improvement of chest computed tomography (ct) findings and viral clearance in upper respiratory tract nasopharyngeal samples. data were obtained from the patient medical records database and included demographic and epidemiological characteristics, clinical symptoms and signs, and laboratory test and radiographic imaging results. the laboratory test results collected included complete blood cell count (cbc), tests of coagulation function and liver and kidney function, electrolyte levels, c-reactive protein (crp), procalcitonin (pct), lactate dehydrogenase (ldh), and creatine kinase (ck). the primary radiographic assessment was chest ct. if there were missing data or clarifications were needed, the information was obtained by communicating directly with the patient, the attending doctor, or other data providers. all data used in the analyses were checked by 2 doctors. the end points included the rate of severe infections, complications, the need for icu admission, the need for mechanical ventilation, and death. these end points were not applied to a fixed time range (ie, within 28 days) as clinical observations were still in progress. all patients who were transferred to the guangzhou eighth people's hospital were diagnosed by a throat swab nucleic acid test administered by the guangdong cdc. on admission, respiratory samples were taken to determine viral load by a reverse transcription polymerase chain reaction (rt-pcr) assay. in brief, upper respiratory throat swab samples were collected from all patients after admission, and the samples were stored in virus medium. an rna isolation kit (da an gene co., ltd, guangzhou, china) was used to extract viral rna from the samples. rt-pcr was performed using the rna detection kit for sars-cov-2 (da an gene co., ltd). the orf1ab and n genes of sars-cov-2 were the amplification target regions. the receiver operating characteristics (roc) curve method was used to determine the internal standard reference cycle threshold (ct) value, which was determined to be 40. if the ct value was ≤40, the sample was considered positive; if the value was >40, the sample was considered negative. as all the continuous variables in this study were not normally distributed, continuous variables were presented as median and interquartile range (iqr). categorical variables were described as numbers and percentages. the wilcoxon-mann-whitney u test was used to test differences between groups for continuous variables, as they did not follow a normal distribution. the chi-square test was used to examine differences of categorical variables. variables with a p value <.10 in bivariate analysis were included in the multivariate logistic regression analysis. forward stepwise binary logistic regression was used for multivariate analysis. variables with a p value <.05 were retained in the final regression model. spss, version 20.0 (ibm corp., armonk, new york, us), was used for data analysis. a total of 275 patients with laboratory-confirmed sars-cov-2 infections were included in the analysis. the median age of the patients (iqr) was 49 (34-62) years, 41.3% were at least 50 years old, 47.7% were males, and 33.1% had at least 1 coexisting medical condition. none of the patients described exposure to the huanan seafood market, and none of the patients were health care workers. based on the who definition [9] , 230 (83.6%) patients had nonsevere disease and 45 (16.4%) patients had severe disease. compared with the nonsevere group, patients with severe disease were older and had a much higher frequency of coexisting medical conditions. additionally, the frequency of imported cases was higher in the severe group than in the nonsevere group (80.0% vs 60.4%; p = .013) ( table 1 ). the median incubation time for all patients was 6 days; however, the incubation time was significantly shorter in the severe group than in the nonsevere group (4 days vs 6 days; p = .004). the median interval between hospital admission and symptom onset was 5 days, but it was significantly longer in the severe group than in the nonsevere group (5 days vs 4 days; p = .034). in all patients, the most common symptoms at the onset of illness were fever (70.5%), dry cough (56%), sputum production (22.6%), and sore throat (13.8%). diarrhea was rare, with only 2.5% of patients reporting this symptom. compared with the nonsevere group, the frequencies of fever, dry cough, sputum production, fatigue, and shortness of breath were much higher in the severe group (table 1) . patients were also divided into imported and local disease groups by epidemiological history. there were no significant differences in the parameters described above between the 2 groups; however, family cluster infections were more common in the local group (supplementary table 1 ). at admission, leukopenia was found in 16.7% of patients, neutropenia in 18.2%, and lymphopenia in 33.5% (table 2 ). other routine blood indices were within the normal ranges. however, the percentages of patients with increased leukocytes and neutrophils and lower levels of lymphocytes were greater in the severe group than in the nonsevere group. in addition, ldh, ck, and aspartate aminotransferase (ast) levels on admission (iqr) were higher in the severe group than in the nonsevere group: incubation period, d 6 (3-9) 6 (3-10) 4 (3) (4) (5) (6) .004 interval between admission to hospital and symptom onset, d 4 (2-7) 4 (2-7) 5 (2-9.5) .034 data are presented as median (interquartile range) and no. (%). p values denote the comparison between the nonsevere group and the severe group. a hepatitis b infection denotes that hepatitis b surface antigen tested positive, with or without elevated alanine or aspartate aminotransferase levels. b cancers refers to any malignancy. all cases were stable disease. albumin (alb) level was decreased in 51.3% of all patients, and more patients in the severe group had decreased alb levels than in the nonsevere group (93.1% vs 45.2%; p < .001). among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, pct, ldh, ck, alb, ast, and d-dimer were associated with disease severity. thus, these variables were included in the multivariate logistic regression. the multivariate analysis indicated that age 50-64 years (reference, 15-49 years), male sex, and decreased alb level were independently associated with disease severity (table 3) . on admission, 38 (14%) patients in the nonsevere group had no abnormalities on chest ct scan, whereas all patients in the severe group had pneumonia. bilateral pneumonia (67.6%) and multiple small patchy shadows and ground-glass shadows (62.1%) were the most common findings (table 2) . pneumonia was defined as appearance of symptoms of fever, coughing, or dyspnea and chest ct showing multiple small patchy shadows and interstitial changes in 1 or both lungs at an early stage, which then progressed to multiple ground-glass shadows and infiltration shadows on both lungs. compared with the nonsevere group, the severe group was more likely to have bilateral involvement (95.6% vs 61.3%; p < .001) and pleural effusion (15.6% vs 3.9%; p = .007). chest ct scan patterns were similar between the imported and local disease groups (supplementary table 2 ). upper respiratory throat swab samples were collected from all patients at admission, and 151 specimens were positive for the orf1ab gene, with a median ct value of 34. of these patients, 25.8% had higher viral loads (ct values < 30), whereas 74.2% had low viral loads (ct values, 30 to 40). a total of 158 specimens were positive for the n gene, with a median ct value of 32, and 41.8% of the specimens had higher viral loads. the levels of viral rna were not different between the severe and nonsevere groups. there was no significant difference in viral load between imported and local disease cases (supplementary table 2 ). during hospitalization, the most common complication was pneumonia (86%), followed by ards (7.6%) and disseminated intravascular coagulation (dic; 1.5%). the rates of all complications were higher in patients with severe disease than in those with nonsevere disease. a total of 237 patients (86.2%) received empiric antibiotic treatment, 226 (82.2%) received antiviral therapy, 64 (23.3%) received systemic corticosteroid treatment, and 26 (9.5%) received immunoglobulin therapy. additionally, 6 patients (2.2%) were administered antifungal medications (table 4 ). approximately half of the patients (55.6%) received oxygen, and 10.2% of patients required noninvasive ventilation. eleven patients (4.0%) required invasive mechanical ventilation, and 6 of the 11 patients received extracorporeal membrane oxygenation (ecmo) and continuous renal replacement therapy (crrt) as salvage therapy. as expected, these treatments were used in significantly more patients with severe disease as compared with those with nonsevere disease (noninvasive ventilation: 55.6% vs 1.3%; p < .001; invasive mechanical ventilation: 24.4% vs 0%; p < .001; ecmo: 13.3% vs 0%; p < .001; crrt: 13.3% vs 0%; p < .001) because application of these treatments was included in the who's definition of severe disease. as of february 10, 2020, 229 patients (83.3%) were still hospitalized. a total of 38 patients (13.8%) had been discharged, and 8 patients (2.9%) had been transferred to another hospital due to serious illness. as of february 10, no patient had died (table 4 ). we investigated the epidemiological, clinical, and laboratory characteristics of 275 patients with covid-19 in guangzhou, guangdong, the most affected province outside of hubei. this is the largest sample size outside wuhan, the center of the epidemic as we know it so far. the most common symptoms were fever and dry cough, and ~16% of the patients had severe disease. there were no health care workers in the patient sample, no cases of in-hospital infection, and no deaths at the time this report was prepared. many studies [10, 11] regarding sars-cov-2 have been published recently. in contrast to studies from the city of wuhan and zhejiang province, in which most patients were males, slightly more than half of our patients were females (53.3%). furthermore, the patients in the present study had milder disease with respect to a lower frequency of symptoms such as fever, dry cough, and shortness of breath. the rates of severe cases and mortality in guangzhou were much lower than reported in wuhan (16.3% and 0%, respectively), which is similar to the rates reported in zhejiang [11] . the rate of gastrointestinal symptoms was low in our study, which is consistent with early reports from wuhan but is contradictory to a recent us study that reported a gastrointestinal symptom rate of 61% [12] . this discrepancy may be attributed to the difference in clinical characteristics between populations or to a change in the virus. however, further studies should be conducted to investigate this issue. the number of infected patients increased sharply in a short period and medical resources were in short supply, which delayed diagnosis and treatment for many patients. in addition, early diagnosis, isolation, and treatment in guangzhou might have collectively contributed to the marked reduction in the mortality rate. to further evaluate the relationship between source of infection and disease severity, patients were divided into an imported group and a local group based on epidemiological history. clinical characteristics and laboratory test results were similar between the groups, but the proportion of imported cases was higher in the severe group (80%). however, this association was not significant in the multiple logistic regression. sars-cov viral particles damage the cytoplasmic component of lymphocytes, which results in lymphocyte apoptosis. thus, patients infected with sars-cov are likely to exhibit lymphopenia. a prior study reported that 35% of patients with nonsevere sars-cov infections had mild lymphopenia [13] . lymphopenia is a prominent feature of severe middle east respiratory syndrome (mers) infection [14] , and it is common in patients with severe sars-cov infection [13] . in our study, 60% of patients with severe infections had some degree of lymphopenia. this suggests that lymphopenia in sars-cov-2 infections may be related to the severity of the disease. patients who are older and those with multiple underlying diseases are more likely to develop severe disease [15] . another study demonstrated that patients treated in the icu were more likely to be older and to have underlying comorbidities, dyspnea, and anorexia than patients who did not require icu admission [10] . this is consistent with the results of our study. studies of other viral diseases, such as rabies, have indicated that the incubation period of viral diseases is significantly related to the severity of the disease. shorter incubation periods are associated with more serious disease, and this is related to the number of cells initially infected by the virus. however, no studies have examined the relationship between the incubation period of covid-19 and disease severity so far. we found that the incubation period was shorter in patients with severe disease, which suggests that the incubation period of covid-19 may be related to disease severity. in addition, patients with bilateral pneumonia diagnosed on admission by ct were more likely to develop severe disease [16] . so it is important to process chest ct scans soon after admission. multivariate logistic regression analysis indicated that older age, male sex, and lower albumin level were independently associated with severe sars-cov-2 infection. alb is synthesized by hepatocytes and is the most abundant protein in plasma. gatta et al. [17] reported that hypoalbuminemia was one of the most important factors affecting the prognosis of patients with sepsis. peires et al. [18] showed that a decrease of alb level in patients with sepsis indicated worsening of the disease and poor prognosis. the mechanism of alb reduction due to sepsis is considered to be due to the excessive inflammatory reaction of the body. the inflammatory reaction leads to the release of oxygen free radicals and prostaglandins from kupffer cells, which can inhibit the synthesis of alb by the liver and promote the consumption and decomposition of protein, thus leading to hypoalbuminemia. so it is important to evaluate alb levels dynamically in these patients. rt-pcr analysis of respiratory or fecal samples, together with serological testing, can confirm the diagnosis of sars-cov infection in most sars patients. however, the sensitivity of detecting viral rna is reported to be 16.4% in nasal swabs, 37.3% in throat swabs, and 66.4% in sputum samples [19] . testing multiple nasopharyngeal and fecal samples increases the sensitivity of detecting viral rna [20] , and no significant correlation between viral load and severity of sars-cov-2 infection has been noted. considering that ct values were comparable between the severe group and the nonsevere group, the progression of sars-cov-2 respiratory failure might not be due to uncontrolled viral replication, but might be related to immunopathological damage. this study has several limitations. first, the definition of the incubation period should be the time from when the pathogen invades the body to the earliest onset of clinical symptoms. the uncertainty of the exact dates (recall bias) might have inevitably affected the assessment of incubation period. in addition, by the deadline for data collection of this study (february 10, 2020), 229 patients (83.3%) were still hospitalized. at the time of manuscript submission, the onset time in some patients may have been shorter than the observation period of 28 days, during which these patients could have developed severe disease, resulting in deviation of clinical observation characteristics. at present, there are no further follow-up data for these patients due to the urgent need for information that may guide clinical decision-making. future study with longer follow-up periods should be conducted to validate the findings of this study. the exposure history was recorded based on patient self-report at admission; all the patients were sober and able to answer questions. therefore, there may inevitably be a certain degree of subjectivity in the exposure history of the patients. we also found that <10% of patients did not know where they were infected, so there may be other unknown potential exposure. moreover, viral load from other specimens is a potentially useful marker of disease severity; however, only throat swabs were available in the present study. most of the patients infected with sars-cov-2 in guangzhou, china were not severe cases, with relatively lower severe ration than that reported in wuhan, and this may be due to earlier diagnosis and treatment. moreover, patients with older age, male, and decreased albumin level were more likely to develop into severe ones. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding composition and divergence of coronavirus spike proteins and host ace2 receptors predict potential intermediate hosts of sars-cov-2 evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster clinical characteristics of coronavirus disease 2019 in china clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical management of severe acute respiratory infection when novel coronavirus (2019-ncov) infection is suspected clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series gastrointestinal symptoms and covid-19: case-control study from the united states multiple organ infection and the pathogenesis of sars t-cell immunity of sars-cov: implications for vaccine development against mers-cov clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study imaging features of 2019 novel coronavirus pneumonia coronavirus as a possible cause of severe acute respiratory syndrome quantitative detection and viral load analysis of sars-cov-2 in infected patients sars-cov-2 viral load in upper respiratory specimens of infected patients financial support. this key: cord-285502-rvv64190 authors: yang, lie; yu, xiao; wu, xiaolong; wang, jia; yan, xiaoke; jiang, shen; chen, zhuqi title: emergency response to the explosive growth of health care wastes during covid-19 pandemic in wuhan, china date: 2020-08-18 journal: resour conserv recycl doi: 10.1016/j.resconrec.2020.105074 sha: doc_id: 285502 cord_uid: rvv64190 during the coronavirus disease 2019 (covid-19) as a worldwide pandemic, the security management of health care wastes (hcws) has attracted increasing concern due to their high risk. in this paper, the integrated management of hcws in wuhan, the first covid-19-outbreaking city with over ten millions of people completely locking down, was collected, investigated and analyzed. during the pandemic, municipal solid wastes (msws) from designated hospitals, fangcang shelter hospitals, isolation locations and residential areas (e.g. face masks) were collected and categorized as hcws due to the high infectiousness and strong survivability of covid-19, and accordingly the average production of hcws per 1000 persons in wuhan explosively increased from 3.64 kg/d to 27.32 kg/d. segregation, collection, storage, transportation and disposal of hcws in wuhan were discussed and outlined. stationary facilities, mobile facilities, co-processing facilities (incineration plants for msws) and nonlocal disposal were consecutively utilized to improve the disposal capacity, from 50 tons/d to 280.1 tons/d. results indicated that stationary and co-processing facilities were preferential for hcws disposal, while mobile facilities and nonlocal disposal acted as supplementary approaches. overall, the improved system of hcws management could meet the challenge of the explosive growth of hcws production during covid-19 pandemic in wuhan. furthermore, these practices could provide a reference for other densely populated metropolises. coronavirus disease 2019 is an emerging respiratory infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), which was first reported in early december 2019 in wuhan, china . covid-19 can be transmitted through aerosols, large droplets, or direct contact with secretions or fomites (shi et al., 2020) . due to its high infectiousness, which necessitates aggressive infection mitigation strategies to reduce the risk to patients and healthcare providers (engelman et al., 2020) . therefore, a tremendous amount of personal protective equipment (ppe) is consumed through both the medical care processes and the regular human activities. especially, a recent research reveals the strong survivability of the coronavirus, which could survive on material surfaces (e.g., metals, glass, and plastics) for up to 9 days (nzediegwu and chang, 2020) . thus, this survivability inevitably causes the explosive growth of health care wastes (hcws) production in an explosive manner. typical hcws are mainly collected from hospitals and can be divided into five categories: sharp waste, infectious waste, tissues waste, chemical waste and medicine waste (yong et al., 2009) . the total production of hcws is usually stable under certain conditions (ahmad et al., 2019) . however, during the pandemic, municipal solid wastes (msws) from designated hospitals, fangcang shelter hospitals, isolation locations and residential areas (e.g. face masks) are of potential infectiousness due to the high infectiousness and strong survivability of covid-19, and need to be collected, transported, storage and treated as part of hcws (mee, 2005 (mee, , 2006a . these kinds of solid wastes with potential infectiousness were defined as epidemic msws in this study. thus, during covid-19 pandemic (engelman et al., 2020; li et al., 2020) , the definition and scope of hcws was obviously extended, especially for covid-19-outbreaking cities or areas like wuhan in china, new york in usa, lombardia in italy and etc., and necessitates the establishment and operation of an emergent management system. as a mega city in the central china, wuhan has a population of 11 million before covid-19 outbreak, and this number decreased to approximate nine million during the lockdown period. two emergent hospitals were urgently constructed to provide 2600 beds for confirmed cases. additionally, 48 designated hospitals (21722 beds) and 23 fangcang shelter hospitals (19757 beds) were successively applied to serve the increasing confirmed cases. fangcang shelter hospitals were reconstructed from exhibition halls, stadia or large public facilities and used for the medical care of mild confirmed cases . furthermore, a series of isolation locations to isolate presumptive cases. tens of thousands of medical care personnels from all parts of china came to wuhan as the support of medical treatment, and all these treatments for patients as well as activities for quarantining people in turn leads to the explosive increase of hcws with an extended scope (e.g. face masks from non-medical regions). as far as we know, this is the first case of locking down a mega city with a population of over 10 million due to the outbreak of pandemic in human history. the study period was from january 23, 2020 (city lockdown) to april 24, 2020 (on-care cases are less than 30), and was divided into three stages, including the first stage (jan. 23-feb. 12), the second stage , and the third stage (mar. 23-apr. 24). the first stage was the initial period of covid-19 pandemic and the production of hcws began to increase. the burst growth of hcws occurred in the second stage and then the amount decreased gradually in the third stage. the number of confirmed patients was extracted from the daily reports of health commission of hubei province and wuhan municipal health commission. a laboratory-confirmed case is defined if the patient has a positive result for sars-cov-2 virus by real-time reverse transcriptase-polymerase chain reaction assay or high-throughput sequencing of nasal and pharyngeal swab specimens ). an on-care case is defined as a patient who is in the process of medical treatment in centralized hospitals or fangcang shelter hospitals. the detailed data of health care wastes (hcws) were provided by hubei solid waste and chemical pollution prevention center. some of the data have been reported in public by the media. the treatment capacity of hcws means the designed limitation of treatment facilities, while the treatment amount of hcws means the real treatment amount in treatment facilities. the schematic of hcws management during covid-19 pandemic in wuhan is demonstrated in fig.1 . apparently, the daily treatment amount of hcws increased slightly during the first stage. subsequently, two emergency hospitals (2600 beds), 48 designated hospitals (21722 beds) and 23 fangcang shelter hospitals (19757 beds) were successively applied. these medical facilities contributed to the burst growth of hcws in the second stage. the peak value of daily treatment amount of hcws was 291 tons on mar. 1, which was nearly 6 times comparing with the routine amount of 50 tons on jan. 23. in the third stage, the number of on-care cases decreased remarkably, on account of the large number of cured patients. it is worth mentioning that the daily treatment amount of hcws is still notably more than that before covid-19 outbreak, probably due to the large consumption of ppe (e.g. face masks, gloves, disinfector). a large amount of disinfection products were consumed for virus inactivation, including chemicals (e.g., 75% alcohol solution, chlorine containing disinfectants) and uv lamps, etc. the average production of hcws per 1000 persons in wuhan varied from 3.64 kg/d to 27.32 kg/d after the pandemic. to meet the urgent treatment desire of tremendously increased production of hcws, the treatment capacity has been promoted sharply via various approaches (fig.1) . the treatment capacity of hcws was significantly improved from 50 tons/d on jan. 23 to 280.1 tons per day on apr. 24. in the first stage, the operation loading rate of hcws treatment facility was 93.71%, which was quite close to full loading operation conditions of treatment facilities. during the first stage of pandemic covid-19, various approaches were employed to increase the treatment capacity of hcws, including mobile facilities, co-processing facilities with msws, emergency facilities, and nonlocal treatment facilities. all of these approaches contributed the rapid enhancement of the disposal capacity of hcws in wuhan. owing to the enhanced disposal capacity, the operation rate of the disposal capacity was only 36.88% on apr. 24, 2020, which was of sufficient security during the covid-19 period. source separation is recommended based on both the segregation of infectious and non-infectious wastes from hospitals in non-epidemic periods (lee and huffman, 1996) . the segregation practices have been reported as follows: infectious wastes were collected in yellow bags; msws were collected in black bags; sharps were collected in plastic containers; and cytotoxic/cytostatic drugs were collected in their original packaging (yong et al., 2009) . nonetheless, non-infectious wastes are also potential to act as the infectious vectors due to the high risk of covid-19. for instance, msws from designated hospitals, fangcang shelter hospitals and isolation locations were packaged and collected as hcws. therefore, all of these hcws were collected with strict segregation packages and managed according to the criterions of infectious wastes (mee, 2008) during the covid-19 epidemic in wuhan. an investigation was conducted to evaluate the risks of the hcws management, showing that the collection had higher importance than the temporary storage and the transportation (eren and tuzkaya, 2019) . the specialized turnover containers (mee, 2008) for hcws collection have been massively supplied by the local government, from 4000 to 19000 (table 1) . additionally, the occupational health risk of staff cannot be ignored and the necessary protective equipment and training has been provided widely. the source management is crucial for the security of the entire system of hcws. after the segregation and the collection ( figure s1 ), hcws are normally delivered to temporary storage sites, which locate near/inside the hospitals (yong et al., 2009) . the storage conditions are strictly controlled based on the current regulation (e.g. areas should be easy to clean, have adequate ventilation, and be properly marked) (mee, 2012) . the waste capacity of each storage site is usually designed based on the waste production of the corresponding hospital. on account of the severe risk of hcws, the stored wastes should be treated within 24 h, when the temperature is higher than 5℃ (mee, 2005) . however, the storage capacities of hospitals and other medical institutions in wuhan were not sufficient due to the burst growth of hcws in the initial stage after covid-19 outbreak. apart from designated hospitals, the storage sites of fangcang shelter hospitals and isolation locations were severely insufficient in the first stage. the amount of the stored but untreated hcws is demonstrated in the high-load period of the residual stored amount is mainly within the second stage of hcws treatment. fortunately, the storage capacity of hcws was rapidly increased by the local administrative departments. 13 extra emergency storage sites were urgently built and the total capacity reached 1118.6 tons (table 1, figure s2 ). therefore, the loading rate of hcws storage facilities was only 17.16%, even on the peak day. these emergency storage sites played a vital role in the security management of hcws in wuhan. hcws transportation refers to the haulage and handling of waste from inside healthcare facilities to treatment sites ( figure s3 ), which can either exist on-site at a hospital or be a central off-site facility (windfeld and brooks, 2015) . according to the current regulations in china (mee, 2003) , the off-site transportation of hcws to the final disposal site should be handled by authorized disposal companies. hcws are transported through pre-established routes (yong et al., 2009) . at all times, the place of origin and collection date, and place of destination of transport vehicles should be strictly monitored and noted (insa et al., 2010) . before covid-19 outbreak, there were 24 licensed transport vehicles available for hcws transportation in wuhan. this number rapidly increased to 82 via emergency dispatching. the improved transportation capacity was confirmed to be sufficient for the daily operation of hcws management in wuhan. the dynamic distribution of various local treatment capacities is presented in fig. 3 . the total capacity of local hcws treatment is significantly improved to meet the challenge of covid-19 spread. the majority (97.38%) of hcws was treated in local facilities, including stationary facilities, mobile facilities and co-processing facilities. during the peak period, some hcws were delivered to three nearby cities for harmless treatment, accounting for 2.62% of the total treatment amount during the study period. before covid-19 outbreak, the local treatment capacity of hcws in wuhan was 50 tons/d by an active centralized incineration plant for hcws. the incineration plant is well equipped with incinerator feeding system, incinerator, thermal energy utilization system, flue gas purification system, residue treatment system, etc. after the lockdown of wuhan, a brand new incineration plant was established on jan. 24, with a capacity of 10 tons/d. in addition, an emergency treatment center (qianzishan) using steam-based centralized treatment was constructed with two phases (each phase with the capacity of 30 tons/d) ( figure s4 ). incineration and steam disinfection are both widely utilized technologies (ababneh et al., 2020; dursun et al., 2011; kaur et al., 2019) , and can meet the requirements of current regulations under standardized management (mee, 2005 (mee, , 2006b . until apr. 23, the capacity of stationary facilities for hcws reached 120 tons/d, accounting for 42.84% of the total capacity. it was worth mentioning that the three stationary facilities were operated at high loading rates, nearly covering the entire study period. for instance, 59.86 tons of hcws were treated in the three stationary facilities, which took up 87.90% of hcws from hospitals and isolation locations on mar. 21. evidently, the stationary facilities played a leading role in the treatment of hcws from various hospitals and isolation locations. 34 mobile facilities using various technologies were rapidly built in designated hospitals ( figure s5 ), fangcang shelter hospitals, and temporary storage sites during the covid-19 period, from procurement (18, 52.94%), social donation (10, according to fig.4 , microwave disinfection, steam disinfection and incineration were applied in these mobile facilities in service. although these mobile facilities were designed and built based on the current regulations and laws, the preferential treatment approaches of hcws are still the stationary facilities due to the actual treatment efficiency and secondary environmental risks (liu et al., 2009; tiller and linscott, 2004; wu et al., 2011) . microwave disinfection and steam disinfection are both effective technologies for the disinfection of hcws (hong et al., 2018; oliveira et al., 2010; . the disinfected hcws should be further treated according to the regulations (mee, 2006a, b) . the licensed transportation from these mobile facilities to ultimate disposal sites is necessary for the security treatment of hcws. regarding mobile incineration facilities, the secondary environmental risk cannot be ignored in the absence of ancillary facilities (mee, 2005) , including thermal energy utilization system, flue gas purification system, residue treatment system, etc. in china, the waste-to-energy incineration has been increasingly adopted for waste treatment (hu et al., 2018; makarichi et al., 2018; yatsunthea and chaiyat, 2020) . moreover, the severe ecological risk would occur without specialized flue gas purification and fly ash treatment (kaur et al., 2019; wu et al., 2011) . these disadvantages of mobile facilities could reasonably explain that 6 mobile facilities were closed, when the second stage (capacity: 30 tons/d) of qianzishan emergency treatment center came into operation on apr. 23. fig. 4 co-processing of hcws with msws is an emergency choice, when the generation of hcws exceeds the capacity of existing treatment facilities. in fact, the generation of msws decreased significantly in the first stage (jan. 23-feb. 12), and then increased slowly in the second stage (feb. 13-mar. 22) and the third stage (mar. 23-apr. 24) (fig. 5) . the generation decline of msws provided a sufficient treatment capacity for the co-processing of hcws. in addition to various sterilization treatments, landfill and incineration are frequently-used for the ultimate treatment of hcws (aung et al., 2019; chen et al., 2013; lee and huffman, 1996) . there are five waste-to-energy incineration plants and two sanitary landfills in service for msws treatment in wuhan. although landfill is still applied for the treatment of hcws in some developing countries niyongabo et al., 2019) , it is not secure for the ultimate disposal of hcws due to the high risk of covid-19. in contrast, waste-to-energy incineration is a considerable option for simultaneous treatment and energy utilization of hcws. it is widely known that various pollutants would be generated along with the generation of flue gases and fly ashes during the incineration process of hcws (xie et al., 2009) , especially for pcdd/fs (wu et al., 2011) , pahs and heavy metals (li et al., 2017; liu et al., 2009 ). therefore, secondary pollution control is the vital factor for evaluating incineration types. according to the regulations for hazardous waste incineration (mee, 2001 (mee, , 2005 , the burning temperature of the incinerator used for medical waste should be higher than 850 ℃. only two waste-to-energy incineration plants (xinghuo mswi and xingou mswi) ( figure s6 ) were available for hcws treatment in wuhan due to the burning temperature (>850 ℃). two selected incineration plants are equipped with grate furnaces, which are beneficial for the removal of persistent organic pollutants (e.g. pcdd/fs) (vandecasteele et al., 2007) . nevertheless, the other three incineration plants are equipped with fluidized bed furnaces, which may cause air pollution due to the lower heat transfer rate between the bed material and medical wastes . therefore, grate-furnace incineration plants are more suitable for the co-processing of hcws, rather than fluidized-bed incineration plants. according the emergency regulation of mee (mee, 2020), the maximum loading amount of hcws in msw incineration plants is only 5% of for the co-processing. consequently, the co-processing capacity of the two selected incineration plants (2000 tons/d for msws) was 100 tons/d. the co-processing amount and percentage of hcws during covid-19 pandemic in wuhan are demonstrated in fig.5 . it was observed that co-processing played a crucial role in the treatment of hcws in wuhan. the total amount of co-processed hcws reached 5806.4 tons, accounting for 46.09% of the total treatment amount of hcws during the study period. the co-processing with msws could notably raise the treatment capacity of hcws based on existing treatment facilities, which could provide a reference for the emergency management of other regions and cities. besides local treatment, some hcws were transported to nearby cities for nonlocal treatment in the second stage (feb.13-mar. 22) (fig. 6 ). three cities, including xiangyang, huangshi and xianning, provided the emergency treatment of hcws from wuhan. licensed vehicles (mee, 2003) were used for the trans-regional transportation of hcws. the transportation process was strictly monitored for security reasons. the accumulated nonlocal treatment amount of hcws reached 330.3 tons, accounting for 2.62% of the total treatment amount during the studied period. although the amount was significantly lower than those of the stationary and co-processing facilities, the contribution of nonlocal treatment could not be ignored in the emergency management of hcws in wuhan. overall, nonlocal treatment could act as an alternative option for other cities and regions during covid-19 pandemic. on the whole, the emergency management of hcws during covid-19 pandemic in wuhan is a successful case, especially considering the fact that this outbreak of pandemic was a sudden case. the efficient and secure management of hcws is believed to contribute remarkably to the effective control of covid-19 spread in wuhan. therefore, several implications are drawn from the actual practices of hcws management in wuhan as indicated above. (a) the implementation of national and local emergency policies could provide operable guidelines for the management of hcws during covid-19 pandemic. mee promulgated a national guideline for the emergency management of hcws (mee, 2020). in addition, wuhan municipal administration and law enforcement committee announced an emergency policy on feb. 12, 2020, which decided to adopt two grate-furnace incineration plants as co-processing facilities. (b) msws of potential infectiousness were defined as hcws during covid-19 pandemic. besides typical hcws, infectious msws in designated hospitals, fangcang shelter hospitals, isolation locations and residential areas were also collected and treated as hcws. (c) the integrated management of hcws, including segregation, collection, storage, transportation and treatment, was significantly enhanced during covid-19 pandemic. the entire process should be monitored to guarantee the secure management of hcws at all time. (d) the co-processing facilities contributed significantly to the efficient and secure treatment of hcws as an emergency approach. especially for those grate-furnace incineration plants, the total treatment capacity of hcws could be rapidly improved even with a co-processing rate of 5%. the high operation temperature (>850 ℃) and ancillary facilities effectively prevent the emission of various pollutants. (e) social participation played an important role in the rapid improvement of treatment capacity of hcws. it was noticed that 10 mobile facilities were donated from various companies for corporate social responsibility, accounting for 29.41% of mobile facilities in wuhan. (f) nonlocal treatment could act as an effective supplement during which the trans-regional transportation of hcws should be strictly monitored for risk control. the detailed emergency management of hcws during covid-19 pandemic in wuhan was investigated in this study. infectious msws in designated hospitals, fangcang shelter hospitals, isolation locations and residential areas were also collected and treated as hcws, and led to the increase of total production of hcws in an explosive manner from 3.64 kg/d to 27.32 kg/d per 1000 persons. the capacities of collection, storage, transportation and treatment facilities were all massively increased to guarantee the safe management of hcws. stationary and co-processing facilities played a crucial role for the efficient treatment of hcws. when the daily production of hcws was close to the acceptable limitation of local treatment facilities, the trans-regional management were applied. the practical experience of emergency management of hcws in wuhan can be highly suggestive to other countries and regions to combat the global pandemic of covid-19, and other respiratory infectious diseases. recycling of pre-treated medical waste fly ash in mortar mixtures lca of hospital solid waste treatment alternatives in a developing country: the case of district swat application of multi-criteria-decision approach for the analysis of medical waste management systems in myanmar generation and distribution of pahs in the process of medical waste incineration assessment of health-care waste treatment alternatives using fuzzy multi-criteria decision making approaches. resources, conservation and recycling adult cardiac surgery and the covid-19 pandemic: aggressive infection mitigation strategies are necessary in the operating room and surgical recovery occupational health and safety-oriented medical waste management: a case study of istanbul life-cycle environmental and economic assessment of medical waste treatment the growing importance of waste-to-energy (wte) incineration in china's anthropogenic mercury emissions: emission inventories and reduction strategies critical review of medical waste legislation in spain. resources, conservation and recycling influence of incinerated biomedical waste ash on the properties of concrete healthcare waste management in asian developing countries: a mini review medical waste management/incineration a close-up on covid-19 and cardiovascular diseases. nutrition, metabolism and cardiovascular diseases tracing source and migration of pb during waste incineration using stable pb isotopes indoor air concentrations of mercury species in incineration plants for municipal solid waste (msw) and hospital waste (hw) the evolution of waste-to-energy incineration: a review pollution control standard for hazardous wastes incineration technical specifications for medical waste transfer vehicles technical specifications for centralized incineration facility construction on medical waste technical specifications for microwave disinfection centralized treatment engineering on medical waste technical specifications for steam-based centralized treatment engineering on medical waste standard of packaging bags, containers and warning symbols specific to medical waste technical specifications for collection, storage, transportation of hazardous waste emergency management and technical guidelines for medical wastes during covid-19 pandemic current treatment and disposal practices for medical wastes in bujumbura improper solid waste management increases potential for covid-19 spread in developing countries. resources, conservation and recycling microwave inactivation of bacillus atrophaeus spores in healthcare waste impact of temperature on the dynamics of the covid-19 outbreak in china evaluation of a steam autoclave for sterilizing medical waste at a university health center integrated municipal solid waste treatment using a grate furnace incinerator: the indaver case the suppression mechanism of pahs formation by coarser-sized bed material during medical waste fluidized bed incineration disinfection technology of hospital wastes and wastewater: suggestions for disinfection strategy during coronavirus disease 2019 (covid-19) pandemic in china medical waste management -a review thermal removal of pcdd/fs from medical waste incineration fly ash -effect of temperature and nitrogen flow rate emissions investigation for a novel medical waste incinerator a very small power plant -municipal waste of the organic rankine cycle and incinerator from medical and municipal wastes medical waste management in china: a case study of nanjing this work was financially supported by the national key r&d program of china (no. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-279976-juz9jnfk authors: xie, mingxuan; chen, qiong title: insight into 2019 novel coronavirus — an updated intrim review and lessons from sars-cov and mers-cov date: 2020-04-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.03.071 sha: doc_id: 279976 cord_uid: juz9jnfk background: the rapid spread of the coronavirus disease 2019 (covid-19), caused by a zoonotic beta-coronavirus entitled 2019 novel coronavirus (2019-ncov), has become a global threat. awareness of the biological features of 2019-ncov should be updated in time and needs to be comprehensively summarized to help optimize control measures and make therapeutic decisions. methods: based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-ncov infection, in comparison with severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) infection. results: the genome of 2019-ncov partially resembled sars-cov and mers-cov, and indicating a bat origin. the covid-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than sars and mers. clinical presentation and pathology of covid-19 greatly resembled sars and mers, with less upper respiratory and gastrointestinal symptoms, and more exudative lesions in post-mortems. potential treatments included remdesivir, chloroquine, tocilizumab, convalescent plasma and vaccine immunization (when possible). conclusion: the initial experience from the current pandemic and lessons from the previous two pandemics can help improve future preparedness plans and combat disease progression. in late december 2019, a pneumonia outbreak of unknown etiology took place in wuhan, hubei province, china, and spread quickly nationwide. chinese center for disease control and prevention (ccdc) identified a novel beta-coronavirus called 2019-ncov, now officially known as severe acute respiratory syndrome coronavirus 2 (sars-cov-2) (gorbalenya et al., 2020) , that responsible for the pandemic. this was the third zoonotic coronavirus breakout in the first two decades of 21 st century that allowing human-to-human transmission and raising global health concerns. chinese government had taken immediate, transparent and extraordinary measures, and reached initial achievements to control the outbreak. as of 11 march 2020, the pandemic in pubmed, web of science, embase, cnki, wanfang, vip, preprint biorxiv and medrxiv databases from the earliest available date to 11 march, 2020. initial search terms were "2019-ncov" or "2019 novel coronavirus" or "sars-cov-2" or "covid-19" or "corona virus disease 2019" or "ncp" or "novel coronavirus pneumonia". further search words were above keywords, "sars" or "sars-cov" or "severe acute respiratory syndrome", "mers" or "mers-cov" or "middle east respiratory syndrome", in combinations of with "spike protein" or "genome" or "reproductive number" or "incubation period" or "serial interval" or "fatality rate" or "clinical characteristics" or "pathology" or "autopsy" or "treatment". j o u r n a l p r e -p r o o f moreover, official documents and news released by national health commission of p.r. china, ccdc, cdc(usa) and who were accessed for up-to-date information on covid-19. only the articles in english or chinese were considered. in this review, we highlight the pandemic potential and pathological indications of emerging coronavirus, comprehensively and systematically summarize the up-to-date knowledge of the biological characteristics of 2019-ncov, including virology and origin, epidemiology, clinical manifestations, pathology and treatment. because of its natural structures and biological features to bind receptors on host cells, the spike protein of 2019-ncov may played an essential role in disease spreading. we summarized all of the four available pathology studies of covid-19 biopsy and autopsy, and compared the results with previous two deadly coronavirus diseases. new therapeutic measures are emerging one after another. potential effective treatments were remdesivir, chloroquine, tocilizumab, convalescent plasma and vaccine immunization (when possible). evidence-based medicine should always be advocated to guide our clinical decision. coronavirus belongs to the subfamily orthocoronavirinae in the family of coronaviridae in the order nidovirales, which mainly caused infections in respiratory and gastrointestinal tract. the 2019-ncov is a novel enveloped beta-coronavirus which has a single stranded positive sense rna genome . concerning the origin of the virus, several phylogenetic analysis suggested the bat to be the most probable animal reservoir. based on genome sequencing, 2019-ncov is about 89% identical to bat sars-like-covzxc21, 82% identical to human sars-cov and about 50% to mers-cov (chan et al., 2020; lu et al., 2020) . as both sars-cov and mers-cov were transmitted from bats to palm civets or dromedary camels, and finally to humans, there should be another animal representing as an intermediate host between bat and human. pangolins were suggested as the possible intermediate hosts, because their genome had approximately 85.5%-92.4% similarity to 2019-ncov, representing two sub-lineages of 2019-ncov in the phylogenetic tree, one of which (gd/p1l and gdp2s) was extremely closely related to 2019-ncov (lam et al., 2020) . other research suggested 2019-ncov was the recombinant virus of bat coronavirus and j o u r n a l p r e -p r o o f snake coronavirus, by comparison in conjunction with relative synonymous codon usage bias among different animal species (ji et al., 2020) . the truth is yet to be discovered. the spike surface glycoprotein of coronavirus plays an essential role in binding to receptors on host cells and determines host tropism. spike protein(s-protein) of 2019-ncov is reported to bind with angiotensin-converting enzyme 2 (ace2), the same receptor of sars-cov to invade host cells; whereas mers-cov uses dipeptidyl peptidase 4 (dpp4) as the primary receptor . the amino acid sequence another research team also discovered an "rrar" furin recognition site by an insertion in the s1/s2 protease cleavage site in 2019-ncov, instead of a single arginine in sars-cov. after quantifying the kinetics mediating the interaction via surface plasmon resonance, ace2 is calculated to bind to 2019-ncov ectodomain with ~15 nm affinity, which is approximately 10-to 20-fold higher affinity than ace2 binding to sars-cov (wrapp et al., 2020) . in all, the binding affinity between 2019-ncov s-protein and ace2 is comparable or even stronger than sars-cov s-protein and ace2. this may explain the rapid development and strong ability of human-to-human transmission in covid-19. the pandemic escalated exponentially at the beginning of 2020, which might only be the tip of the iceberg due to delayed case reporting and deficiency in testing kits . the onset of first cluster cases were reported an exposure history to the j o u r n a l p r e -p r o o f huanan seafood(wild animal) wholesale market in wuhan. however, phyloepidemiologic analyses suggested that huanan market was not the origin of 2019-ncov. the virus was imported from elsewhere and boosted in the crowded market (yu et al., 2020) . the proportion of infected cases without an exposure history and in health care workers gradually increased. all of the evidence indicated the human-to-human transmission ability of 2019-ncov, which may already be spread silently between people in wuhan before the cluster of cases from huanan market was discovered in late december. person-to-person transmission may occur mainly through droplet or contact transmission. according to guan's latest pilot study, 2019-ncov was detected positive in the gastrointestinal tract specimens (stool and rectal swabs) as well as in saliva and urine, and even in esophageal erosion and bleeding site of severe peptic ulcer patients . four important epidemiological parameters of 2019-ncov were reviewed in comparison with those of sars-cov and mers-cov(shown in table 1 ). representing the average number of new infections generated by an infectious person in a totally naïve population. for r0˃1, the number of infected is likely to increase; for r0 ˂1, transmission is likely to decline and die out. the reproductive number updated along with the development of the outbreak and interventions. r0 was estimated to be around 3 for sars (bauch et al., 2005) and ˂1 for mers (bauch and oraby, 2013) . the preliminary r0 of 2019-ncov was reported as 2.24-3.58 . several research groups reported estimated r0 of the outbreak depending on distinct estimation methods and the validity of underlying assumptions. liu et al. (2020) reviewed all of the 12 references of an estimated r0 ranged from 1.4 to 6.49, with a mean of 3.28 and a median of 2.79. in clinical studies, a 425-case study by 22 january 2020, reported an r0 of approximately 2.2(95%ci, 1.4-3.9) , while another 4021-case study by 26 january 2020, estimated 3.77(95%ci, 3.51-4.05) . the discrepancy may be due to sample number and different stages of the pandemic. incubation period is defined as the interval from initial exposure to an infectious agent to onset of any symptoms or signs it causes. a long incubation period may lead to a high rate of asymptomatic and subclinical infection. the first prediction of mean incubation period was 5.2 days (95%ci, 4.1-7.0 days), with the 95th percentile of the distribution at 12.5 days, based on 2019-ncov exposure histories of the first 425 cases in wuhan . a 4021-case study reported 4.75 days (interquartile range: j o u r n a l p r e -p r o o f 3.0-7.2 days) . another 88-exported-case study calculated the mean incubation period to be 6.4 days (95%ci, 5.6-7.7 days), using known travel histories to and from wuhan and symptom onset dates (backer et al., 2020) . all these literatures lay the foundation to set 14 days as the medical observation period if any exposure occurred. a latest study collected 1099 cases from 552 hospitals in 31 provinces in china and declared a median incubation period of 3.0 days, ranging from 0 to surprisingly 24.0 days. an adjustments in screening and control policies may be needed. the 2019-ncov generally has a longer incubation time than sars-cov (4.0 days, 95% ci 3.6-4.4 days) (lessler et al., 2009 ) and mers-cov (range 4.5-5.2 days) (park et al., 2018) . serial interval is the interval from illness onset in a primary case to illness onset in the secondary case. the mean serial interval was estimated at 7.5 days(95% ci, 5.3-19days) using contact tracing data from early wuhan cases in 2019-ncov pandemic, which was shorter than the 8.4-day mean serial interval reported for sars (lipsitch et al., 2003) and 12.6-day for mers (cowling et al., 2015) . another estimation of the mean serial interval from 26 infector-infectee pairs was surprisingly 2.6 days, which was shorter than the median incubation period, suggesting a substantial proportion of secondary transmission before illness onset (nishiura et al., 2020) . the cfr in early studies of covid-19 involving relatively small samples of confirmed cases in wuhan, varied from 4.3% to 14.6% huang et al., 2020; , but that may not be able to reflect the truth. the cfr in wuhan was undoubtedly higher than cfr outside of wuhan. the reported cfr ranged 1.4%-3.06% in large nationwide case studies . prognosis factors such as male, elderly patients aged≥ 60 years, underlying disease, severe pneumonia at baseline and a delay from onset to diagnosis >5 days substantially elevated the cfrs . cfrs in patients with cardiovascular disease, diabetes, hypertension and respiratory disorders were as high as 10.5%, 7.3%, 6.0% and 6.3%, respectively. according to who announcement, sars accounted for 8096 cases and 774 death, with a cfr of 9.6% (who, 2004 clinical presentation of covid-19 greatly resembled viral pneumonia such as sars and mers. most cases are mild cases(81%), whose symptoms were usually self-limiting and recovery in two weeks (wu and mcgoogan, 2020) . severe patients progressed rapidly with acute respiratory distress syndrome (ards) and septic shock, eventually ended in multiple organ failure. general information of four inpatient case studies with relatively comprehensive data were summarized in supplementary table 1. the 2019-ncov was more likely to infect elderly men with comorbidities. males were more susceptible to 2019-ncov infection, same as sars-cov and mers-cov studies (badawi and ryoo, 2016) , due to x chromosome and sex hormones' role on innate and adaptive immunity (jaillon et al., 2019) . chronic underlying diseases (mainly hypertension, cardio-cerebrovascular diseases and diabetes) may increase the risk of 2019-ncov infection , which is similar to mers-cov infection (badawi and ryoo, 2016) . smoking may be a negative prognostic indicator for covid-19 guan et al., 2020) . clinical information of the above four selected inpatient case studies were summarized in supplementary table 2. onset of symptoms were usually mild and nonspecific, presenting by fever, dry cough and shortness of breath. very few covid-19 patients had prominent upper respiratory tract and gastrointestinal symptoms (eg, diarrhea) huang et al., 2020) , compared to 20-25% of patients with mers-cov or sars-cov infection developed diarrhea (assiri et al., 2013) . however, only 43.8% of covid-19 patients had an initial presentation of fever, and developed to 87.9% following hospitalization , compared to as high as 99% and 98% frequent in sars-cov and mers-cov infection (badawi and ryoo, 2016) . those patients without fever or even asymptomatic may be left un-quarantined as silent infection source, if the surveillance methods focused heavily j o u r n a l p r e -p r o o f on fever detection. moreover, the onset of symptoms may help physicians identifying patients with poor prognosis. patients admitted to the icu were more likely to report pharyngeal pain, dyspnea, dizziness, abdominal pain and anorexia . in terms of laboratory findings, a substantial decrease in the total number of lymphocytes could be used as an index in the diagnosis of 2019-ncov infection, indicating a consumption of immune cells and an impairment to cellular immune function . non-survivors developed more severe lymphopenia over time . initial proinflammatory plasma cytokine concentrations were higher in covid-19 patients than in healthy adults. icu patients had even higher plasma levels of il2, il7, il10, gscf, ip10, mcp1, mip1a, and tnfα compared to non-icu patients . there were numerous differences in laboratory findings between patients admitted to the icu and those not, including higher white blood cell and neutrophil counts, higher levels of d-dimer, creatine kinase, and creatine in icu patients . typical chest ct manifestation of covid-19 pneumonia were initially small subpleural ground glass opacities that grew larger with crazy-paving pattern and consolidation. after two weeks of growth, the lesions were gradually absorbed leaving extensive opacities and subpleural parenchymal bands in recovery patients. however, guan et al. ( 2020) demonstrated that patients with normal radiologic findings on initial presentation consisted of 23.9% and 5.2% of severe and non-severe cases respectively, which add the complexity to disease control. (nicholls et al., 2003) . thrombi were seen in all six autopsies of sars-cov infected patients, with even huge thrombus formation in part of pulmonary vessels. coagulation function disorders were reported in most of the severe covid-19 patients, by elevated levels of d-dimer and prolonged prothrombin time, some of whom ended in disseminated intravascular coagulation huang et al., 2020; . this may explain some sudden death of clinical recovery patients and serve as an indication for disease severity. in an autopsy study, the only one patient without usage of corticosteroids demonstrated increased cd3+ lymphocyte than five other specimen treated by corticosteroids (pei et al., 2005) . it suggested an inhibition of immune system similarities. the human monoclonal antibody could efficiently neutralize sars-cov and inhibit syncytia formation between s-protein and ace2 expressing cells (sui et al., 2004) . appropriate modification of the monoclonal antibody may be effective for treatment of covid-19. what's more, potential therapies targeting the renin-angiotensin system, to increase ace2 expression and inhibit ace may be there are no effective antiviral treatment for coronavirus infection, even the strong candidates as lopinavir/ritonavir and abidol exhibited no remarkable effect on clinical improvement, day 28 mortality or virus clearance (chen et al., 2020) . expectation and attention were shifted to "remdesivir" which may be the most potential wide-spectrum drug for antiviral treatment of 2019-ncov. remdesivir is an adenosine analogue, which incorporates into novel viral rna chains and results in pre-mature termination. it is currently under clinical development for the treatment of ebola virus infection (mulangu et al., 2019) . wang et al. (2020b) revealed that remdesivir were highly effective and safe in the control of 2019-ncov infection in vero e6 cells and huh-7 cells. a successful appliance of remdesivir on the first 2019-ncov infected case in the united states when the his clinical status was getting worsen, were recently released (holshue et al., 2020) . animal experiments also showed superiority of remdesivir over lopinavir/ritonavir combined with interferon-β, by reducing mers-cov titers of infected mice and improving the lung tissue damage (sheahan et al., 2020) . the effectiveness and safety of remdesivir can be expected by the clinical trial lead by dr bin cao. the 2019-ncov infection is associated with a cytokine storm triggered by over-activated immune system xu et al., 2020b) , similar to sars and mers. the aberrant and excessive immune responses lead to a long-term lung function and structure damage in patients survived from icu. ongoing trials of il-6 antagonist tocilizumab, which shown effective against cytokine release syndrome resulting from car-t cell infusion against b cell acute lymphoblastic leukemia, may be expanded to restore t cell counts and treat severe 2019-ncov infection (le et al., 2018) . the available observational studies and meta-analysis of corticosteroid treatment suggested impaired antibody response, increased mortality and secondary infection rates in influenza, increased viraemia and impaired virus clearance of sars-cov and mers-cov, and complications of corticosteroid therapy in survivors (zumla et al., 2020) . therefore, corticosteroid should not be recommended for treatment of 2019-ncov, or use on severe patient with special caution. a review (nichol et al., 2003) . in conclusion, it still remains a challenging task to fight the 2019-ncov of unknown origin and mysterious biological features, and to control an outbreak of covid-19 with such a high r0, a long incubation period and a short serial interval, by limited treatment and prevention measures. lessons learned from the mers and sars outbreaks can provide valuable insight into how to handle the current pandemic. the successful public health outbreak response tactics of chinese government, such as hand hygiene, wearing masks, isolation, quarantine, social distancing, and community containment, can be copied by other countries according to their national situation. as the pandemic is still ongoing and expanding, experiences and research literatures from china and other countries will increase. the 2019-ncov should be monitored of any possible gene variation of antigenic drift or antigenic conversion, to avoid another round of outbreak. another lessons from this pandemic will be awe for nature and love for life. funding source: this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. ethical approval: the ethical approval or individual consent was not applicable. all authors declare no conflict of interest. all authors 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elderly lung pathology of fatal severe acute respiratory syndrome serial interval of novel coronavirus (2019-ncov) infections. medrxiv(preprint) 2020 mers transmission and risk factors: a systematic review lung pathology and pathogenesis of severe acute respiratory syndrome: a report of six full autopsies a report on the general observation of a 2019 novel coronavirus autopsy comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s1 protein that blocks receptor association evaluation of convalescent plasma for ebola virus disease in guinea chloroquine is a potent inhibitor of sars coronavirus infection and spread clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china. jama 2020a remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-ncov) in vitro decoding the evolution and transmissions of the novel pneumonia coronavirus (sars-cov-2) using whole genomic data summary of probable sars cases with onset of illness from 1 who . who mers global summary and assessment of risk who. novel coronavirus(2019-ncov) situation report-51 2020 cryo-em structure of the 2019-ncov spike in the prefusion conformation genome composition and divergence of the novel coronavirus (2019-ncov) originating in china characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72314 cases from the chinese center for disease control and prevention evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission pathological findings of covid-19 associated with acute respiratory distress syndrome liqun fang. epidemiological and clinical features of the 2019 novel coronavirus outbreak in china single-cell rna expression profiling of ace2, the putative receptor of wuhan 2019-ncov a novel coronavirus from patients with pneumonia in china reducing mortality from 2019-ncov: host-directed therapies should be an option crrt(%) 7 9 1.5 0.8 key: cord-287499-zcizdc7s authors: thompson, hayley a; imai, natsuko; dighe, amy; ainslie, kylie e c; baguelin, marc; bhatia, sangeeta; bhatt, samir; boonyasiri, adhiratha; boyd, olivia; brazeau, nicholas f; cattarino, lorenzo; cooper, laura v; coupland, helen; cucunuba, zulma; cuomo-dannenburg, gina; djaafara, bimandra; dorigatti, ilaria; elsland, sabine; fitzjohn, richard; fu, han; gaythorpe, katy a m; green, will; hallett, timothy; hamlet, arran; haw, david; hayes, sarah; hinsley, wes; jeffrey, benjamin; knock, edward; laydon, daniel j; lees, john; mangal, tara d; mellan, thomas; mishra, swapnil; mousa, andria; nedjati-gilani, gemma; nouvellet, pierre; okell, lucy; parag, kris v; ragonnet-cronin, manon; riley, steven; unwin, h juliette t; verity, robert; vollmer, michaela; volz, erik; walker, patrick g t; walters, caroline; wang, haowei; wang, yuanrong; watson, oliver j; whittaker, charles; whittles, lilith k; winskill, peter; xi, xiaoyue; donnelly, christl a; ferguson, neil m title: sars-cov-2 infection prevalence on repatriation flights from wuhan city, china date: 2020-08-24 journal: j travel med doi: 10.1093/jtm/taaa135 sha: doc_id: 287499 cord_uid: zcizdc7s we estimated sars-cov-2 infection prevalence in cohorts of repatriated citizens from wuhan to be 0.44% (95% ci: 0.19%–1.03%). although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in wuhan city, china, in the absence of large-scale population testing early in the epidemic. highlight: we estimated sars-cov-2 infection prevalence in cohorts of repatriated citizens from wuhan to be 0.44% (95% ci: 0.19%-1.03%). although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in wuhan city, china, in the absence of large-scale population testing early in the epidemic. the world health organization declared covid-19 a global pandemic on 11 th march 2020. 1 cases of atypical pneumonia caused by the sars-cov-2 virus were first detected in wuhan city, china in late 2019. the growing scale of the outbreak and the strict travel and movement restrictions implemented in january 2020 prompted foreign governments to repatriate citizens from the then epicentre of transmission. 2 between january 29 th and february 27 th , 56 flights repatriated a total of 8,597 individuals from wuhan to 55 countries. this letter details sars-cov-2 infection prevalence over these repatriation flights. estimating infection prevalence in repatriated individuals is useful especially early in an outbreak of a novel pathogen when local case ascertainment at the origin is low and relies on symptomatic testing. for example, if infection prevalence in repatriates is high this could indicate a highly transmissible and widely circulating pathogen. repatriation flights were identified from international and local news outlets and government press releases. we tracked the total number of repatriates per flight, final destinations, number tested on arrival, during and before release from quarantine, and of those who tested positive, the number symptomatic or asymptomatic where available (for downloadable data table of identified flights see our public github repository: https://github.com/mrc-ide/repatriationcovid-19). as testing protocols differed by country, we present the infection prevalence only for the 17 repatriation flights where all individuals (n=2,433) were tested upon arrival regardless of symptoms. as transmission during the flight itself could not be ruled out, we did not consider individuals who later tested positive during the quarantine period. by focusing on flights where all passengers were tested for sars-cov-2 infection with real-time reverse transcription polymerase chain reaction (rt-pcr), regardless of symptoms, a more accurate estimate of infection prevalence can be obtained compared to relying on symptomatic surveillance testing alone. we calculated the infection point prevalence per flight as the number of positive rt-pcr test results on arrival divided by the total population tested and the corresponding exact 95% binomial confidence intervals. we used a binomial mixed-effects model to obtain a pooled estimate of infection prevalence over this time frame, accounting for the heterogeneity between different repatriated populations. 3, 4 per flight infection prevalence ranged from 0 to 1.9% and of the 2,433 passengers tested immediately upon arrival, 13 individuals tested positive, resulting in a pooled infection prevalence in repatriates of 0.44% (95% ci: 0.19%-1.03%) (figure 1 ). over the 5 flights leaving wuhan between 30 th january and 1 st february inclusive (flights closest to the reported peak of the epidemic in wuhan) where everyone was tested on arrival, the pooled infection prevalence was 0.88% (6/685, 95% ci: 0.39%-1.93%). the infection risk for foreign nationals and tourists could differ from the general population due to socio-economic status, living and/or working conditions, and exposure patterns. in addition, following the travel ban on january 23 rd symptomatic individuals may have been prevented from boarding these flights. therefore, prevalence from repatriated flights can be considered a conservative estimate of infection prevalence in the wider population. compared to the estimated infection prevalence of 3.6% (95% ci: 2.0-6.1%) and 6.3% (95% ci: 0.8-20.8%) amongst repatriates from european countries to greece in late march, our estimates of prevalence in repatriates from wuhan suggest relatively low levels of community transmission in wuhan during this period despite flights occurring close to the reported peak of the epidemic. 5 more accurately than pcr positivity in repatriated populations, or symptomatic surveillance in local communities, retrospective local serological surveys can provide an insight into the scale of an outbreak as seroprevalence can be used as a measure of the cumulative incidence of infection. several serological surveys have been conducted since the epidemic subsided in wuhan. a survey conducted between march 15 th and april 28 th measured a seroprevalence of 3.27% (95% ci: 3.02-3.52%) in asymptomatic individuals visiting a general hospital in the jianghan district, wuhan, when adjusted for age and sex, and 2.72% (95% ci: 2.49-2.95) when adjusted for assay sensitivity and specificity. 6 another survey conducted between march 30 th and april 10 th measured seroprevalence to be 3.8% (95% ci: 2.6-5.4%) in healthcare workers (hcws), 3.8% (95% ci 2.2-6.3%) in hotel staff, and 3.2% (95% ci: 1.6-6.4%) in family members of hcws. 7 however, it should be noted that these are high-risk populations and not necessarily representative of the general population of wuhan. in addition, there is evidence that antibodies to sars-cov-2 wane quickly and so serosurveys may not capture all past infections within a population. 8 the repatriation flights we considered represent a globally diverse population of foreign nationals who were residing in wuhan city leading up to the outbreak for variable periods of time and for a variety of reasons: students, work-related travel, visiting friends and families and tourism. it is important to note that it is unclear how the risk of infection posed to these individuals compared to the risk of infection within the general population in wuhan city. we assume the infection prevalence in repatriated individuals can be used as a lower bound for infection prevalence in the general population. while this assumption is hard to quantify and validate it does impact the interpretation of our results and should be borne in mind. despite this, characterising infection prevalence from repatriated cohorts highlights a way to help bridge the gap between symptom-based surveillance which may under-estimate true infection prevalence and seroprevalence surveys which are difficult to conduct during epidemic peaks. author contributions: hat, ni, cad, nmf conceived the study; hat, ni, ad, wg, gcd, kamg, hf collected and extracted the international flight data and information on testing strategies; hat and ni carried out the analysis; hat wrote the first draft with input from ni and ad; all authors contributed to the final draft. funding: this work was supported by joint centre funding from the uk medical research council and department for international development. the authors have declared no conflicts of interest. world health organization. who director-general's opening remarks at the media briefing on covid-19 -11 world health organization. coronavirus disease (covid-2019) situation reports random effects meta-analysis of event outcome in the framework of the generalized linear mixed model with applications in sparse data the binomial distribution of meta-analysis was preferred to model within-study variability high prevalence of sars-cov-2 infection in repatriation flights to greece from three european countries seroprevalence and epidemiological characteristics of immunoglobulin m and g antibodies against sars-cov-2 in asymptomatic people in wuhan, china seroprevalence of immunoglobulin m and g antibodies against sars-cov-2 in china rapid decay of anti-sars-cov-2 antibodies in persons with mild covid-19 key: cord-344688-uu3b529c authors: song, xue-jun; xiong, dong-lin; wang, zhe-yin; yang, dong; zhou, ling; li, rong-chun title: pain management during the covid-19 pandemic in china: lessons learned date: 2020-04-22 journal: pain med doi: 10.1093/pm/pnaa143 sha: doc_id: 344688 cord_uid: uu3b529c nan it was late january, during the cold winter before the lunar new year, when wuhan began its 76-day lockdown in response to an outbreak of covid-19. the rest of china followed suit shortly thereafter with the implementation of strictly enforced quarantine measures (1, 2) . the chinese central government issued a nation-wide order by listing covid-19 as a level 2 infectious disease warranting priority management (2) , which has been invoked in the past for deadly infectious diseases such as smallpox, anthrax, and cholera. the subsequent emergence and spread of sars-cov-2 around the world has ignited a global crisis, with the world health organization (who) issuing a global health pandemic notice and urging the avoidance of non-essential travel (3) . in china, while non-essential workers were requested to stay home, those working in healthcare, emergency services, and disaster control found themselves with more responsibility than ever, mobilized like troops during war. in the initial stages of the pandemic spanning late january to early february, medical systems in wuhan faced overwhelming shortages of health care workers and key medical resources including medical-grade personal protective equipment, as well as limited space in hospitals for managing the surge of patients with covid-19. in the face of these challenges, the central government quickly organized. a total of 42,600 health care providers and workers as well as millions of tons of medical supplies were sent to wuhan and its neighboring areas in the hubei province from all over the country (4), with additional aid coming from other countries and various international humanitarian aid organizations (5, 6) . those working on the front lines in wuhan have been serving as part of the ongoing fight against the covid-19 pandemic, a largescale global public health challenge. having born witness to such ongoing devastation, the world is recognizing the importance of examining our existing public health and health care systems, their potential to be maximally effective during the pandemic, and how they can be improved. here, we report some of our personal experiences as chinese physicians and scientists working in the field of pain medicine in wuhan as well as shenzhen, another large metropolis in china severely hit by covid-19. we discuss strategies that have been helpful in pain management for our patients during the pandemic and provide recommendations based on the lessons we learned. though first reports of sars-cov-2 emerged in december 2019, the government and the public ignored these warnings that emerged from the heart of wuhan, failing to realize the potential threat of the novel coronavirus. as a result, members of the public, hospitals, and medical workers did not realize they were being exposed to sars-cov-2 until hospitals were overwhelmed. the numbers of patients with fever, pneumonia, and other related symptoms rose exponentially, quickly using up most available resources in hospitals. in order to concentrate available resources to help patients with the most severe conditions, most wuhan medical services not directly involved in intensive care were partially or completely shut down, with their resources redistributed to intensive care units and covid-19 related procedures. these closures included the closure of pain management departments, posing a challenge for patients with medical conditions causing severe chronic pain such as cancer, as well as for vulnerable populations who rely on our services such as the elderly and disabled. in our pain management departments, we implemented a series of practical strategies to better take care of our most vulnerable patients during the epidemic. during government-mandated quarantine, patients were allowed to file requests for outpatient care. after screening by the strict control requirements, patients who appeared in pain clinic were roughly triaged into different levels of care. the first level included patients with mild to moderate pain with relatively clear etiopathogenesis and who were relatively few comorbidities and in good condition. they were given prescription medications to manage their pain at home along with necessary telemedicine support. those who have had close contact with any individuals diagnosed with or suspected to have covid-19 or who had recently travelled to or from the epidemic area were required to self-quarantine at home and report for further observation. the second level of patients included those with mild to moderate pain and those who either had covid-19-like symptoms or had close contact with individuals diagnosed with covid-19. the third level included those with severe pain or with emergency conditions. these patients received immediate treatment in clinic or were admitted as inpatients for further testing and treatment. for patients triaged to levels 2 or 3, those who presented with any symptoms and/or suspicious from physical examinations that might indicate a covid-19 infection were immediately sent to an isolation ward for further testing and treatment. for inpatients, contact between the patient and health care workers was minimized by scheduling the minimal number of necessary pain treatments, and recovered patients were discharged and supported with telemedicine aid. for those patients with severe pain, we arranged necessary pain treatment including surgery as needed. among our priorities was the timely identification of patients in our pain clinic who were at high risk of covid-19 infection in order to provide aid to patients with severe cases of covid-19, to reduce transmission, and to ensure the proper allocation of limited medical resources. with the help of public health systems, we were able to keep most patients home and provide them with necessary medical services including telemedicine support. these strategies brought tremendous benefits to both health care providers and patients and allowed our pain clinics to continue to function during the epidemic. telemedicine became a convenient and effective way to provide necessary medical services to patients with chronic pain during the initial periods of the epidemic, as it allowed patients with nonemergent conditions to remain at home and allowed hospitalized patients who had been discharged early to maintain continuity of care. via telemedicine, we have been able to provide our patients with instructions for administering prescription and non-prescription drugs as well as guidance for physical at-home exercises for pain relief. when possible, bedside procedures were performed during home visits for patients in urgent need. for instance, in our pain departments in wuhan and in shenzhen, some patients with cancer pain continued to receive continuous home treatment with programed intrathecal injection of opioids. we arranged regular home visits for these patients and provided minimally necessary management such as drug refills. during the nation-wide quarantine, city traffic was also greatly reduced, allowing physicians to make home visits more easily. patients 6 with severe pain needing urgent treatment or with complex conditions were still seen at our pain clinic in-person or referred to other departments for further observation and treatment. the very first outpatient in the pain clinic at wuhan fourth hospital to be an increasing concern among medical providers is that the fear of missing a covid-19 infection can lead to the failure to recognize other urgent medical issues. at our shenzhen hospital, a 34 year old man visited the pain clinic with moderate rightsided rib pain and mild fever. this patient had travelled from wuhan one day before the city's lockdown and had already served two weeks of quarantine in shenzhen. medical staff immediately suspected covid-19. he was sent home for another twoweek quarantine with telemedicine follow-up. during this second quarantine, the patient had persistent fever, worsening pain, and was partially paralytic when we saw him in our clinic two weeks later. only at this point was the patient found to have a spinal neurotoma in the right 8 th thoracic region, with his temporary partial paralysis resulting from tumor compression of the spinal cord. the patient received surgical intervention and did well post-operatively. he was also confirmed negative for covidsome of our patients hospitalized with covid-19 complained of mild to moderate body pain. their covid-19 associated pain was similar to patterns of pain we have seen in some outpatients as described previously, suggesting viral-induced myalgias. this pain may have also been due long hospital bed stays causing pain in the joints, spine, muscles and other soft tissues, as well as physically manifested pain associated with covid-19 related psychological stress. throughout their hospitalizations, we made sure to schedule regular visits to their isolation wards and provided appropriate pain consultant and management. the first lesson we learned was that we must ensure that key information regarding serious infectious diseases is as accurate and as transparent as possible with timely updates. as viruses have the potential to be spread to anyone, it is immensely important to keep the public informed of ways to stay hygienic and minimize the spreading of disease. public administration and media should be honest and responsible in order to facilitate public awareness as well as reduce false rumors that can cause widespread panic and unease. the right to public discourse including constructive criticism of ongoing public health efforts should be protected and even encouraged in order to achieve optimal strategies in addressing various aspects of the pandemic. humility in the face of the unknown is a strength. globally, countries should take firm action and implement preventive and protective measures. governmental support and coordination of efforts is necessary to ensure sufficient access to and distribution of medical resources for communities and health care systems in need. according to the who, quarantine and personal protection are two of the best ways to limit the spread of infectious respiratory diseases (7) . wuhan's lockdown and china's nation-wide quarantine dramatically reduced the spread of covid-19. protecting oneself means protecting others, because one's own safety depends on the safety of the whole community. since the early stages of covid-19 in wuhan, chinese people were required to wear masks to reduce the spread of disease (8), a strategy which has also been recommended by who for most respiratory infectious diseases (7). wuhan's experience provided us with both tragic and encouraging information about the importance and effectiveness of personal protection. a report showed that, in some of the wuhan's hospitals, 54 physicians and nurses were infected with the sars-cov-2 virus from late january to march 2020. of those infected, 22% were working in high risk departments such as infectious disease and intensive care units, while the majority (78%) worked in departments with less direct exposure to covid-19 patients (9) . the red cross society of china reported that 35% of infected doctors and nurses nationwide (n=2971) worked in high-risk departments and 65% in low-risk departments (10) . amazingly, the 42,600 physicians and nurses sent to wuhan from dozens of other provinces and cities to provide medical support to the city, none were infected with covid-19 (11) despite working day and night on the front lines, likely because they were equipped with the adequate personal protective equipment. these data provide strong evidence that sufficient personal protection can prevent the spread of covid-19. the epidemic provided many medical professionals an opportunity to incorporate telemedicine into pain management for the first time due to the urgent need for remote health care services. for many of patients with different types of chronic pain, telemedicine support in addition to necessary in-person visits may be a much better strategy for outpatient treatment, even outside of epidemic conditions, as it is both cost-effective and does not compromise quality care for patients with chronic pain. telemedicine is increasingly being recognized as a valuable tool to both healthcare providers and patients and is worthy of further evaluation and implementation worldwide, particularly in china, where telemedicine support has not been widely used and there is great demand for both inpatient and outpatient health care. the national health council has recently emphasized the online services to further strengthen the prevention and control of epidemic situation in hubei (12). during quarantine, patients with chronic pain were forced to stay home, while many patients who would have qualified for in-person clinic visits chose to stay home due to fear of covid-19 infection. now that quarantine is being lifted in many parts of china, many are still understandably wary of seeking in-person health care. we must consider strategies to encourage those with health issues needing management to seek outpatient care, as well as continue to provide telemedicine support. meanwhile, health care providers should be aware that pain may be related to covid-19 infection 11 in a variety of forms as we discussed in our cases-as an early sign of infection, or as a sequela of infection and iatrogenic effects such as prolonged bedrest and psychological stress. of course, pain may very well be a manifestation of a non-covid-19 related process. these patients can be better served with our improved strategies of pain management. we may prepare ourselves to see more patients who previously had covid-19 infection visiting pain clinic as the epidemic slows. chinese national health council: document no wuhan city government document no.1. 2020. regarding coronavirus pneumonia epidemic world health organization director-general's statement on the advice of the ihr emergency committee on novel coronavirus joint prevention and control mechanism of state council of china: press conference the red cross society of china: aid programs for anti-sars-cov-2 wuhan customs: notice on customs clearance of import donations used for prevention and control of new type coronavirus pneumonia world health organization: infection prevention and control during health care when covid-19 is suspected. interim guidance office of the chinese national health council: circular on the issuance of technical guidelines for the prevention and control of new forms of coronavirus infection in medical institutions (1 st version clinical characteristics of 54 medical staff with covid-19: a retrospective study in a single center in wuhan the red cross society of china: byte beat medical big data foundation joint prevention and control mechanism of state council of china: caring the frontline workers joint prevention and control mechanism of state council of china: notice on developing online services to further strengthen the prevention and control of epidemic situation in hubei province key: cord-280892-net44oxu authors: zhan, yu-xin; zhao, shi-yu; yuan, jiao; liu, huan; liu, yun-fang; gui, ling-li; zheng, hong; zhou, ya-min; qiu, li-hua; chen, jiao-hong; yu, jiao-hua; li, su-yun title: prevalence and influencing factors on fatigue of first-line nurses combating with covid-19 in china: a descriptive cross-sectional study date: 2020-08-07 journal: curr med sci doi: 10.1007/s11596-020-2226-9 sha: doc_id: 280892 cord_uid: net44oxu nurses’ work-related fatigue has been recognized as a threat to nurse health and patient safety. the aim of this study was to assess the prevalence of fatigue among first-line nurses combating with covid-19 in wuhan, china, and to analyze its influencing factors on fatigue. a multi-center, descriptive, cross-sectional design with a convenience sample was used. the statistical population consisted of the first-line nurses in 7 tertiary general hospitals from march 3, 2020 to march 10, 2020 in wuhan of china. a total of 2667 samples from 2768 contacted participants completed the investgation, with a response rate of 96.35%. social-demographic questionnaire, work-related questionnaire, fatigue scale-14, generalized anxiety disorder-7, patient health questionnaire-9, and chinese perceived stress scale were used to conduct online survey. the descriptive statistic of nurses’ social-demographic characteristics was conducted, and the related variables of work, anxiety, depression, perceived stress and fatigue were analyzed by t-tests, nonparametric test and pearson’s correlation analysis. the significant factors which resulted in nurses’ fatigue were further analyzed by multiple linear regression analysis. the median score for the first-line nurses’ fatigue in wuhan was 4 (2, 8). the median score of physical and mental fatigue of them was 3 (1, 6) and 1 (0, 3) respectively. according to the scoring criteria, 35.06% nurses (n=935) of all participants were in the fatigue status, their median score of fatigue was 10 (8, 11), and the median score of physical and mental fatigue of them was 7 (5, 8) and 3 (2, 4) respectively. multiple linear regression analysis revealed the participants in the risk groups of anxiety, depression and perceived stress had higher scores on physical and mental fatigue and the statistically significant positive correlation was observed between the variables and nurses’ fatigue, the frequency of exercise and nurses’ fatigue had a statistically significant negative correlation, and average daily working hours had a significantly positive correlation with nurses’ fatigue, and the frequency of weekly night shift had a low positive correlation with nurses’ fatigue (p<0.01). there was a moderate level of fatigue among the first-line nurses fighting against covid-19 pandemic in wuhan, china. government and health authorities need to formulate and take effective intervention strategies according to the relevant risk factors, and undertake preventive measures aimed at reducing health hazards due to increased work-related fatigue among first-line nurses, and to enhance their health status and provide a safe occupational environment worldwide. promoting both medical and nursing safety while combating with the pandemic currently is warranted. physiological fatigue and psychological fatigue [1] . nurse fatigue refers to a "work-related condition that ranges from acute to chronic in nature and can result in over-whelming sense of tiredness, decreased energy, and exhaustion, ultimately accompanied by impacting physical and cognitive functions" [2] . fatigue in nurses is complex and arises in response to individual, unit, and health care system demands [3] . kahriman et al reported that 83% of medical errors were positively correlated with nurses' fatigue [4] . the emergence of corona virus disease 2019 (covid19) in wuhan, china was in december 2019 [5] . on march 11, 2020 , the world health organization declared covid-19 as a global pandemic with the spread of this worst global crisis [6] . all on-the-job nurses in wuhan were fully engaged in the continuous combating with the prevention and control of the pandemic as the first-line nurses at the first time. the tremendous psychological burden and rescue challenge greatly aggravated the symptoms of fatigue among the first-line nurses in wuhan, and easily led to various psychological abnormalities [7] . previous study showed that there was a strong relationship between fatigue and the lifestyles and psychological states [8] . it was reported that a fall in resistance to the existing physical, mental and emotional stress in nurses might lead to anxiety, depression and ultimately fatigue [9, 10] . the sudden outbreak of sars in 2003 had a psychological impact on nurses. studies have shown that nurses are reluctant to go home for fear of infecting relatives, colleagues and friends [11] [12] [13] . health care workers spent hours each day putting on and taking off airtight protective equipment, which aggravated the exhaustion that the workers were experiencing from the increasing workload with the outbreak of sars [14] . the nurses' stress was found to be mainly due to the lack of protective gear and basic equipment, especially in the early phase of the ebola virus disease outbreak [15] . in 2014, the ebola outbreak was also a challenge for the physical and mental health of health care professionals. despite shift hours and the risk of infection, the challenging treatment environment created anxiety, depression, fatigue and social isolation for health care professionals [16] . national health commission of china had published several guideline documents aimed to settle the emergency psychological crisis through establishing psychological assistance hotline and a series of interventions for the medial personnel during the pandemic. furthermore, it would be necessary to carry out widespread surveillance to monitor and manage the risk of fatigue possibly involved in work-related and negative mental status among the first-line nurses. at present, we found no large sample study on fatigue status and risk factors of the first-line nurses in wuhan. the aim of this study is to evaluate the prevalence of fatigue status among first-line nurses responsible for rescue of covid-19 in wuhan, and to analyze the influencing factors associated with physical and mental fatigue of nurses. the findings of this study may be used to provide strategies to better assist health care administrators in addressing the physical and mental health of nurses domestically and internationally, and so as to supply references for the medical and health management to implement effective intervention to relieve the mental burden and reduce the fatigue level, contribute to construction of the safe occupational environment and promote medical and nursing safety. a descriptive cross-sectional survey was conducted with a convenience sample of nurses from 7 hospitals in wuhan, china from march 3 to 10, 2020. to be eligible, all participants were the registered nurses. all procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 helsinki declaration and its later amendments or comparable ethical standards. the including criteria for population included the nurses who have participated in the first-line nursing work of covid-19 patients from january 1 till now. the nurses without nurse qualification certificate, foreign aid nurses, trainee nurses from other hospitals, and nurses who were continuously off duty from january 1 to the investigation period (maternity leave, sick leave, personal leave, etc.) were excluded from this study. according to the multi-factor analysis sample estimation method of 6-10 times variables of the total number of items in the questionnaire, the minimum sample size was 610. considering 20% of the invalid filling rate of the questionnaire, it was expected that at least 732 questionnaires would be conducted. finally 2768 questionnaires were completed, and 2667 of them were valid, for a survey response rate of 96.35%. in this study, questionnaire stars were used to make two-dimensional code, and wechat was used to distribute the questionnaire online. the research established a questionnaire survey group, which was mainly responsible for the distribution and collection of questionnaires in 7 hospitals respectively. after obtaining approval of ethics committee of the researcher's hospital and the consent and cooperation from 7 respective hospitals, each chief nurse in charge of hospitals was approached to be familiar with the purpose and procedure of the investigation. the researchers trained 7 investigators in a unified way, including the aim, composition and filling requirements of the questionnaire. the survey group checked the questionnaires one by one and eliminated the invalid ones. exclusion criteria of invalid questionnaire were as follows: inconsistency in logic of answering, such as filling in contradictions and inconsistencies, answering time less than 300 s, simple repetition and abnormal answering, and informed disagreement. in order to ensure the accuracy of the data, the research group strictly implemented pre-control of the quality. (1) questionnaire design: on the basis of consulting and referring to domestic and foreign literature, the scale was selected, modified and supplemented in combination with the opinions of public health management and nursing management experts to ensure the universality and specificity of the questionnaire; (2) answer setting: all items were set as required questions to ensure the integrity of the questionnaire; the way of filling in the questionnaire was set as one time for each equipment answer to avoid repeated answers; (3) pre-survey: the research designer, investigator and some respondents participated in the pre-survey of the questionnaire, and discussed and revised the design of the questionnaire and the setting of items. the revised questionnaire was used to carry out the pre-survey again to test the reliability of the method. (4) formal investigation: convenient sampling method was adopted, and the trained investigators of each hospital used the guidance to fill in the instruction uniformly, so as to prevent investigation bias. the investigators used consistent language to explain when the respondents had questions. (5) data processing: the data were encoded, input, summarized and checked by two members of the research group, and logical correction was carried out. problems found were corrected in time, and invalid questionnaires were eliminated. this questionnaire included general information about the age, gender, education level, years of working experiences, marital status, fertility status, professional titles, lifestyles within the last month such as average length of daily break and night sleep and exercise. this questionnaire asked information about the participants' current working status in hospital respectively. the scale was developed by king's college hospital in the uk, which was mainly used to measure the severity of fatigue symptoms, evaluate clinical efficacy, and screen fatigue cases in epidemiological research [17] . there are 14 items in the scale which reflect the severity of fatigue from different perspectives: items 1-8 reflect physical fatigue, and items 9-14 reflect mental fatigue. the scores are added from items 1 to 8 to get the scores of physical fatigue, and the scores are added from items 9 to 14 to get the scores of mental fatigue, while the total score of fatigue is the sum of the scores of physical and mental fatigue. the highest physical fatigue score is 8, the highest mental fatigue score is 6, the highest total score is 14, the total score ≥7 implies that fatigue status exists. the higher the score, the more serious the reflection of fatigue. the total cronbach's alpha coefficient is 0.7725, and the half coefficient is 0.7725, which indicates the scale has good internal consistency [18] . the cronbach's alpha coefficient was 0.850 in our study. the scale was developed by spitzer et al in 2006 according to the diagnostic criteria of generalized anxiety disorder for screening of generalized anxiety disorder and evaluation of symptom severity [19] . the scale consists 7 items, each of which describes a typical symptom of generalized anxiety disorder. the scale is graded according to the status and frequency of its occurrence in the past two weeks. the total score is formed by adding the scores of each item of the scale, ranging from 0-21. according to the scoring criteria, the results of scores are divided into four degrees: scores for 0-4, 5-9, 10-14 and 15-21, corresponding to none, mild, moderate and severe level of anxiety respectively [20] . the higher the score, the more serious the anxiety. gad-7 is easy to implement, and has good reliability and validity in different populations. the cronbach's alpha coefficient of gad-7 in chinese version is 0.898 [21] . the cronbach's alpha coefficient was 0.947 in our study. the scale was based on the nine criteria of depression in the handbook of diagnosis and statistics of mental disorders published by the american psychiatric association [22] . the scale consists 9 items and the total score is composed of the scores of each item in the scale, ranging from 0 to 27. according to the scoring criteria, the results of scores are divided into five degrees: score 0-4, 5-9, 10-14, 15-19, 20-27, corresponding to none, mild, moderate, excessively moderate and severe level of depression respectively [23] . the higher the score, the more serious the depression. the cronbach's alpha coefficient of phq-9 in chinese version is 0.857 [24] . the cronbach's alpha coefficient was 0.933 in our study. the scale was widely used in the mental health assessment of the occupational population. it was revised by yang et al according to the foreign version of the perceived stress scale (pss) into chinese version [25] . the scale consists of 14 items reflecting stress tension and loss of control, and participants are required to answer according to their own feelings [26] . a score of 0-24 indicates normal pressure; 25-42 indicates high pressure; 43-56 indicates excessive pressure. the scale has high homogeneity and internal consistency among different populations in china, and cronbach's alpha coefficient is 0.797 [25] . the cronbach's alpha coefficient was 0.823 in our study. data were analyzed using the ibm statistical package for social sciences (spss) version 23.0. descriptive statistics were used to present participants' social-demographic and work-related factors and the prevalence of fatigue. mann whitney test and kruskal wallis test were used to analyze the fatigue status of nurses in different social-demographic characteristics, work-related variables, anxiety, depression and perceived stress levels; and pearson's correlation analysis was conducted to examine the relationships between the anxiety, depression, perceived stress levels and fatigue of nurses; multiple stepwise linear regression analysis was performed to identify the influence of aforementioned variables on first-line nurses' fatigue. an alpha-level of p<0.05 was set for significance in all analyses. of the 2667 nurses investigated in this study, 3.04% (n=81) were male, 96.96% (n=2586) were female; the median age was 30 (26, 35) years of age; the median year of working experiences was 8 (4, 13) years; 58.98% were married (n=1573), 38.73% were unmarried (n=1033), 2.29% were divorced and others (n=61); 39.26% were unmarried and childless (n=1047), 7.54% were married and childless (n=201), 53.20% were married and childbearing (n=1419). the characteristics of social-demographic are shown in table1. the median score of fatigue of first-line nurses was 4 (2, 8) . the median score of physical fatigue was 3 (1, 6), the median score of mental fatigue was 1 (0, 3). furthermore, 35.06% nurses (n=935) of the all participants had a total score of ≥7, the median score of them was 10 (8, 11), the median scores of physical and mental fatigue of participants with high level of fatigue were 7 (5, 8) and 3 (2, 4) respectively. general data were used as independent variables and scores of physical fatigue and mental fatigue were used as dependent variables for nonparametric test. the results showed that age, years of working experiences, marriage and fertility status, average length of daily break and night sleep and exercise variables had an impact on the score of physical fatigue; years of working experiences, marriage and fertility status, average length of daily break and night sleep and exercise variables had an impact on the score of mental fatigue, and the difference was statistically significant (p<0.05). the results are shown in table 1. work-related variables were used as independent variables and scores of physical and mental fatigue were used as dependent variables for nonparametric test. the results showed that the total number of days of rescue work, average daily working hours, frequency of night shifts, direct participation in the rescue of patients with covid-19, professional protection training, professional psychological assistance, occupational exposure, infection with covid-19, experience of negative events (the relatives, friends and colleagues of participants were seriously, critically ill or even dead due to the pandemic), and the degree of personal fear of covid-19 variables had influence on the score of physical fatigue; the average daily working hours, frequency of night shifts, direct participation in the rescue of patients with covid-19, professional protection training, occupational exposure, experience of negative events (the relatives, friends and colleagues of participants were seriously, critically ill or even dead due to the pandemic), and the degree of personal fear of covid-19 variables could influence the score of mental fatigue, and the difference was statistically significant (p<0.01). the results are shown in table 2. anxiety, depression and perceived stress were independent variables, and the scores of physical fatigue and mental fatigue were used as dependent variables for nonparametric test. 2667 nurses were divided into group of "yes" or "no" which indicated whether they were in risk of abnormal mental status or not, according to the scoring criteria of anxiety, depression and perceived stress scales respectively. the results showed that the total number of each risk group of anxiety, depression and perceived stress was 1062 (39.82%), 1458 (54.65%) and 1298 (62.00%), meanwhile, the median scores of physical fatigue in each risk group of them were 6 (4, 8), 5 (3, 7) and 5 (3, 7) , the median scores of mental fatigue in each risk group of them were 3 (1, 4), 2 (1, 4) and 3 (1, 4), respectively. the results showed that anxiety, depression and perceived stress could influence the scores of physical and mental fatigue. the difference was statistically significant (p<0.01). the results of descriptive and univariate analyses of the factors are shown in table 3, and those of the bivariate correlation analyses between anxiety, depression, perceived stress variables and fatigue are shown in table 4. observed between the average number of weekly exercise and nurses' fatigue (b=-0.266; p<0.001). it was also found that average daily working hours had a significantly positive correlation with nurses' fatigue (b=0.270; p<0.001). meanwhile, anxiety and perceived stress were also positively associated with nurses' fatigue, which means that anxiety (b=0.068; p=0.003) and perceived stress (b=0.103; p<0.001) increase the nurses' fatigue. in addition, the average night shift times every week had a low positive correlation with nurses' fatigue (b=0.070; p=0.036). in our study over a third nurses had a substantial symptoms of tiredness among first-line nurses in wuhan, accordant with the findings reported in study conducted in united states [27] . the result showed the incidence of fatigue was moderate, 35.06% nurses of the all participants had a total score of ≥7, the median score was 10 (8, 11), the median score of physical (2, 4) respectively. during the acute sars outbreak, 89% of health care workers who were in high-risk situations reported psychological symptoms. nurses' fatigue has been recognized as a threat to nurses' health and patient safety [12] . fatigue is not only a status, but also a process. it has been reported that the incidence of fatigue is 35.3%-50.00% in the recent relative studies [27, 28] . if we do not pay attention to the reasonable arrangement of rest, nurses are prone to fatigue syndrome. considering the extremely high risk of tiredness symptom among first-line health care workers in wuhan, their physical and mental health may require special attention. as revealed in the multiple linear regression models of fatigue, average daily working hours had a significantly positive correlation with nurses' fatigue. it has been proved that extended working hours result in the escalating exhaustion, increased traumas and decreased nursing actions [8, 9] . in our study, we found that the mean score of nurses with daily working hours of 4-6 was the lowest. on the contrary, in groups of 8-10 hours and 10-12 hours, the mean score was higher. engaging in the rescue nursing work of patients with covid-19 was a series of challenges. due to the particularity of the pandemic, close use of the protective clothes, glasses and n95 masks for a long time were prone to increase physical discomfort, such as pressure injury, difficulty in nursing practice, even hard to guarantee physiological needs, resulting in physical consumption and affecting work efficiency to a certain extent. when nurses continued to struggle with the pandemic, as the working hours were prolonged and volatile, nurses' psychological states would constantly be disturbed by external work, and the physical fatigue of nurses might also be affected by the continuous efforts in the front line. meanwhile, mental fatigue has a certain impact, and eventually becomes a major hidden risk for safe nursing work. the finding of present study showed that the frequency of weekly night shift had a low positive correlation with nurses' fatigue. the previous study provided evidence supporting the association of work shift length with fatigue [29] . it was found that night shift of 3-4 times per week indicated much higher level of fatigue, and the more frequent night shift, the higher fatigue level in our study. nursing work is both physically and mentally laborious. in the earlier stage of the pandemic, most nurses from different departments were dispatched to the isolation wards urgently, plunged into rescue work with immense obligation, accompanied by the higher frequency of night shift with 8 h in the initial period, consecutive works with insufficient rest during the night on-duty resulted in the physical and mental burnout. sagherian et al [30] gave a strong evidence that in nurses who experienced shift work schedules, working long hours, disturbed circadian rhythm, fatigue eventually became unavoidable and carrying out optimal nursing performance was a challenge. based on our findings, it was also found after decreased the frequency of night shift to 1-2 times per week through effective managements and other creative and innovative workplace scheduling, the level of nursers' fatigue declined significantly. this study reported that the frequency of exercise and nurses' fatigue had a statistically significant negative correlation, and nurses without taking any exercises showed higher level of physical fatigue than in the exercise groups. healthy lifestyle can effectively improve the process of nurses' health promotion and physical activity or exercise had been proved to be linked with an increase in sleep quality and to reduce chronic fatigue [31] . despite other lifestyle variables did not enter the multivariate analysis lastly, the subsequent lifestyle-related variables which were statistically significant in univariate analyses needed to be noticed, for nurses in groups of 30-60 min and over 60 min for daily lunch break, and nurses with sufficient night sleep, showed lower scores than in the group without lunch break and adequate night sleep. previous study indicated a significant relationship between insufficient rest period and fatigue [30] . the intense rescue work and shortage of human resources can lead to the repeated restriction of rest, substantially impair cognitive performance and decrease alertness among the first-line nurses, resulting in the distinctly greater level of fatigue. psychological health related factors were included in our study. at present, a series of studies [32] [33] [34] about mental health research of rescue nurses in wuhan indicated that nurses experienced continuous and aggravated negative psychological problems in many aspects, including anxiety, depression and stress, etc., which were consistent with the results in this study. in the present study, the risk symptoms of anxiety, depression and perceived stress in nurses had significant influences on physical and mental fatigue. the higher level of anxiety, depression and perceived stress existed, the more serious degree of physical and mental fatigue emerged. a statistically significant positive correlation was observed between the variables and fatigue through pearson's correlation analysis (p<0.01). our results were consistent with those in the previous studies that fatigue was associated with levels of anxiety and depression [35, 36] . most first-line nurses are females, whose personality characteristics are sensitive, fragile and prone to psychological crises such as insecurity and fear, which leads to aggravation of fatigue. in addition, some first-line nurses are lack of experience in infectious disease rescue and emergency care technology, which also brings great psychological stress. there was a moderate level of fatigue among the first-line nurses fighting against covid-19 pandemic in wuhan, china. individuals, health authorities and government need to formulate and take effective intervention strategies according to the relevant risk factors, and undertake preventive measures aimed at reducing health hazards due to increased work-related fatigue among first-line nurses, and to enhance their health status and provide a safe occupational environment worldwide. fatigue has a detrimental effect on nurses' overall perceptions of patient safety [37] . work-related fatigue includes physiological, cognitive, emotional and sensory elements that result as a consequence of high work volume and insufficient time for energy recovery. the physical and mental fatigue is likely present among nurses. physical fatigue is caused by physical labor and load, which is characterized by general discomfort and reduced ability to produce strength or power. mental fatigue is caused by mental task and stress, resulting in elevated level of fatigue and decreased level of concentration, motivation and alertness [38] . the persistence in healthy lifestyle is encouraged, moderate exercise is conducive to relieve the state of nervous tension, eliminate tension, release psychological pressure, promote deep sleep, and optimal rest [32, 31] . methods for nurses to deal with psychological crisis or emotional response, such as appropriate emotional catharsis allow themselves to have negative emotions, and detect and adjust them timely; find suitable relaxation ways; change cognition and attitude; maintain full understanding between nurses and patients; seek social support when necessary; share their feelings and experiences with colleagues and peers; choose to keep in touch with family and friends; increase the family background resources; make up for the lack of resources brought by high work family conflict, in order to improve work passion and alleviate psychological problems, maintain physical and mental integrity and activeness. the complexity and multidimensional nature of nursing work may lead to fatigue, and health care institutions need to better understand the factors that contribute to nurses' fatigue and consider accurate mitigation strategies. fatigue risk management systems (frms) [39] was recommended to set up in hospitals to provide a comprehensive approach to reduce risks from fatigue, including instituting workplace policies, establishing procedures to protect tasks that are vulnerable to fatigue-related errors, promoting education for managers and nurses, taking fatigue-related factors into the considerations of investigation on adverse events. the hospital officials should ensure a better working environment for medical staff, appropriate working hours and frequency of night shift, eliminate job burnout, improve the work immersion level of nurses, and reduce the occurrence of adverse events. it is suggested that countries and regions with the pandemic should provide strong support for rescue nurses to lessen work-related fatigue in daily working. it is necessary to request the support of superior departments, allocate the human resources of nurses reasonably, according to the dynamic and flexible principle, adjust the working mode and working length according to the workload, and reduce unnecessary too-prolonged work for first-line nurses. every person and each organization are involved in the rescue work when encountering the pandemic. government should establish and improve the response mechanism for major public health emergencies [6] , and give full play to the role of the government system in each region combating with the pandemic, concentrate and integrate the advantageous resources, establish a complete medical and life support system, and provide strong social support for the medical staff and organizations participating in current rescue. providing humanistic care to all the rescue staff, including solving the necessary problems of dining, accommodation, life, transportation, so as to ensure their strong enforce to participate in and promote the improvement of team performance while reducing the conflict experience, may be beneficial for relieving their negative mental stress. the organization should provide support on mental health knowledge with the aim of mastering the psychological stress reaction process and performance of nurses appropriately, implement targeted mental health assessment and intervention, strengthen the psychological crisis intervention during and after the pandemic situation, which could cut down the negative emotions of medical staff effectively. the present research has several limitations. first, a descriptive cross-sectional design was used, and no cause-and-effect relationships were established. thus, it would be necessary to conduct a longitudinal study and ascertain the variables with a cause-effect relationship. secondly, the study was based on a questionnaire survey with self-report instruments, and all of the variables were measured in terms of participants' subjective perceptions, the bias is not avoidable, which can affect the response reliability. future studies using random sampling frames can enhance the external validity of the findings. nevertheless, we made efforts to control for the personal and professional characteristics of participants to provide the clearest possible image of working as first-line nurses combating with covid-19 in wuhan, china. further prudent investigation using multiple modes of inquiry should be performed and deeper interviews during periodical examinations may be needed on this topic to diagnose chronic fatigue syndrome. this study is of great significance to the rescue nursing work of the pandemic currently. first, health care authorities should be aware of this issue and pay more attention to the physical and mental state of nurses, for it could lead to adverse health conditions for nurses working in current severe situation of pandemic prevention and control. the long-term fatigue of nurses not only damages individual physical and mental health, increases psychological crisis events for nurses under the rescue condition, but also reduces the efficiency and quality of rescue work, patients' disease recovery and safety might be affected. it is imperative to strengthen the support and guarantee system of national government and health care settings for rescue nurses all over the world. to sum up, addressing fatigue and managing risk across industries have received growing attention in the occupational health literature. while fatigue in nurses is a significant challenge in health care, concrete guidelines and methods to reduce fatigue or mitigate its negative effects on safety and performance are lacking. findings from the present research could promote more comprehensive awareness of the contributing factors in the rescue work-related system and psychological variables relate to increased fatigue levels, ultimately guide the design of relevant and appropriate fatigue mitigation interventions, and undertake measures to lessen fatigue in practice context of combating with the pandemic at present. defining and measuring fatigue an integrative review fatigue among 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nurses during the outbreak of covid-19 fatigue in intensive care nurses and related factors demographic and occupational predictors of stress and fatigue in french intensive-care registered nurses and nurses' aides: a cross-sectional study fatigue, burnout, work environment, workload and perceived patient safety culture among critical care nurses impact of fatigue on performance in registered nurses: data mining and implications for practice addressing occupational fatigue in nurses: current state of fatigue risk management in hospitals, part 1 authors acknowledge all participants who responded to the surveys and the nursing administrators for the cooperation with their effort and time in conducting the present study. the authors declare that there is no conflict of interest regarding the publication of this article. key: cord-255905-ti9b1etu authors: qiu, chengfeng; xiao, qian; liao, xin; deng, ziwei; liu, huiwen; shu, yuanlu; zhou, dinghui; deng, ye; wang, hongqiang; zhao, xiang; zhou, jianliang; wang, jin; shi, zhihua; da, long title: transmission and clinical characteristics of coronavirus disease 2019 in 104 outside-wuhan patients, china date: 2020-03-06 journal: nan doi: 10.1101/2020.03.04.20026005 sha: doc_id: 255905 cord_uid: ti9b1etu background: cases with coronavirus disease 2019 (covid-19) emigrated from wuhan escalated the risk of spreading in other cities. this report focused on the outside-wuhan patients to assess the transmission and clinical characteristics of this illness. methods: contact investigation was conducted on each patient who admitted to the assigned hospitals in hunan province (geographically adjacent to wuhan) from jan 22, 2020 to feb 12, 2020. demographic, clinical, laboratory and radiological characteristics, medication therapy and outcomes were collected and analyzed. patients were confirmed by pcr test. results: of the 104 patients, 48 (46.15%) were imported cases and 56 (53.85%) were indigenous cases; 93 (89.42%) had a definite contact history with infections. family clusters were the major body of patients. transmission along the chain of 3 &ldquo:generations” was observed. mean age was 43 (rang, 8-84) years (including 3 children) and 49 (47.12%) were male. most patients had typical symptoms, 5 asymptomatic infections were found and 2 of them infected their relatives. the median incubation period was 6 (rang, 1-32) days, of 8 patients ranged from 18 to 32 days. just 9 of 16 severe patients required icu care. until feb 12, 2020, 40 (38.46%) discharged and 1 (0.96%) died. for the antiviral treatment, 80 (76.92%) patients received traditional chinese medicine therapy. conclusions: family but not community transmission occupied the main body of infections in the two centers. asymptomatic transmission demonstrated here warned us that it may bring more risk to the spread of covid-19. the incubation period of 8 patients exceeded 14 days. hospital-associated infections in wuhan 2, 6 . until we know this information about it also hard to assess how bad this novel coronavirus is going to get. province geographically adjacent to wuhan, hubei province, high-efficiency transport between the two provinces may lead to a rapid spread of covid-19 in hunan province. this report included the hospitalized patients with covid-19 to assess the transmission and clinical characteristic of two hospitals, which designated as the treatment center for the ncp in huaihua and shaoyang cities, hunan province, china. these findings could provide value information to better understand such new illness. in this study, we recruited confirmed patients with covid-19 from two hospitals, the first people's hospital of huaihua and the central hospital of shaoyang which designated as the treatment center of huaihua and shaoyang city, huanan province, china from jan 22, 2020 to feb 12, 2020 . according to the guidelines of china 7 , patient was confirmed by the positive result from the real-time reverse-transcription-polymerase-chain-reaction (rt-pcr) assay of nasopharyngeal or throat swab. suspected infectors that did not confirmed by pcr were excluded. for the study population, imported case was defined as an infector who emigrated from wuhan (who ever lived in or traveled to wuhan), the rest of study patients were defined as indigenous cases. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint we carefully surveyed the contact history of every patients, including whether he or she ever lived in or travelled to wuhan, or had closely contacted with people returning from wuhan during two months before their illness onset. in addition, the history of contacting with animals and eating game meat was also screened. if necessary, we directly communicated with the attending physician, patients or their family members. demographic, clinical, laboratory and radiological characteristics, medication therapy (ie, antiviral therapy, antibacterial therapy, corticosteroid therapy and traditional chinese medicine therapy), underlying comorbidities, symptoms, sign and chest computed tomographic images were obtained from electronic medical records. outcomes were followed till feb 12, 2020. standard questionnaire and form were used for contact investigation and data collection. the data were independently reviewed by two trained physicians (ye deng and xin liao) and checked by another two physicians (hongqiang wang and da long) respectively. every one signed data authenticity commitment and stamp official seal. the date of onset symptom was defined as the day when the case firstly developed symptoms related to ncp. acute respiratory distress syndrome (ards) was defined according to the berlin definition 8 . acute kidney injury was identified by an abrupt decrease in kidney function including changes in serum creatinine (scr) (≥0.3mg/dl or 265.5μmol/l) when they occur within a 48-hour period, other diagnostic items according to evaluation, and management of acute kidney injury: a kdigo summary 9 . liver function abnormal was all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint defined as abnormal of liver enzymes or bilirubin. cardiac injury was identified by the serum levels of cardiac biomarkers (eg, troponin i) which is above the 99 th percentile upper reference limit or new abnormalities shown in electrocardiography and echocardiography 2 . in this study, case confirmation accords to the positive results of pcr. nasopharyngeal swab was collected from suspected patients. sample collection and extraction followed the standard procedure. the primers and probe target to open reading frame (orf1ab) and nucleoprotein (n) gene of covid-19 were used. the procedure and reaction condition for pcr application was followed by the manufacture's all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. this study was approved by the ethics committee of the first people's hospital of huaihua (ky-2020013102) and the central hospital of shaoyang (ky-202000103), china. considering the infectious of ncp, we conducted an oral informed consent with every patient instead of written informed consent (www.chictr.org.cn chi ctr2000029734). normally distributed continuous variables were described as mean and standard deviation (sd). for non-normally distributed continuous variables, we used median and interquartile range (iqr) or range. categorical variables were expressed as ratio and percentages (%). differences in means of normally distributed continuous variables were compared using student's t-test (two groups) and the non-normally distributed continuous variables compared using mann-whitney u test. categorical variables were compared using the χ 2 test or fisher exact test. a two-sided p-value 0.05 was considered statistically significant. all statistical all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint tests were performed using spss version 25.0. since china firstly reported the outbreak of a cryptic pneumonia to who on december 31, 2019. the causative agent was soon identified as a novel coronavirus on jan 7, 2020. as the sharply increased number of ncp in wuhan, china ordered a shutdown of wuhan city on jan 23, 2020. hunan province, geographically closed to wuhan, immediately launched a level one emergency response to prevent the infection spreading. the other cities also responded strict control measures in succession. from jan 22, 2020 to feb 12, 2020, a total of 104 cases were confirmed in the two centers of hunan province, 48 (46.15%) were imported cases and 56 (53.85%) were indigenous cases. since feb 6, 2020, imported case no longer appeared in the two centers (figure 1 a) . the cumulative number of confirmed cases increased smoothly in the two centers (figure 1 b), newly confirmed cases per day ranged from 0 to 11, a slight increase of newly confirmed cases was observed from jan 22, 2019 to feb 4, 2020, and then the number turned to a little decline lasted to feb 12, 2020 (figure 1 b) . the stable of the two centers was quite different from the sharply growth of patients in wuhan in recent month. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint with the aim to better understand the transmission characteristics of covid-19 in outside-wuhan cities. we carefully clarified the contact history of each patients. of the 104 patients, 93 (89.42%) patients had a clear contact history with the infections, 11 (10.53%) were sporadic cases that hardly identified a definite contact history. as showed in table 1 , all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint cluster infections including couples, relatives, friends and colleagues transmitted through a close domestic life or dinner. family clusters accounted the most infections of covid-19 in this study population. cluster 6 (2 cases) and 14 (7 cases) infected via taking the same public vehicle together. nosocomial transmission did not happen so far in the two centers. six clusters (table 1, were found in this study. in cluster 5, c89 was infected from his wife c45. with the aim to fast screen the potential infections, their family members took the pcr test. their son-in-law (c'1) and their grandson (c'2) (c'1 and c'2 not included in this study population) got positive results in another hospital, but till now all of them had never developed any symptoms. in cluster 17, c'3 (not included in this study population) returned shaoyang city from wuhan on jan19, 2020, three relatives of c'3 were identified as covid-19 infection after several days of closely contacted with c'3. none of them had contacted with the other suspected infectors during those days. her sister-in-low (c37) was confirmed on feb 1, 2020, her sister (c44) and mother (c49) were confirmed on feb 4, 2020. but so far c'3 had never developed any symptoms. weather c'3 is an asymptomatic infection did not been identified by pcr test, but the same contact history and the similar onset time of her three relatives indicate that c'3 was an asymptomatic covid-19-carrier. in cluster 19, c'4 (not included in this study population) contacted with her college who traveled from wuhan, and soon confirmed by pcr positive result. as an asymptomatic patient, c'4 infected c92 (c'4's all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint mother), c94 (c'4' s father-in-law) and c102 (c'4' s daughter), c102 also had no symptoms with a positive result of pcr test. as showed in table 2 palpitation (1[0.96%]) as onset symptoms. the median incubation duration was 6 days, ranged from 1 to 32 days; 8 patients got more longer incubation duration (18, 19, 20, 21, 23, 24 , 24 and 32 days) that more than 14 days. median time from onset to confirmation was 6 (rang, 0-17) days. there were 16 (15.38%) patients were identified as severe, the ratio of male vs. female was 11:5 and median age was 53 (rang, 18-81); 9 (8.65%) patients required icu care, the ratio of male vs. female was 4:5 and median age was 59 (rang, 18-84). of the 9 icu patients, 3 received invasive ventilation and 4 received noninvasive ventilations. some patients presented with organ function damage, including 5 (4.81%) with liver function abnormal, 3 (2.14%) developed with cardiac injury and 2 (1.89%) developed with acute kidney injury. ards occurred in 13 (12.50%) patients. for the period from admission to all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint developed ards, the median time was 2 (1-8) days. as we followed until feb 12, 2020, 40 (38.46%) had discharged and 1 (0.96%) died, the rest 63 (60.58%) patients stayed in hospital. as showed in table 3 author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint there were 75 of 94 (79.79%) patients lesions involving both lungs. data of initial chest thin-section ct imaging findings in two discharged patients (c56, figure 4 a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the yet fundamental information gaps exist on how to accurately assess the transmission efficiency. while the controversy of sharply increased cases and medical shortage in the early and outbreak stage in wuhan, patients in wuhan may have limitation to fully reflect the true epidemiological characteristics of this illness. evidence has suggested person-to-person transmission of covid-19 via droplets or skin touch 2, 3, 11 . the data of this study showed all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint a notable feature is clustering occurrence, most patients were infected from their family members, relatives or friends through a close contact. only 11 (10.53%) of this study patients were sporadic cases that hardly identified infector source, suggesting that community transmission of covid-19 is not developed rapidly in the two cities (huaihua and shaoyang); this also matches the smooth growth of total confirmed cases. of note, strict control measures by the local government produced a powerful effect on the slowing spread. we are eager to know how infectious the virus is. except the confirmed cases, whether the asymptomatic covid-19-carriers has the infectious is unclear. three cases (c37, c44 and c49) infected from the same person (c'3) who ever traveled to wuhan. but until now, c'3 did not develop any symptoms. though we did not take a pcr test to confirm whether c'3 was a virus-carrier, the same contact history and the similar onset time of her three relatives indicate that c'3 was an asymptomatic covid-19-carrier. five asymptomatic patients were found in this study, one patients (c'4) who infected three family members (c92, c94 and c102) provide evidence that the asymptomatic transmission risks the spread of covid-19, which brings more difficult to cut off the epidemic's transmission route. we surveyed eight infected couples, a total of 3 infants were closely lived with their parents, but none of them was infected. just 3 children were infected from their parents or relatives. these observations further demonstrated that infant and child are not so susceptible as adult, that is consistent with the previous reports 2,3,6,12 . unlike the other reported populations, no nosocomial transmission was found in the two centers 2 . the safeguard of protective equipment and the strengthen of nosocomial infection control may play key roles in the zero accident of hospital-related infection. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint unlike some earlier reports 3,6 , here no gender difference was found among this study patients (47.12% patients were male). this is consistent with a recent report of 138 wuhan patients 2 . this report further provides the evidence that male and female may have the same susceptibility of this illness. this study patients were younger than that of reported patients. it may be related to the patients' job characteristics and social relationship. with the spring festival coming, young or middle-aged people are more likely to attend social activity, which results in person-to-person transmission. common symptoms of onset were similar to the reported patietns [1] [2] [3] . the atypical symptoms such as diarrhea, nausea and runny nose bring us more difficult to diagnose precisely. the incubation duration ranged from 1 to 32 days with the median time of 6 days which was similar to the reported patients 13 . a recent report warned us the incubation duration may extend to 24 days 14 . we also found the incubation duration of 8 patients ranged from 18 to 32 days, indicating that it may exceed 14 days which reported with the initial infections 3 . patients who required icu care just presented 8.65%. with the increased awareness of early discovery and timely treatment, organ function damage was occurred just in few patients, that is quite different from observation of patients in wuhan patients. the higher rate of discharge (38.46%) and lower mortality (0.96%) of this study population may mainly attribute to the relatively superior treat conditions, including enough healthcare worker and single ward for every patient. in addition, psychological intervention was also performed to patients. studies suggested that covid-19 may attacks human's immune system which resulted in cytokine storm 3 . the lymphocyte counts of this study patients were below the normal. here 17 of 19 patients showed a significant decrease in cd4 cell counts and 9 of 17 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint patients showed a decrease in cd8 cell counts, it is a pity that rest of the patients did not take the test. we still don't know the pathogenic mechanism of covid-19, so we should take a route test of the cd4 and cd8 counts for better understanding of this illness. though no antiviral treatment for covid-19 infection has been proves to be effective 15, 16 . antiviral and supportive treatment are the major therapy for ncp. 103 of 104 patients of this study received one or more antiviral drugs, including lopinavar/ ritonavir, interferon α atomization and abidol. lopinavar/ ritonavir was proved to be substantial clinical benefit against sars 17 19, 20 . evidence suggests corticosteroids did not decrease the mortality of patients with sars and mers, but rather delayed the clearance of viral 19, 21 . chinese guideline recommends a short treatment of corticosteroids in server ncp 7 this study has several limitations. first, just two centers of hunan province were included, there is limited information based on the data to fully assess the transmission and all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.20026005 doi: medrxiv preprint clinical characteristics in outside-wuhan cities. second, all patients were confirmed by rt-pcr through nasopharyngeal or throat swab, it could not reflect viral load change in blood or organs. until now it is confused about whether the severity of ncp is related to changes of viral load in blood. third, the follow-up period is not long enough to examine the outcomes of all the included patients. in conclusion, this report gives showed that timely control measures after the wuhan all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the notes, c indicates the cases who have been confirmed as covid-19 pneumonia in the two centers. x indicates the cases who did not included in this study population but have been confirmed as covid-19 pneumonia or as virus-carrier. c' indicates asymptomatic infections. * the others include the confirmed cases returning from wuhan but did not infect others. sporadic cases include the indigenous patients who did not identified the source of infection. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the distribution of the 2019-ncov epidemic. 2020 clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical features of patients infected with 2019 novel coronavirus in wuhan a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the distribution of the 2019-ncov epidemic and correlation with population emigration from wuhan, china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study national health commission p. new coronavirus pneumonia prevention and control program acute respiratory distress syndrome: the berlin definition diagnosis, evaluation, and management of acute kidney injury: a kdigo summary (part 1) importation and human-to-human transmission of a novel coronavirus in vietnam epidemiological and clinical features of the 2019 novel coronavirus outbreak in china early transmission dynamics in wuhan, china, of novel all rights reserved. no reuse allowed without permission author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the clinical characteristics of 2019 novel coronavirus infection in china the novel chinese coronavirus (2019-ncov) infections: challenges for fighting the storm return of the coronavirus: 2019-ncov role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings treatment of middle east respiratory syndrome with a combination of lopinavir-ritonavir and interferon-beta1b (miracle trial): study protocol for a randomized controlled trial corticosteroids as adjunctive therapy in the treatment of influenza clinical evidence does not support corticosteroid treatment for 2019-ncov lung injury sars: systematic review of treatment effects emerging coronavirus 2019-ncov pneumonia drugs one or two antiviral drugs, no.,% (n=104) drugs, no.,% (n=104) % (n=104) % (n=104) % (n=104) % (n=104) all rights reserved. no reuse allowed without permission.author/funder, who has granted medrxiv a license to display the preprint in perpetuity.the copyright holder for this preprint (which was not peer-reviewed) is the key: cord-282652-2w3bx6p8 authors: sun, haoyang; dickens, borame lee; chen, mark; cook, alex richard; clapham, hannah eleanor title: estimating number of global importations of covid-19 from wuhan, risk of transmission outside mainland china and covid-19 introduction index between countries outside mainland china date: 2020-02-20 journal: nan doi: 10.1101/2020.02.17.20024075 sha: doc_id: 282652 cord_uid: 2w3bx6p8 background the emergence of a novel coronavirus (sars-cov-2) in wuhan, china in early december 2019 has caused widespread transmission within the country, with over 1,000 deaths reported to date. other countries have since reported coronavirus disease 2019 (covid-19) importation from china, with some experiencing local transmission and even case importation from countries outside china. we aim to estimate the number of cases imported from wuhan to each country or territory outside mainland china, and with these estimates assess the risk of onward local transmission and the relative potential of case importation between countries outside china. methods we used the reported number of cases imported from wuhan and flight data to generate an uncertainty distribution for the estimated number of imported cases from wuhan to each location outside mainland china. this uncertainty was propagated to quantify the local outbreak risk using a branching process model. a covid-19 introduction index was derived for each pair of donor and recipient countries, accounting for the local outbreak risk in the donor country and the between-country connectivity. results we identified 13 countries or territories outside mainland china that may have under-detected covid-19 importation from wuhan, such as thailand and indonesia. in addition, 16 countries had a local outbreak risk estimate exceeding 50%, including four outside asia. the covid-19 introduction index highlights potential locations outside mainland china from which cases may be imported to each recipient country. conclusions as sars-cov-2 continues to spread globally, more epicentres may emerge outside china. hence, it is important for countries to remain alert for the possibilities of viral introduction from other countries outside china, even before local transmission in a source country becomes known. the emergence of a novel coronavirus (sars-cov-2) in wuhan, china in early december 2019 has caused widespread transmission within the country, with over 1,000 deaths reported to date. other countries have since reported coronavirus disease 2019 (covid19) importation from china, with some experiencing local transmission and even case importation from countries outside china. we aim to estimate the number of cases imported from wuhan to each country or territory outside mainland china, and with these estimates assess the risk of onward local transmission and the relative potential of case importation between countries outside china. we used the reported number of cases imported from wuhan and flight data to generate an uncertainty distribution for the estimated number of imported cases from wuhan to each location outside mainland china. this uncertainty was propagated to quantify the local outbreak risk using a branching process model. a covid-19 introduction index was derived for each pair of donor and recipient countries, accounting for the local outbreak risk in the donor country and the betweencountry connectivity. we identified 13 countries or territories outside mainland china that may have under-detected covid-19 importation from wuhan, such as thailand and indonesia. in addition, 16 countries had a local outbreak risk estimate exceeding 50%, including four outside asia. the covid-19 introduction index highlights potential locations outside mainland china from which cases may be imported to each recipient country. as sars-cov-2 continues to spread globally, more epicentres may emerge outside china. hence, it is important for countries to remain alert for the possibilities of viral introduction from other countries outside china, even before local transmission in a source country becomes known. the emergence of a novel coronavirus (sars-cov-2) in wuhan city, china at the end of 2019, has caused large numbers of cases of coronavirus disease 2019 and deaths in wuhan. 1-3 as of 11 th february 2020, there are increasing reports of large scale transmission and numbers of cases in other places in china. 4, 5 in addition, there are now reports of cases in multiple countries outside of china, and limited reports of transmission within countries outside of china. 5 from january 23 rd travel from wuhan was halted by the chinese government, and in addition many countries have implemented measures such as airport screening, testing of patients reporting symptoms who have recent travel from china, 5 quarantining arrivals from wuhan and/or china or halting travel altogether. as with many infectious diseases, there is a risk of under reporting of cases, as some people who are infected do not seek care, some who seek care are not diagnosed and, in some settings, those who are diagnosed may not reported. there are also particular issues in an outbreak of a novel pathogen due to difficulties in mobilizing the response and in development of testing capacities, as well as changes over time in the definition of sars-cov-2 infection symptoms. there are therefore concerns the reported cases in countries outside of china may be an under-report of what is actually occurring. previous work has estimated significant under reporting of covid-19 cases in a number of countries such as indonesia, cambodia and thailand. 6 a detailed understanding of the geographical distribution of case importation will help to guide resources to places with currently limited capacity to test, and provide support to perform control measures and support for clinical care. flight data has been used to determine connectivity between countries and therefore risk of onward transmission from china to other countries. early in the outbreak, bogoch et al. listed the countries at most risk of importations given the number of flights from wuhan. 7 their ranking ultimately followed closely the countries that first reported imported cases, albeit with some countries predicted to report that did not. since then others have used flight and other data to highlight countries at most risk of importation of sars-cov-2 from china. 8, 9 these papers have then used the infectious disease vulnerability index (idvi) as an assessment of how at risk a country is to local transmission. 8, 9 in countries where importations are occurring, it will be important to quantify the risk of onward transmission occurring and the extent of this transmission. kucharski et al. 10 considered this generally given the number of importations using a probabilistic model, and wu et al estimated a probability of transmission within cities outside china. 4 however risk estimates of importations to countries outside china have been focused on the risk of importations from mainland china, with the risk being correlated with the connectivity of places in mainland china to other countries. [7] [8] [9] as transmission increasingly occurs in countries outside mainland china it may also become important to consider the risk of importations to and from other countries. indeed there have already been cases outside of china, only reporting travel history to countries outside of china, such as from singapore to the uk, 11 and from thailand, singapore and japan to south korea. 12 in light of this, there is some urgency to assessing the relative risks of onward transmission between countries outside of china. therefore in this paper we estimate 1) the number of imported cases globally from wuhan (using flight data and the currently reported cases), then using our estimates of the number of imported cases and current estimates of r0 for sars-cov-2 we estimate, 2) the probability of an outbreak in countries outside mainland china, and finally given this outbreak risk and the flights between countries outside mainland china, we estimate 3) the risk index for importations occurring from and to countries outside mainland china. there is, of course, large uncertainty in these values and we propagate the uncertainty through the estimates. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.02.17.20024075 doi: medrxiv preprint we used the information on the date, location, and travel history of each reported covid-19 case, which was synthesized and made publicly available by the ncov-2019 data working group. 13 for each country or territory outside of mainland china, we collated data on the total number of reported covid-19 cases imported from wuhan only (not from other places in china), based on the epidemiological data updated as of 7 th february-15 days since the wuhan shutdown (table s1) . for a small number of cases, we were unable to identify the cities from which they were imported. we included these into our data as having originated from wuhan to avoid producing false positive results when we later on identified countries that may have under-detected sars-cov-2 importation from wuhan. we used the monthly number of air ticket bookings during 2017 from the official airline guide 14 to approximate the volumes of air passengers for each origin-destination route. for each country or territory outside of mainland china (denoted by ), we assumed that the total number of covid-19 cases imported from wuhan ( ) followed a poisson distribution with rate parameter proportional to the number of air travelers from wuhan during january 2020 ( → , ), with an unknown coefficient 0 to be estimated from data (more detail in supporting information): to date, the reported total number of imported cases from wuhan ( ) differ substantially between countries even after adjusting for the volumes of air passengers arriving from wuhan. we assumed this was due to inter-country variation in case detection and reporting rates. we ranked countries based on the ratio between the reported case count and passenger volume → , , and assumed all the imported covid-19 cases from wuhan have been successfully detected and reported by countries having the top 10 rankings, to provide a conservative estimate for 0 and hence the number of cases imported from wuhan to the rest of the countries we consider. in the equation below, θ refers to the set of the aforementioned countries having the highest rankings, and the posterior of 0 follows a gamma distribution if we impose a uniform prior: the posterior predictive distribution of the estimated number of covid-19 cases imported from wuhan to each country ∉ θ is thus a gamma-poisson mixture. alternatively, this can be viewed as a negative binomial distribution that models the number of failures before the (∑ + 1 ∈θ ) th success in a series of independent and identical bernoulli trials, each with probability of . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint ⁄ . subsequently, we computed the 95% uncertainty interval for the total number of covid-19 cases imported from wuhan to each country ∉ θ. the left tail probability p( ≤ ) can also be used to identify countries that may have under-detected covid-19 importation from wuhan. next, we propagated the uncertainty in the estimated number of imported covid-19 cases from wuhan, and estimated the probability that a local outbreak would occur and sustain for at least three generations (hereinafter referred to as "local outbreak risk") for each country or territory outside mainland china. we modelled the offspring distribution of each case as a negative binomial distribution, with mean equal to the basic reproduction number estimated by riou et al. 15 , and dispersion parameter assumed to be equal to that of sars-cov. 16 using the first-step analysis, the local outbreak risk can be mathematically derived, where we created two scenarios for each country: (1) only the reported cases imported from wuhan were immediately isolated, but the rest of the estimated cases were not (main analysis) and (2) immediate isolation of 95% of the estimated imported cases from wuhan. here, we assumed that immediately isolated cases were not able to cause any secondary infection throughout their infectious periods, and hence the local outbreak risk estimation was conservative. for the main analysis, we truncated the uncertainty distribution of the imported case count derived earlier using the reported case count, to ensure that the estimated total number of cases imported from wuhan was always greater than or equal to the reported case count. countries with a local outbreak risk above 0.5 in our main analysis were named as potential donor countries, and subsequently assessed for their relative potential of exporting sars-cov-2 to any recipient country or territory outside mainland china, described as follows. for each recipient country outside mainland china , we derived a covid-19 introduction index → (on a relative scale) that ranks potential donor countries in terms of their viral exportation potential. this was expressed as the product of the probability of travelling from a potential donor country to a recipient country in february, and the local outbreak risk , where the total population size in each potential donor country ( ) was based on the data published by the socioeconomic data and applications centre 17 . in addition, we also derived the total covid-19 introduction index estimate for each recipient country ( •→ ) by summing over all the potential donor countries : . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.02.17.20024075 doi: medrxiv preprint outside of mainland china, most countries or territories we estimate as having a large number of covid-19 cases imported from wuhan are located in asia (figure 1 and table s1 ). outside asia, we estimate united states, australia, and united kingdom as having the highest imported case count estimates (figure 1 and table s1 ). in addition, we also identify countries whose reported number of imported cases from wuhan is less than the 5 th percentile of the posterior predictive distribution of our imported case estimates (table 1) , suggesting under-detected cases imported from wuhan in these countries or territories. in particular, we estimate that thailand received 97 (95% ci: 66-136) imported cases from wuhan-the largest among all the countries analyzed but have only reported ~20 cases (table 1) . for indonesia there have not been any reported covid-19 cases imported from wuhan, and yet we estimate at least 19 (95% ci: 10-30) imported cases. if we assume each country has immediately isolated all the reported cases imported from wuhan (and therefore truncated transmission), but not isolated the extra cases we estimated and that no extra control measures are put in place, we estimate that the chance that local transmission would occur and sustain for at least three generations exceeds 50% for a total of 16 countries or territories, including four outside asia: australia, canada, united kingdom, and united states ( table 2 ). in a second scenario, where we assume that 95% of all the imported cases from wuhan were immediately isolated, the estimated local outbreak risk reduces substantially, with only thailand having a local outbreak risk estimate greater than 50%. still, the estimated risk of local transmission sustaining for at least three generations is not negligible (> 20%) in many other countries or territories, including japan, taiwan, hong kong, south korea, united states, malaysia, and singapore ( table 2 for the countries or territories having a local outbreak risk estimate greater than 50% in the main analysis, and figure 2 & table s2 for results obtained for all countries or territories outside of mainland china). for countries where we estimate a large number of unreported cases, the local outbreak risk is ranked higher in the first scenario than the second scenario, as the extra estimated cases not being detected means a higher risk of onward transmission compared to countries where we estimate higher detection (table 2 ). for each recipient country or territory outside mainland china, we assess the relative potential of covid-19 introduction from each donor country that has a local outbreak risk estimate exceeding 50%. for example, hong kong, singapore, and australia are found to have the highest covid-19 introduction index estimates when we consider the united kingdom as the recipient country. using the united kingdom, united states, south korea, and south africa as recipient country examples, we highlight the top donor countries or territories based on the covid-19 introduction index estimate for each of these countries (figure 3 ). the covid-19 introduction index estimates for all pairs of donor-recipient countries create a network of ranked possible importation links between countries outside mainland china (table s3a ). the total covid-19 introduction index estimate from all the potential donor countries is highest for taiwan followed by japan (full list of estimates shown in table s3b ). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint table 2 : countries or territories having a local outbreak risk greater than 50% in the main analysis (i.e. assuming immediate isolation of all the reported cases imported from wuhan). in an alternative scenario, we assumed that each country or territory was able to isolate 95% of all the cases imported from wuhan, and the risk of local outbreak was re-computed (shown in the last column). figure 1 : posterior median estimate of the number of covid-19 cases imported from wuhan, for each country or territory outside mainland china. for the countries having the top 10 highest ratios between the reported number of imported cases and the volume of passengers from wuhan (used as the top reporting rate in our analysis), the reported case counts were shown instead. figure 2 : estimated probability that a local outbreak will occur and sustain for at least 3 generations following the importation from wuhan ("local outbreak risk") for each country or territory outside mainland china: (a) assuming immediate isolation of all the reported cases imported from wuhan; (b) assuming immediate isolation of 95% of all the imported cases from wuhan occurs. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.02.17.20024075 doi: medrxiv preprint this study quantifies, with uncertainty, the estimated number of cases imported from wuhan to countries outside mainland china. as we use information from the places with the highest ratio of the reported case count to the volume of passengers from wuhan, we are only estimating the number of importations if these places with the highest ratio are capturing all imported cases. therefore our estimates should be viewed as a lower bound on the number of imported infections, given possible mild and asymptomatic infections. even given this, we estimate that indonesiawhich has reported 0 cases to date-would be expected to have more cases than this, in line with estimates from lipsitch et al. 6 . in addition, in places that have identified some cases-such as thailand, japan, south korea, taiwan and hong kong, the us and malaysia-we estimate that the imported number of cases from wuhan is even higher than those reported. in some of these places, testing may be already increasing, but if not, our results would suggest that these places should be targets for increased screening and testing for sars-cov-2. we next probabilistically determine the risk of local transmission within countries outside mainland china. there is of course currently great uncertainty in these estimates, however some of the countries we estimate with the highest probability have indeed reported (limited) local transmission such as thailand, the us, singapore, taiwan, japan and the south korea 18 . this information was not used to generate our estimates, but provides some validation for the model. in countries such as singapore, intensive contact tracing of cases and testing of all pneumonia cases was implemented 19 , increasing the likelihood of finding community transmission. the impact of control measures after initial detected cases is not included in our model, but may alter the risk of onward transmission and should be considered in further iterations of the model as in other modelling work considering impact interventions under different transmission scenarios. 20, 21 other countries that we estimate to be at high risk of local transmission, but that have not yet detected transmission 18 include indonesia, cambodia, canada and the philippines. for all these places, our results suggest there could be a consideration of expanding testing of pneumonia or influenza like illness cases beyond those who have currently travelled, to find community transmission as soon as possible after it occurs, as has been ongoing in singapore 19 and has been recommended recently in some areas of the us 22 . we estimate that in the first wave of inter-country spread not including mainland china the countries at highest risk are still mainly within asia, the pacific, north america and europe. the first importations of cases to and from countries outside mainland china have already occurred, including from singapore to the uk, 23 and thailand, japan and singapore to the south korea. 12 singapore was second highest on our uk donor risk result list after hong kong and japan, singapore and thailand were numbers 4, 5 and 6 on the south korea's list after macao, hong kong and taiwan. given our results and these observations, it would seem prudent for planning to consider the scenario in which the number of countries that may be both recipient and donors of importations will be increasing. once transmission is confirmed in a possible donor country, our estimates of the risk transmission index are no longer needed, and the number of reported cases and the volume of traffic between countries are what will become important (see table s3 ). however it must be considered that transmission may not always be detected quickly in all possible donor countries so estimates of the risk of transmission in donor countries may remain useful for planning. though many of the countries at risk of second wave importations are similar to those at risk from wuhan, there are some countries that we did not estimate as having the highest numbers of importations from wuhan, but become at increased risk as we consider donor countries outside mainland china. these include india, new zealand, spain and mexico, as they have greater links to countries outside mainland china than to wuhan, china. with the first imported case in africa recently reported in egypt 24 (which was estimated to have the highest link with mainland china by lai et al. 8 ,) we must assess where we are in the timeline of the outbreak with respect to importations to africa, and including the risk of importation from not only mainland china could be important here. not included in our analysis currently is the risk of importation from places in china outside wuhan. there have yet not been enough importations from outside wuhan to use our current method, and there is currently much uncertainty on the numbers of cases in china to use this data. however as this changes, methods using both types of data could be considered here. the links between other places in china may follow similar patterns to wuhan and therefore our risk of countries vulnerable for outbreaks and sourcing onward transmission may be similar, but there may be places that are differentially connected to wuhan and other places in china and so will become at increased risk as importations from china continue. in addition, flights from other places in china to different countries will be truncated at different times for different countries depending on if and when countries halted incoming flights from china. we also currently don't consider travel across land or sea borders in our analysis. there are other limitations to our analysis. we assume that r0 in places outside of wuhan is similar to that estimated from early transmission in wuhan, however we do not know how variation in climate, population structure, contact patterns, control measures such as contact tracing and quarantine, and other factors may impact transmission. this is an important area for future research based on what is observed in different places and the extension of the analysis to explicitly model transmission in each recipient country can be undertaken as more becomes known. in summary, we estimate a number of imported cases from wuhan that were undetected. given these importations, we estimate a high risk of onward transmission within a number of countries outside mainland china, particularly in those places where cases were not detected, as these undetected cases could not be isolated, and transmission truncated. given our results of high risk of onward transmission we highlight the importance of wider testing to pick up community transmission as soon as possible after transmission occurs. we also highlight countries that become at increased risk of importation as transmission occurs outside china, and provide results for each country to assess the countries that pose their highest risk of importation. genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features of patients infected with 2019 novel coronavirus in wuhan nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study using predicted imports of 2019-ncov cases to determine locations that may not be identifying all imported cases. medrxiv pneumonia of unknown etiology in wuhan, china: potential for international spread via commercial air travel assessing spread risk of wuhan novel coronavirus within and beyond china preparedness and vulnerability of african countries against introductions of 2019-ncov. medrxiv early dynamics of transmission and control of 2019-ncov: a mathematical modelling study. medrxiv ncov-2019 data working group. no title. epidemiological data from the ncov-2019 outbreak: early descriptions from publicly available data definitive flight information, aviation intelligence and analytics pattern of early human-to-human transmission of wuhan superspreading and the effect of individual variation on disease emergence all pneumonia patients in public hospitals in singapore being tested for coronavirus: moh, health news & top stories -the straits times effectiveness of airport screening at detecting travellers infected with novel coronavirus (2019-ncov) feasibility of controlling 2019-ncov outbreaks by isolation of cases and contacts. medrxiv the us will begin testing patients with flu-like symptoms for coronavirus in an expanded effort to contain the outbreak coronavirus: third uk patient "caught coronavirus in singapore key: cord-283891-m36un1y2 authors: hu, bisong; qiu, jingyu; chen, haiying; tao, vincent; wang, jinfeng; lin, hui title: first, second and potential third generation spreads of the covid-19 epidemic in mainland china: an early exploratory study incorporating location-based service data of mobile devices date: 2020-05-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.048 sha: doc_id: 283891 cord_uid: m36un1y2 abstract objectives the outbreak of atypical pneumonia caused by the novel coronavirus (covid-19) has currently become a global concern. the generations of the epidemic spread are not well known, yet these are critical parameters to facilitate an understanding of the epidemic. a seafood wholesale market and wuhan city, china, were recognized as the primary and secondary epidemic sources. human movements nationwide from the two epidemic sources revealed the characteristics of the first-generation and second-generation spreads of the covid-19 epidemic, as well as the potential third-generation spread. methods we used spatiotemporal data of covid-19 cases in mainland china and two categories of location-based service (lbs) data of mobile devices from the primary and secondary epidemic sources to calculate pearson correlation coefficient,r, and spatial stratified heterogeneity, q, statistics. results two categories of device trajectories had generally significant correlations and determinant powers of the epidemic spread. bothr and q statistics decreased with distance from the epidemic sources and their associations changed with time. at the beginning of the epidemic, the mixed first-generation and second-generation spreads appeared in most cities with confirmed cases. they strongly interacted to enhance the epidemic in hubei province and the trend was also significant in the provinces adjacent to hubei. the third-generation spread started in wuhan from january 17 to 20, 2020, and in hubei from january 23 to 24. no obvious third-generation spread was detected outside hubei. conclusions the findings provide important foundations to quantify the effect of human movement on epidemic spread and inform ongoing control strategies. the spatiotemporal association between the epidemic spread and human movements from the primary and secondary epidemic sources indicates a transfer from second to third generations of the infection. urgent control measures include preventing the potential third-generation spread in mainland china, eliminating it in hubei, and reducing the interaction influence of first-generation and second-generation spreads. an outbreak of atypical pneumonia caused by the 2019 novel coronavirus (covid-19) was recognized from middle january, 2020, in wuhan city, china. the novel coronavirus that infects human was first reported in wuhan, hubei province, china, on december 31, 2019 (zhu et al. 2020) . early confirmed cases were mainly linked to a seafood wholesale market in wuhan (li et al. 2020a; zhu et al. 2020) . epidemiological studies indicate that the covid-19 epidemic has a basic reproductive number between 2 and 3 (li et al. 2020a; wu et al. 2020) , which is lower than the 2003 severe acute respiratory syndrome (sars) (lipsitch 2003; riley et al. 2003) . wuhan is a main transportation hub in central china, several million travelers ventured outward from the epidemic outbreak source in the first half of january, 2020, due to annual chinese (lunar) new year holiday migrations. the large-scale outbreak started on january 19 (the first confirmed case reported outside hubei province). although strict transportation screening measures were activated by many cities in the next 3-4 days, the epidemic rapidly spread nationwide in a week. moreover, covid-19 infections have been identified in other countries and the current epidemic has become a global concern (cohen and normile 2020; holshue et al. 2020; rothe et al. 2020; . the world health organization (who) declared the covid-19 outbreak as a public health emergency of international concern (pheic) on january 30 (who 2020b) . there is evidence that the epidemic outbreak in china and elsewhere spread along the paths of travel from wuhan (li et al. 2020b) , and local outbreaks could appear in other major cities of china with time lags (wu et al. 2020) . massive human movements via railways and domestic/international airlines from wuhan, and the timing of chinese new year, has enabled the virus to spread nationwide and worldwide (peeri et al. 2020) . control measures (e.g., travel quarantine and restrictions) in wuhan were effective to delay the overall epidemic progression in mainland china and reduce the international case importations (chinazzi et al. 2020) . the huanan seafood wholesale market and wuhan were recognized as the primary and secondary epidemic centers, respectively, and therefore, the movements of populations from the two sources influenced the generations of the covid-19 epidemic in mainland china, especially during the very early epidemic stage before the transportation measures activated by wuhan and other cities. the first-generation (primary) spread of the epidemic was in part reflected by the human movement from the primary source (i.e., the seafood market), and the secondgeneration (secondary) spread was reflected by that from the secondary center (i.e., wuhan city). they varied and interacted by region and time during the early epidemic progression, and had the potential clues to identify the third-generation spreads in various regions, which are mainly caused by the local cases instead of the imported ones. here, using location-based service (lbs) data of mobile devices, we analyzed the spatiotemporal association of the confirmed covid-19 cases and human movements from the sources of the epidemic outbreak, and revealed the first, second and potential third generation spreads of the covid-19 epidemic in mainland china. we collected spatiotemporal data of covid-19 cases in mainland china from the daily bulletins of the national health commission of the people's republic of china (nhc) and various provincial/municipal health commissions. some publicly available news and media were utilized as supplemental data. the final epidemic dataset was comparatively verified through the public platform of the 2019-ncov-infected pneumonia epidemic from the chinese center for disease control and prevention (china cdc 2020a) . the dataset of the covid-19 cases includes the following fields: date (starting from january 10, 2020), province code/name, city code/name, and numbers of daily new suspected/confirmed cases. from the above dataset, we can generate the cumulative number of daily confirmed cases at a specific city s and until a given end date t, which is denoted by ys,t. the human movement of populations from two epidemic sources (the huanan seafood wholesale market and wuhan), were considered to be associated with the spatiotemporal epidemic spread. the datasets of lbs requests from mobile devices were provide by wayz inc., shanghai, china. the device trace datasets cover over 80% mobile devices supported by the three telecommunication operators in china. the lbs-requesting statistics are implemented every two hours with highresolution location information. the raw data indicate the individual trajectories of numerous mobile devices with high-resolution spatiotemporal information, and can be easily aggregated in a specific spatial scale and within a given time step. for a subpopulation from the epidemic center, we can aggregate the device trace data from the start date to a given end date t, and the corresponding cumulative number at a specific city s is denoted by xs,t. multiple lbs requests within a time step are only counted once by a same device. private individual information was deleted from the raw data of the mobile devices, and in this study, the device trace data was aggregated to the administrative cities and the epidemic date, i.e., the mobile device traces were associated with the j o u r n a l p r e -p r o o f epidemic dataset according to date and location. these aggregated statistics of mobile device traces are expected to be representative of the human migrations from the epidemic sources. two epidemic sources were considered, including the seafood wholesale market and wuhan city. the devices which activated their lbs requests in the market in november 2019 indicated the potential first-generation cases of the covid-19 epidemic. and the potential second-generation cases were those which were activated in wuhan in december 2019 and then traveled to other regions in january 2020. , ( ) and , ( ) are used to denote the spatiotemporal trajectories of the above two subpopulations of mobile devices, respectively. all the processing and aggregation of mobile device trace data were implemented by the provider. the final datasets include the daily counts of two categories of trajectories in all the administrative cities in mainland china. the cumulatively summed device traces had a spatially distributed consistency with the population distribution in mainland china ( figure 1 ). two categories of trajectories mainly spread to the provinces adjacent to hubei and several developed areas a longer distance from hubei, such as guangdong province, zhejiang province and beijing. we considered the spread of the epidemic from the source in various space and time domains, and the corresponding associations with human movements were analyzed in several temporal divisions and spatial scales. seven areas were delineated, including i) wuhan city, ii) hubei province excluding wuhan, iii) hubei province, iv) hubei's adjacent provinces (anhui, chongqing city, henan, hunan, jiangxi and shaanxi), v) mainland china excluding hubei, vi) mainland china excluding wuhan, and vii) mainland china. date periods were generated using three key date stamps, including january 10, 2020 (when the first 41 confirmed cases were reported in wuhan), january 19 (when the large-scale outbreak started) and january 26 (the end of the first week of the largescale outbreak). based on the above datasets of covid-19 cases in mainland china and two categories of location-based service data of mobile devices from the epidemic sources, we calculated their pearson correlation coefficient, r, and spatial stratified heterogeneity (ssh), q, statistics. pearson correlation is usually used to evaluate the linear association between two variables and calculated as follows: (1) where rxy denotes the correlation coefficient of covid-19 spatiotemporal spread and human migrations from the epidemic source, within the period from the start date to a given end date t. ys,t is the cumulative number of daily confirmed cases at city s and xs,t is the cumulative number of device trajectories from the epidemic source, with the mean values of ̄ and , respectively. n is the number of the administrative cities in mainland china. in this study, we calculated two pearson correlations with the spatiotemporal data of two categories of trajectories, , ( ) and , ( ) , to explore the associations between the epidemic spread and the human migrations from the seafood market and wuhan, respectively. the geodetector q statistic is generally applied to quantitatively evaluate the ssh of an explained j o u r n a l p r e -p r o o f variable (wang et al. 2010 (wang et al. , 2016 , and assess the determinant power of explanatory variables and their interaction, without linear assumptions (yin et al. 2019) . the fundamental formula of the q statistic is given by: where q is the determinant power of the factor to the objective. n is the number of objective variable observations and σ 2 indicates the variance of all the observations. the objective is stratified into l stratums, denoted by h =1, 2, …, l, which is determined by the determinant factor. nh is the number of observations and ℎ 2 is the corresponding variance within stratum h. the value of q ranges from 0 to 1. we calculate q statistic to assess the determinant power of human migrations from the epidemic source to covid-19 spatiotemporal spread. similarly, the spatiotemporal data of two categories of trajectories can be applied to calculate two q statistics for the two epidemic sources. within the period from the start date to a given end date t, we implemented the stratification by the equalinterval division after ordering the trajectory data, xs,t, and divided all the observations into 5 strata to calculate the q statistic of the cumulative trajectories, xs,t, to the cumulative cases, ys,t. this is a common stratification way to deal with the numerical independent variables (yin et al. 2019) , which can reduce the subjective influence of various stratifications to q statistics. moreover, for two or more determinant factors, an interaction q statistic can be calculated to measure their interaction influences (e.g., are they independent, or do they weaken/enhance each other?) (wang et al. 2010) . in this study, two categories of trajectories, , ( ) and , ( ) , were used to implement the stratifications and the corresponding q statistics were calculated, respectively, which are denoted by q (m) and q (w) . while the stratification was generated by the intersection between the above two individual stratifications, an interaction q statistic, q (m∩w) , can be calculated, where the symbol "∩" denotes the intersection between two strata layers. various interaction types can be defined according to the comparison between q (m) , q (w) and q (m∩w) (wang et al. 2010) . for instance, "q (m∩w) > q (m) and q (w) " indicates a bi-enhancement interaction between two categories of trajectories in facilitating the spread of the epidemic (see wang et al. 2010 for more details about the interaction q statistic). analyses in this study were performed with the use of the r software package (r foundation for statistical computing) and thematic mapping was implemented in the arcgis platform (esri). similar to the spatial distributions of the mobile device traces (figure 1 ), the pearson correlations r and q statistics between the cumulatively summed cases and two categories of trajectories up to january 26, 2020 had a spatially distributed consistency with the population distribution among the administrative cities in mainland china ( figure 2 ). two categories of trajectories had generally significant correlations and determinant powers of the epidemic spread, and both r and q decreased in distance from the epidemic sources. the first-generation and second-generation transmissions of the infection simultaneously appeared in many cities at the early stage of the outbreak. specifically, devices activated in the market displayed higher values of r and q in several small and medium cities than devices activated in wuhan city (figures 2a and 2c) . it is clear that many cities executed a quick response and activated transportation control measures, which helped control the first-generation epidemic spreads. the r and q statistics of the devices activated in wuhan, however, indicate that the second-generation spread still influenced many cities in the first week of the outbreak ( figures 2b, 2d and table 1 ). the market trajectories received a much higher pearson correlation value to confirmed cases in wuhan (r=0.6160, p<0.001) than hubei province excluding wuhan (r=0.3741, p<0.001) and mainland china excluding hubei (r=0.3319, p<0.001) . the correlations of wuhan trajectories were 0.7438, 0.5874 and 0.5183 in the above three areas, respectively. the temporal correlation curves of both market and wuhan trajectories have obvious decreasing trends from january 17 to 20, 2020 in wuhan ( figure 3a) , which indicates the potential start date of the third-generation epidemic spread. one week after this, market trajectories had higher pearson correlation values than wuhan trajectories, and the first-generation spread still had a serious influence in wuhan ( figure 3a) . similarly, in hubei province excluding wuhan, the potential start date of the third-generation spread was from january 23 to 24 ( figure 3b) . moreover, the second-generation spread played a dominant role in the areas outside wuhan, especially in hubei province excluding wuhan and the provinces adjacent to hubei, since wuhan trajectories had much higher values of correlations ( figures 3b and 3c ). we found no obvious turning dates in the areas outside hubei ( figures 3c and 3d) , and the potential third-generation spread remains to be determined. the curves have remained stationary since january 22 in mainland china excluding hubei ( figure 3d ). the transportation control measures activated by many cities since january 21 appeared to have been successful in partially controlling the first-generation and second-generation epidemic spreads outside hubei province. we focused on the first week of the large-scale outbreak and calculated the q statistics of the two device-activation categories in introducing cumulative confirmed cases in various areas (table 1) . the determinant powers of both categories were extremely high and consistent in wuhan (q=0.8909, p<0.05). their temporal curves had the obvious decreasing trends from january 17 to 20 ( figure 4a ), which validated the start date of the third-generation spread in wuhan. similar validation was observed in hubei province excluding wuhan ( figure 4b ). two categories of trajectories can explain nearly 100% ssh of the epidemic spread in wuhan before the large-scale outbreak and the ssh increased constantly since the third-generation spread stage ( figure 4a ). the market and wuhan trajectories had close determinant powers in introducing the epidemic spread in hubei province (q=0.4153, q=0.4261, respectively, and p<0.001). the q statistics reported that these two categories explained 41.53% and 42.61% ssh of the confirmed cases in hubei. the determinant powers of the epidemic spread in hubei province excluding wuhan were 0.2084 (p<0.01) and 0.2513 (p<0.001), respectively. the q statistic values decreased in distance outside wuhan or hubei and showed that the determinant powers in mainland china excluding hubei were 0.1610 (p<0.001) and 0.1723 (p<0.001), respectively. in the first week of the outbreak, wuhan trajectories received higher values of q statistics than market trajectories in hubei province excluding wuhan and in provinces bordering hubei ( figures 4b and 4c) . the second-generation spread contributed more influence in the areas surrounding the epidemic source. however, both two categories had close q statistic values in mainland china excluding hubei ( figure 4d ). the epidemic outside hubei province appeared as a balanced pattern of mixed first-generation and second-generation spreads. furthermore, the q statistics increased constantly outside hubei province, indicating the increasing ssh of the epidemic spread ( figures 4c and 4d ). more attention should be given to control of the trend of second-generation spread and to eliminate potential third-generation spread. taking into consideration of the interaction influences of two categories of trajectories, the interaction q statistics were calculated in various areas (table 1) . all the interaction types were bienhancement which indicates that two determinant factors (i.e., two categories of trajectories originated from two epidemic sources) enhance each other (the interaction q statistic is higher than each single q statistic but lower than the sum of two single q statistics). the determinant powers and interactions of two categories of trajectories in introducing the epidemic spread decreased in distance from the source to the rest of the nation. the interaction q statistic was 0.1925 (compared to the single q statistics of 0.1610 and 0.1723) in mainland china excluding hubei. the interaction q statistic was 0.0786 (compared to the single q statistics of 0.0657 and 0.0642) in mainland china. although the interaction strength was weak, the combination of both trajectory categories still carried more information about the spread of the epidemic throughout the country. the interaction q statistic of two categories of trajectories in hubei province excluding wuhan was 0.4063, which was close to the sum of two single q statistics (0.2084 and 0.2513) and much higher than each one individually. this interaction indicates strong bi-enhancement in facilitating the spread of the epidemic. two categories of trajectories could significantly enhance each other to explain the ssh of the epidemic spread from wuhan to other areas in hubei province. the majority of the earliest cases of the covid-19 atypical pneumonia were linked to the seafood wholesale market in wuhan, which is the most severely-affected city of the covid-19 outbreak. the movements of populations from these two epidemic sources provided potential first-generation and second-generation spreads nationwide and worldwide. here, based on lbs-requesting mobile device traces and spatiotemporal confirmed covid-19 case data, we applied pearson correlation and geodetector q statistics to analyze the spatiotemporal association between the confirmed cases' dynamic and human movements. our findings provide important foundations to quantify the effect of human movement on the epidemic spread, to judge the epidemic generations, and to inform ongoing and future control strategies. we concentrated on two datasets of lbs-requesting mobile devices associated with two sources linked to the first-generation and second-generation spreads provincewide and nationwide. their traces were aggregated by date in administrative cities and linked to the spatiotemporal confirmed cases. it is notable that the covid-19 outbreak had a strong consistency with human migrations from the epidemic sources. the confirmed cases had a clear linear correlation with two categories of trajectories from the sources to the rest of the nation. moreover, both trajectory categories could generally indicate the epidemic spread in hubei province and explain to a certain extent the ssh of the spread from wuhan to the rest of hubei province and throughout the rest of china. our analyses provide a new perspective to explore the spread of the epidemics linked to human movement. during the first week of the large-scale outbreak, the epidemic spread showed a spatially distributed consistency with the population distribution in mainland china. the majority of cities with confirmed cases had a mixed pattern of first-generation and second-generation spreads at the very beginning of the outbreak. many cities activated quick response within 3-4 days and achieved efficient results in inhibiting the first-generation spread outside hubei province. however, it still had a significant impact in hubei province, especially playing the dominant role inside wuhan city. furthermore, among the other cities in hubei province, the first-generation and second-generation spreads enhanced each other with a much higher interaction q statistic. this might be another signal to identify the potential start date of the third-generation spread in a specific area. due to the quick response and strict control measures in many cities, the interaction enhancement of the firstgeneration and second-generation spreads had a weak strength outside hubei province. there is no evidence that any third-generation spread appeared outside hubei in mainland china in the first week of the outbreak. nevertheless, hubei's adjacent provinces require more effective control measures, since the first-generation and second-generation spreads had an increasing trend. our analyses determined an appropriate approach to explore the spatiotemporal association between the epidemic transmission and human movement. two categories of lbs-requesting mobile devices were used in this study to identify the potential close contacts to the primary and secondary epidemic sources. the datasets covered most devices with lbs requests in the given region and time period. however, the linkage between mobile devices and populations could be subject to information loss (e.g., users may replace their mobile devices with new ones). it is also extremely difficult to cover 100% potential close contacts in our datasets. the close contacts of these two populations while traveling before/after the outbreak were not collected, and therefore we cannot estimate the potential third-generation cases and their movements. this limitation involves future work with more universal-source data and high-performance computing capabilities. the covid-19 epidemic data were collected through publicly available sources, and we processed the data of confirmed cases and device traces in the spatial scale of cities. small-scale analyses could be more helpful to construct epidemic control programs in counties or communities within a city. the spatiotemporal association between the spread of the epidemic and human movements indicates a transfer from second to third generations of the infection. this approach has made it possible to assess the start date of the third-generation spreads of covid-19 epidemic and the interactions between first-generation and second-generation spreads across various regions all over the country. the proposed technique incorporating location-based service data of mobile devices can help identify the spatiotemporal generations at the early stage of the covid-19 epidemic. it can be easily implemented and extended to the early exploratory study of other epidemics similar to covid-19. the results indicate the spatiotemporal characteristics of the epidemic spread associated to human movements from epidemic sources and the potential spatiotemporal risks at the early stage of the outbreak. control measures varying by location and time could be executed in different levels for various regions. for instance, cities with obvious third-generation spread require the strictest controls on both the exportations and the inside quarantine, cities should pay more attention to the importations and the inside quarantine if the first-generation and second-generation spreads have the strong interactive enhancements, and other cities require to focus on the control of the importations. in conclusion, we found that the third-generation spread of the covid-19 outbreak probably started during january 17 to 20, 2020 in wuhan, the potential start date of the third-generation spread in hubei province excluding wuhan was from january 23 to 24, and the mixed first-generation and second-generation spreads strongly interacted to enhance the epidemic. the trend of the interactions between the first-generation and second-generation spreads was significant in the provinces adjacent to hubei. the associations between the epidemic spread decreased with distance and had different temporal pattens from the epidemic sources, implying the potential epidemic generation-togeneration evolution on regional spatial scales. at the very beginning of the outbreak, the mixed first-generation and second-generation spreads appeared in most cities with confirmed cases. no obvious third-generation spread was detected outside hubei province. the strict transportation measures implemented in many cities appeared to have been effective in preventing any thirdgeneration spread nationwide. the urgent control measures in hubei province include weakening the third-generation spread and the interaction influence of the first-generation and secondgeneration spreads. even with strict control strategies, effective measures to reduce transmission in the community are still required (li et al. 2020a) . a large increase in migration due to people returning from travel after the new year holiday also introduces challenges to epidemic control . we recommend the urgent control measures of preventing potential thirdgeneration spread in mainland china, eliminating it in hubei, and reducing the interaction influence of first-generation and second-generation spreads. no individual data was collected and the ethical approval or individual consent was not applicable. the lbs-requesting mobile device data were provided by wayz inc., shanghai, china and are not available for distribution due to the constraint in the consent. the dataset of the covid-19 cases is available from multiple public sources. this work was supported by the national natural science foundation of china (41531179) , the national science and technology major project of china (2016yfc1302504) and the science and technology major project of jiangxi province, china (2020ybbgw0007). the funders had no role in study design and conduct; data collection, management, analysis and interpretation; manuscript preparation, writing and review; decision to submit the manuscript for publication. conceptualization we declare no competing interests. public platform of 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the neural tube defects study of the heshun region, china a measure of spatial stratified heterogeneity emergency committee regarding the outbreak of novel coronavirus (2019-ncov) nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study. the lancet mapping the increased minimum mortality temperatures in the context of global climate change a novel coronavirus from patients with pneumonia in china we thank dr. adam thomas devlin at the school of geography and environment, jiangxi normal university for the assistance in the proofreading work for the manuscript. j o u r n a l p r e -p r o o f key: cord-285315-7r44j3q9 authors: bein, berthold; bachmann, martin; huggett, susanne; wegermann, petra title: sars-cov-2/covid-19: empfehlungen zu diagnostik und therapie date: 2020-04-09 journal: anasthesiol intensivmed notfallmed schmerzther doi: 10.1055/a-1146-8674 sha: doc_id: 285315 cord_uid: 7r44j3q9 covid-19, a new viral disease affecting primarily the respiratory system and the lung, has caused a pandemic with serious challenges to health systems around the world. in about 20% of patients, severe symptoms occur after a mean incubation period of 5 – 6 days; 5% of patients need intensive care therapy. morbidity is about 1 – 2%. protecting health care workers is of paramount importance in order to prevent hospital acquired infections. therefore, during all procedures associated with aerosol production, a personal safety equipment consisting of a ffp2/ffp3 (n95) respiratory mask, gloves, safety glasses and a waterproof overall should be used. therapy is based on established recommendations issued for patients with acute lung injury (ards). lung protective ventilation, prone position, restrictive fluid management and an adequate management of organ failures are the mainstays of therapy. in case of fulminant lung failure, veno-venous extracorporeal membrane oxygenation may be used as a rescue in experienced centres. new, experimental therapies evolve with ever increasing frequency; currently, however, there is no evidence based recommendation possible. if off-label and compassionate use of these drugs is considered, an individual benefit-risk assessment is necessary, since serious side effects have been reported. . die verantwortliche spezies ist nach wie vor unbekannt, fledermäuse gelten als wahrscheinlichste quelle [3] . ausgehend von wuhan verbreitete sich das virus in ganz festlandchina mit einer deutlichen häufung in der provinz hubei [4] . in allen betroffenen ländern zeigte sich initial eine exponentielle zunahme der erkrankungen, welche durch teils drastische maßnahmen zur verminderung sozialer kontakte in einigen ländern (vr china, taiwan, singapur) jedoch abgeflacht werden konnte [5] . die exponentielle infektionscharakteristik beruht wahrscheinlich auf der hohen kontagiosität von sars-cov-2. die entsprechende kennziffer (basisreproduktionsziffer) liegt in einer metaanalyse von 12 studien, die bis zum 7. februar 2020 veröffentlicht wurden, aktuell mit im mittel 3,28 angesteckten pro infizierten über der von sars. merke jeder infizierte hat im durchschnitt 3,28 andere personen angesteckt [6] . die case fatality rate (zahl der infizierten, die verstirbt; letalität) von sars-cov-2 beträgt aktuellen berechnungen nach nur 1,4 %, wobei das risiko für eine symptomatische infektion mit zunehmendem alter ansteigt (ca. 4 % pro jahr bei erwachsenen zwischen 30-60 jahren) [7] . patienten über 59 jahre haben ein 5-fach erhöhtes risiko, an covid-19 zu versterben. kinder sind häufig nicht oder nur in geringem ausmaß betroffen, können jedoch die erkrankung übertragen; mit einer größeren zahl schwer betroffener kinder wird aber derzeit nicht gerechnet [8] . die inkubationszeit beträgt im mittel zwischen 5-6 tage (spanne: 0-14 tage). das virus wird bei infizierten noch bis 30 tage nach erkrankungsbeginn nachgewiesen, was es erschwert, asymptomatische patienten nach durchgemachter infektion als geheilt zu klassifizieren [9] . inwieweit sich nach durchgemachter infektion eine immunität ausbildet und wie lange diese bestehen bleiben würde, ist aktuell nicht mit ausreichender evidenz zu beantworten [10] ; tierexperimentelle daten deuten aber darauf hin, dass sich vergleichbar mit anderen viruserkrankungen eine immunität ausbildet, die eine klinisch apparente neuinfektion verhindert [11] . bei covid-19 handelt es sich im wesentlichen um eine infektion der oberen und unteren atemwege. die starke vermehrung des virus im nasen-rachen-raum wird ebenfalls als ursache für die hohe kontagiosität angesehen [12] . ansonsten ähnelt die klinische charakteristik anderen viruserkrankungen, die die lunge befallen: fieber, husten, abgeschlagenheit. nach den verfügbaren daten aus der volksrepublik china sind mehr als 80 % der betroffenen patienten asymptomatisch oder zeigen eine milde symptomatik, bei ca.15 % entwickeln sich schwerere allgemeinsymptome inkl. einer pneumonie, und ca. 5 % der patienten sind kritisch krank mit entwicklung einer sepsis, eines septischen schocks oder eines multiorganversagens [13 -18] (▶ tab. 1). abhängig von intensität und zeitpunkt der testung können abweichende zahlen beobachtet werden. dies scheint z. b. in italien der fall zu sein. bei den kritisch kranken patienten kann sich das klassische bild eines ards ausbilden mit hyalinen membranen, konsolidierten lungenarealen und atelektasen [19] . in der computertomografie des thorax bei aufnahme imponieren in über 50 % der fälle milchglasinfiltrate und bilaterale verschattungen [16] ; im konventionellen röntgenbild [20] zeigen sich ebenfalls in > 50 % der fälle bilaterale verschattungen. bei über 80 % der patienten zeigt sich zum aufnahmezeitpunkt eine lymphozytopenie; im labor waren bei einer kohorte von 173 patienten aus wuhan mit schweren krankheitsverläufen das crp (≥ 10 mg/l, 81,5 %), die ldh (≥ 250 u/l, 58,1 %) und die d-dimere (≥ 0,5 mg/l, 59,8 %) erhöht, während das procalcitonin nur bei 13,7 % der patienten ≥ 0,5 ng/l lag [16] . in anderen kohorten wird auch von erhöhten d-dimeren und erhöhtem serum-ferritin berichtet [21, 22] . generell scheinen ältere männer mit komorbiditäten häufiger schwer zu erkranken und häufiger zu sterben. ungefähr die hälfte der patienten mit covid-19 leidet unter chronischen begleiterkrankungen, überwiegend kardiovaskulären und zerebrovaskulären komorbiditäten und diabetes mellitus [23] . einige patienten mit schweren verläufen zeigten koinfektionen mit bakterien und pilzen. in der kultur wurden u. a. acinetobacter baumannii, klebsiella pneumoniae, aspergillus flavus, candida glabrata und candida albicans gefunden [23] . [18, 27] . insofern kommt neben einer strikten beachtung der basishygiene einer adäquaten ausstattung des personals mit schutzausrüstung eine entscheidende bedeutung zu. aufgrund der hohen kontagiosität wird die verwendung einer ffp2/ffp3-(face filtering piece-)maske bei allen verrichtungen am patienten mit aerosolbildung empfohlen. außerdem müssen eine schutzbrille und eine wasserdichte schürze oder ein wasserdichter kittel getragen werden [28] . ffp-masken der klassen 2 und 3 zeichnen sich durch eine sehr niedrige gesamtleckage aus, was ihre gute schutzwirkung gegen aerosole ("tröpfcheninfektion") erklärt; andererseits ist eine arbeit mit ffp2/ffp3-atemschutz wegen des hohen widerstands nur für einen begrenzten zeitraum möglich [29] . da im rahmen der pandemie mit einer unzureichenden versorgung mit ffp2/ffp3-masken gerechnet werden muss, muss im notfall auch über alternative konzepte nachgedacht werden. die surviving sepsis campaign (ssc) zitiert in ihren kürzlich publizierten empfehlungen zur behandlung von patienten mit covid-19 eine aktuelle metaanalyse, in der keine überlegenheit von speziellen "respiratory masks" (analog unseren ffp2/ffp3-masken) gegenüber konventionellem mund-nasen-schutz bezüglich einer ansteckung von medizinischem personal, das infektiöse patienten betreut hatte, gefunden werden konnte [30] . auch in einer randomisierten studie zur behandlung von patienten, unter denen sich auch solche mit coronavirusinfektion befanden, war der mund-nasen-schutz der n95-spezialmaske nicht unterlegen [31] . in einer notlage können maßnahmen ohne aerosolproduktion auch mit einem mund-nasen-schutz statt ffp2/ffp3-maske durchgeführt werden. bei ca. 20 % der patienten kommt es zu einer schwereren symptomatik (▶ tab. 1), bei ca. 5 % ist eine intensivtherapie erforderlich. die lunge reagiert auf das schädigende agens sars-cov-2 ähnlich wie auf andere viren, die das respiratorische system befallen. es zeigen sich pathophysiologische veränderungen, die von patienten mit influenza-oder sars-viruspneumonien bekannt sind. das bedeutet konkret, dass die behandlung von patienten mit covid-19 zuallererst auf "best standard care" beruht, also auf einer optimalen anwendung evidenzbasierter therapieempfehlungen, die für die therapie des akuten lungenversagens (acute respiratory distress syndrome, ards) erarbeitet wurden [33] . die anlässlich der coronapandemie ganz aktuell publizierten empfehlungen der surviving sepsis campaign (ssc) umfassen insgesamt 50 aussagen, die mit unterschiedlichem empfehlungsgrad versehen wurden [34] . schon früher bestand interesse an chloroquin als möglicherweise antiviral wirksamer substanz; positive resultate in zellkulturen und tierexperimenten konnten jedoch nicht in der klinischen praxis verifiziert werden [41] . aktuell existiert ein letter to the editor [42] , in dem von positiven effekten bei 100 patienten im rahmen einer chinesischen multicenterstudie berichtet wird. in der verumgruppe seien die exazerbation der pneumonie verhindert, die befunde der radiologischen bildgebung verbessert und der krankheitsverlauf insgesamt verkürzt wor-den. relevante nebenwirkungen seien nicht aufgetreten. eine peer reviewed publikation dazu liegt derzeit nicht vor; in einer übersichtsarbeit wird empfohlen, chloroquin nur unter den bedingungen des "monitored emergency use of unregistered interventions" einzusetzen [43] . evidenzbasiert kann für keine dieser therapien derzeit eine empfehlung ausgesprochen werden. in jedem fall ist vor verwendung einer substanz als off-label use eine individuelle nutzen-risiko-abwägung erforderlich, da auch die jeweiligen nebenwirkungen beachtet werden müssen [44] . großes interesse besteht auch bezüglich einer notfalltherapie mittels extrakorporaler membranoxygenierung (ecmo) [45] . dieses therapieverfahren ist mittlerweile in der behandlung des therapierefraktären lungenversagens als venovenöses verfahren (vv-ecmo) etabliert und scheint zumindest in einer subgruppe mit einem überlebensvorteil assoziiert zu sein [46, 47] . einigkeit besteht darin, dass diese therapie nur in erfahrenen zentren durchgeführt werden sollte. analog zu anderen mindestmengen in der medizin scheint eine zahl von mindestens 20 venovenösen ecmo-runs pro jahr hier ein sinnvolles eingangskriterium zu sein [20] . eine kleine subgruppe von covid-19-patienten erleidet während der infektion einen sog. zytokinsturm, der durch die überschießende und exzessive freisetzung von proinflammatorischen zytokinen (z. b. il-2, il-7, interferon-γ, tnf-α) ausgelöst wird [22] . in dieser subgruppe waren außerdem das serum-ferritin und il-6 bei verstorbenen signifikant erhöht [48] . diese beobachtung ist die rationale für eine antiinflammatorische therapie mit z. b. interferon β-1b, dem il-1-blocker anakinra, dem il-6-rezeptorblocker tocilizumab und kortikosteroiden. evidenzbasierte daten existieren für keine der hier erwähnten therapeutischen alternativen; kortikosteroide könnenanalog zu den empfehlungen zur therapie des septischen schocksbei patienten mit sehr hohen vasopressor-dosen im rahmen einer hydrokortisontherapie (200 mg/24 h) erwogen werden. bei patienten im septischen schock mit hohen zytokinkonzentrationen (z. b. ab einem il-6 ≥ 1000 pg/ml) konnte in fallserien das outcome durch die verwendung eines zytokinfilters (cytosorbents, berlin) verbessert werden [49] . voraussetzung ist ein extrakorporaler kreislauf (hämofiltration und/oder ecmo), in den der filter eingebaut werden kann. bei patienten, die obige voraussetzungen erfüllen, könnte die zytokinentfernung eine interessante therapieoption darstellen. auf eine anpassung der antibiotikadosierungen ist ggf. zu achten. johns hopkins coronavirus resource center. coronavirus covid-19 global cases by the center for systems science and engineering (csse) at johns hopkins university. im internet the epidemiology and pathogenesis of coronavirus disease (covid-19) outbreak the proximal origin of sars-cov-2 epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (covid-19) during the early outbreak period: a scoping review response to covid-19 in taiwan novel coronavirus: where we are and what we know estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china covid-19 in children: initial characterization of the pediatric disease characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china healthcare professionals: frequently asked questions and answers reinfection could not occur in sars-cov-2 infected rhesus macaques. biorxiv. cold spring harbor laboratory sars-cov-2 viral load in upper respiratory specimens of infected patients clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study. lancet clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical characteristics of coronavirus disease 2019 in china clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72314 cases from the chinese center for disease control and prevention acute respiratory distress syndrome awmf. s3-leitlinie invasive beatmung und einsatz extrakorporaler verfahren bei akuter respiratorischer insuffizienz, 1. aufl, langversion, stand 04.12.2017. im internet risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in wuhan, china covid-19: consider cytokine storm syndromes and immunosuppression epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study laboratory readiness and response for novel coronavirus (2019-ncov) in expert laboratories in 30 eu/eea countries coronavirus sars-cov-2 -hinweise zur testung von patienten auf infektion mit dem neuartigen coronavirus sars-cov-2 coronavirus sars-cov-2 -optionen zum management von kontaktpersonen unter medizinischem personal bei personalmangel covid-19: protecting health-care workers hygieneanforderungen respiratorisch übertragbare infektions-erkrankungen. im internet infektionsprävention im rahmen der pflege und behandlung von patienten mit übertragbaren krankheiten compounds with therapeutic potential against novel respiratory 2019 coronavirus. antimicrob agents chemother 2020 n95 respirators vs. medical masks for preventing influenza among health care personnel sektion 2 endoskopie der deutschen gesellschaft für pneumologie und beatmungsmedizin acute respiratory distress syndrome surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease 2019 (covid-19) authors intensive care medicine (icm) and critical care medicine (ccm). intensive care med empfehlungen zur intensivmedizinischen therapie von patienten mit covid-19 extravascular lung water predicts progression to acute lung injury in patients with increased risk best practice & research clinical anaesthesiology: advances in haemodynamic monitoring for the perioperative patient who rät doch nicht von ibuprofen ab: ibuprofen und covid-19: who rudert zurück. im internet a trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 potential interventions for novel coronavirus in china: a systematic review of chloroquine and covid-19 breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid-19 associated pneumonia in clinical studies a systematic review on the efficacy and safety of chloroquine for the treatment of covid-19 treating covid-19 -off-label drug use, compassionate use, and randomized clinical trials during pandemics planning and provision of ecmo services for severe ards during the cov-id-19 pandemic and other outbreaks of emerging infectious diseases efficacy and economic assessment of conventional ventilatory support versus extracorporeal membrane oxygenation for severe adult respiratory failure (cesar): a multicentre randomised controlled trial extracorporeal membrane oxygenation for severe acute respiratory distress syndrome clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan, china hemoadsorption by cytosorb in septic patients: a case series key: cord-298563-346lwjr8 authors: kaplan, edward h. title: containing 2019-ncov (wuhan) coronavirus date: 2020-03-07 journal: health care manag sci doi: 10.1007/s10729-020-09504-6 sha: doc_id: 298563 cord_uid: 346lwjr8 the novel coronavirus 2019-ncov first appeared in december 2019 in wuhan, china. while most of the initial cases were linked to the huanan seafood wholesale market, person-to-person transmission has been verified. given that a vaccine cannot be developed and deployed for at least a year, preventing further transmission relies upon standard principles of containment, two of which are the isolation of known cases and the quarantine of persons believed at high risk of exposure. this note presents probability models for assessing the effectiveness of case isolation and quarantine within a community during the initial phase of an outbreak with illustrations based on early observations from wuhan. the novel coronavirus 2019-ncov first appeared in december 2019 in wuhan, china [1] . most of the initial cases were linked to the huanan seafood wholesale market, but person-to-person transmission was established quickly while viral transmission prior to the appearance of symptoms remains controversial [2, 3] . from the same family as the sars and mers coronaviruses (10% and 35% fatality rates respectively [4, 5] ), 2019-ncov has also led to serious cases of pneumonia, albeit with a lower estimated fatality rate of 2-3% at the present time [6] . given that a vaccine cannot be developed and deployed for at least a year, preventing further transmission relies upon standard principles of containment, two of which are the isolation of known cases and the quarantine of persons believed at high risk of exposure (with the latter extended inside china to prevent travel to or from wuhan, and globally via the cancellation of air travel to and from china). what follows are some probability models for assessing the effectiveness of case isolation of infected individuals and quarantine of exposed individuals within a community during the initial phase of an outbreak with illustrations based on early observations from wuhan. the good news is that in principle, case isolation alone is sufficient to end community outbreaks of 2019-ncov transmission provided that cases are detected efficiently. quarantining persons identified via tracing backwards from known cases is also beneficial, but less efficient than isolation. to begin, suppose someone has just become infected. absent intervention, assume that this infected person will transmit new infections in accord with a time-varying poisson process with intensity function λ(t) denoting the transmission rate at time t following infection. the expected total number of infections this person will transmit over all time (the reproductive number r 0 ) equals and as is well-known, an epidemic cannot be self-sustaining unless r 0 > 1 [7, 8] . it follows that a good way to assess isolation and quarantine is to examine their effect on r 0 . but first, we take advantage of another epidemic principle, which is that early in an outbreak, the incidence of infection grows exponentially. so, suppose that the rate of new infections grows as ke rt where r is the exponential growth rate, and let ι 0 denote the initial number of infections introduced at time 0. it follows that which is to say that the rate of new infections at chronological time t is the cumulation of all past infections times the chronological time t transmission rate associated with those past infections. simplifying and recognizing that e −rt λ(t) goes to zero (r 0 is finite) yields the euler-lotka equation in the disease outbreak context, eq. 3 can be understood as the composite of all sources of current infections. among all persons newly infected, the fraction whose infectors were infected between t and t + t time units ago equals is thus the probability density for the duration of time an infector has been infected as sampled from the infectors of those just infected. back to wuhan, where detailed study of the first 425 confirmed 2019-ncov cases was reported in [1] . using only case data up to january 4, the exponential growth rate r was directly estimated to equal 0.1/day [1] . contact tracing from identified index cases was able to establish links to their presumed infectors. while it was not possible to pinpoint exact dates of infection, the dates at which symptoms in both infectees and (presumed) infectors occurred were determined, and the difference in these dates taken as a proxy for the elapsed time since infection of the infector (see [7] for technical issues that arise from this approach). the resulting frequency distribution was then used to estimate b(t), which was fit as a gamma distribution with mean (standard deviation) of 7.5 (3.4) days [1] . given these estimates of r and b(t), λ(t) = e rt b(t) and consistent with what was reported in [1] as well as other studies employing different methods [9, 10] . we can now model containment. starting with case isolation, suppose that an infected person is detected at time t d days following infection, and is isolated for τ i days. the effect of doing this is to erase all infections that would have been transmitted between times t d and t d +τ i . following the poisson model, the expected number of transmissions blocked equals clearly the sooner an infected person is detected (the smaller t d ) and the longer a person is isolated (the larger τ i ), the greater the number of infections that can be prevented. suppose that newly infected persons self-recognize their infection at the time when symptoms appear. this optimistic scenario equates the detection time to the incubation time for 2019-ncov, and this incubation time distribution was reported to follow a lognormal distribution with a mean of 5.2 days and a 95th percentile of 12.5 days (which implies a standard deviation of 3.9 days) [1] . denoting the incubation time density by f t d (t), the expected number of transmissions blocked by case isolation of duration τ i upon the appearance of symptoms, β i , is given by substituting λ(t) and f t d (t) as previously described yields β i 's of 1 however, assuming that the time to detection is equal to the incubation time is very optimistic. indeed, the wuhan study revealed that the average time from onset of illness to a medical visit was 5.8 days [1] , comparable to the incubation time. to obtain a more sobering view of isolation, suppose that an individual's time to detection is twice the incubation time. using the lognormal incubation density cited above, the new detection time distribution will also be lognormal but now with a mean (standard deviation) of 10.4 (7.8) days. applying eq. 6 yields β i 's of 0.84, 1.07 and 1.1 for isolations of 7, 14 and unlimited days. even lifetime isolation fails to reduce transmission below threshold if the time to detection takes too long. given the amount of attention generated by news coverage and public service announcements, this second scenario is overly pessimistic. the real message is the importance of rapid (self) detection. what of quarantine? screening and quarantining individuals potentially exposed elsewhere upon entry to a community (as has been the case at airports) certainly can prevent the importation of new infections and their subsequent transmission chains, though at the cost of containing uninfected persons. beyond this, quarantine (typically at home where it is recommended that the exposed person not share immediate space, utensils, towels etc. with others) is meant for apparently healthy individuals discovered to be at risk of exposure via contact tracing with the idea that should they in fact have become infected, they would become ill without transmitting the virus and then report for isolation. however, quarantining uninfected contacts offers no benefit presuming the potential infector has already been identified and isolated, so the key question is whether such tracing would reach already infected but previously unidentified contacts in time to make a meaningful reduction in disease transmission. to present an optimistic view of tracing-driven quarantine, suppose that a newly infected person (referred to as the index from the standpoint of contact tracing) is immediately identified. instantaneous interview and tracing leads to the quarantine of our index's prior contacts, one of whom happens to be the infector (who is immediately isolated upon discovery). said infector, however, has already been infectious for some time before being identified via the index case. indeed, the probability density for the duration of time the infector has already been infected is given by eq. 4. suppose that the infector is placed in quarantine for τ q days. the expected number of transmissions that would be blocked, β q , is given by while the equations for β i and β q have the same structure, there is a key difference. the elapsed time from infection until an infected person enters isolation directly depends upon the time to recognize symptoms, which is related fundamentally to the incubation time distribution. the elapsed time from infection until an infected person enters quarantine/isolation via contact tracing, however, depends upon sampling from those newly infected and looking backwards to estimate the infector's elapsed duration of infection. using the previously estimated models for b(t) and λ(t), eq. 7 yields β q 's of 1.05, 1.33 and 1.36 for τ q 's of 7, 14, and unlimited days. the 14 day quarantine proposed in [1] would reduce the effective reproductive number to 2.26 − 1.33 = 0.93, which is just under threshold. again, this is an optimistic view of contact tracing, for identification of the infector is presumed instantaneous at the index's time of infection. taking into account the detection delay in recognizing the index case would similarly delay the identification of the infector via contact tracing, reducing the number of transmissions that could be prevented as a result. there is no either/or choice between quarantine and isolation. using both leads to an infected person being detected at the minimum of the time a person selfdetects due to symptoms and the time a person would be identified via contact tracing. the expected number of infections prevented then follows from eq. 6 after substituting the probability density for the minimum of the two detection times. to illustrate, assume independence between self-identification and contact-tracing detection times, that self-identification occurs at twice the incubation time, contact identification times follow b(t) as previously, and quarantine/isolation is unlimited in duration. the associated β i q denoting expected infections averted via isolation and quarantine now equals 1.64, which reduces the reproductive number from 2.26 to 0.62, well below the epidemic threshold. the preceding analysis has focused on reducing the reproductive number below 1, yet doing so can still lead to a large total number of infections. for example, reducing the reproductive number to 0.9 would lead to ten times as many infections in total as the extant number at the start of containment, as total infections in such a "minor" outbreak scales as 1/(1 − r 0 ) [11] . the modeling above is meant to be illustrative and surely could be improved in many ways. appropriate characterization of underlying statistical uncertainty, better operational modeling of how actual isolation, quarantine and contact tracing operate [12] (including voluntary selfquarantine by untraced persons who might have been exposed), consideration of the costs of intervention as well as the public health benefits, and characterizing the appropriate level of resources to devote to this outbreak relative to other arguably more pressing public health concerns are all subjects deserving careful study. additional common-sense precautions such as regular handwashing, the use of facemasks, and other measures not considered here should help make such outbreaks even more manageable. one important suggestion is that people should receive flu shots, for in addition to protecting against influenza, vaccination would reduce the number of false positive 2019-ncov cases reported since fewer people would have the common symptoms of both flu and coronavirus, and if a vaccinated person did get sick, it would raise the probability that the case is coronavirus as opposed to flu and make it more likely said person would seek care [13] . there are other practical aspects to explore, including the development of a less-precise but more rapid diagnostic mechanism, determining how long one can safely delay ill patients with symptoms from coming to the hospital to help alleviate congestion, and figuring out how quickly airborne infection isolation rooms (negative pressure units) can be created by hacking the ventilation system in ordinary wards to increase isolation capacity [14] . nonetheless, the modeling results obtained are reassuring. containment via isolation and quarantine has the capacity to control a community 2019-ncov outbreak. early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia transmission of 2019-ncov infection from an asymptomatic contact in germany study claiming new coronavirus can be transmitted by people without symptoms was flawed middle east respiratory syndrome coronavirus transmission a novel coronavirus outbreak of global health concern estimation in emerging epidemics: biases and remedies infectious diseases of humans: dynamics and control nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study report 3: transmissibility of 2019-ncov mrc centre for global infectious disease analysis. imperial college modeling to inform infections disease control analyzing bioterror response logistics:the case of smallpox act now to prevent an american epidemic: quarantines, flu vaccines and other steps to take before the wuhan virus becomes widespread implementing a negative-pressure isolation ward for a surge in airborne infectious patients acknowledgments i thank ron brookmeyer, forrest crawford, gregg gonsalves, robert heimer, albert ko, barry nalebuff, david paltiel, greg zaric and an anonymous referee for comments; any errors are my own. key: cord-283985-8mdnkegz authors: yang, chayu; wang, jin title: a mathematical model for the novel coronavirus epidemic in wuhan, china date: 2020-03-11 journal: math biosci eng doi: 10.3934/mbe.2020148 sha: doc_id: 283985 cord_uid: 8mdnkegz we propose a mathematical model to investigate the current outbreak of the coronavirus disease 2019 (covid-19) in wuhan, china. our model describes the multiple transmission pathways in the infection dynamics, and emphasizes the role of the environmental reservoir in the transmission and spread of this disease. our model also employs non-constant transmission rates which change with the epidemiological status and environmental conditions and which reflect the impact of the on-going disease control measures. we conduct a detailed analysis of this model, and demonstrate its application using publicly reported data. among other findings, our analytical and numerical results indicate that the coronavirus infection would remain endemic, which necessitates long-term disease prevention and intervention programs. a severe outbreak of respiratory illness started in wuhan, a city of 11 million people in central china, in december 2019. the causative agent is the novel coronavirus which was identified and isolated from a single patient in early january and subsequently verified in 16 additional patients [1] . the virus is believed to have a zoonotic origin. in particular, the huanan seafood market, a live animal and seafood wholesale market in wuhan, was regarded as a primary source of this epidemic, as it is found that 55% of the first 425 confirmed cases were linked to the marketplace [2] . meanwhile, recent comparisons of the genetic sequences of this virus and bat coronaviruses show a 96% similarity [3] . this is the third zoonotic human coronavirus emerging in the current century, after the severe acute respiratory syndrome coronavirus (sars-cov) in 2002 that spread to 37 countries and the middle east respiratory syndrome coronavirus (mers-cov) in 2012 that spread to 27 countries. typical symptoms of covid-19 infection include dry cough, fever, fatigue, a number of modeling studies have already been performed for the covid-19 epidemic. wu et al. [11] introduced a susceptible-exposed-infectious-recovered (seir) model to describe the transmission dynamics, and forecasted the national and global spread of the disease, based on reported data from december 31, 2019 to january 28, 2020. they also estimated that the basic reproductive number for covid-19 was about 2.68. read et al. [12] reported a value of 3.1 for the basic reproductive number based on data fitting of a seir model, using an assumption of poisson-distributed daily time increments. tang et al. [13] proposed a deterministic compartmental model incorporating the clinical progression of the disease, the individual epidemiological status, and the intervention measures. they found that the control reproductive number could be as high as 6.47, and that intervention strategies such as intensive contact tracing followed by quarantine and isolation can effectively reduce the control reproduction number and the transmission risk. imai et al. [14] conducted computational modeling of potential epidemic trajectories to estimate the size of the disease outbreak in wuhan, with a focus on the human-to-human transmission. their results imply that control measures need to block well over 60% of transmission to be effective in containing the outbreak. in addition, gao et al. [15] developed a deep learning algorithm to analyze the infectivity of the novel coronavirus and predict its potential hosts. their results indicate that bats and minks may be two animal hosts of this virus. most of these models have emphasized the significant role of the direct, human-to-human transmission pathway in this epidemic [16] , as highlighted by the facts that the majority of the infected individuals did not have any contact with the marketplaces in wuhan, that the number of infections has been rapidly increasing, and that the disease has spread to all provinces in china as well as more than 20 other countries. in particular, a large number of infected individuals exhibit a relatively long incubation period so that they do not show any symptoms and are unaware of their infection for as long as 10-14 days, during which time they can easily transmit the disease to other people through direct contact. on the other hand, the models published thus far have not taken into account the role of the environment in the transmission of covid-19. for example, it is reported that environmental samples taken from the areas of the huanan seafood market have come back positive for the novel coronavirus [4] , suggesting that the pathogen may be transmitted through the environmental reservoir. when infected individuals cough or sneeze, they may spread the virus to the environment through their respiratory droplets which then may go on to infect other people with close contact of the same area. such transmission would especially be facilitated during the early period of the disease outbreak when the general public was not aware of the infection risk, infected individuals were not isolated, and most people did not wear face masks. even worse, there is a possibility that the virus may survive in the environment for several days, increasing the risk of contamination via surfaces and fomites [17, 18] . such environmental survival was confirmed for sars-cov [19] . a most recent study, based on the review of 22 types of coronaviruses, reveals that coronaviruses such as sars-cov, mers-cov and endemic human coronaviruses can persist on inanimate surfaces like metal, glass or plastic for up to 9 days [20] , providing strong evidences for the pathogen's environmental survival. additionally, the novel coronavirus has been found in the stool of some infected individuals [5] , which may contaminate the aquatic environment, and fecal-oral contact remains a possible route of transmission for this disease. in the present paper, we present a new mathematical model for covid-19 that incorporates multiple transmission pathways, including both the environment-to-human and human-tohuman routes. in particular, we introduce an environmental compartment that represents the pathogen concentration in the environmental reservoir. a susceptible individual may contract the disease through the interaction with the contaminated environment, with an infectious but asymptomatic individual, or with an infectious and symptomatic individual. meanwhile, the transmission rates in our model depend on the epidemiological status and environmental conditions which change with time. in particular, when the infection level is high, people would be motivated to take necessary action to reduce the contact with the infected individuals and contaminated environment so as to protect themselves and their families, leading to a reduction of the average transmission rates. such varied transmission rates also reflect the strong disease control measures that the chinese government has implemented, including large-scale quarantine, intensive tracking of movement and contact, strict isolation, extending the lunar new year holiday, and advising the public to stay home and avoid spreading infection. the remainder of this paper is organized as follows. in section 2, we present our model and assumptions, and conduct a detailed mathematical analysis. in section 3, we conduct numerical simulation by incorporating the infection data reported for the city of wuhan. in section 4, we conclude the paper with some discussion. we divide the total human population into four compartments: the susceptible (denoted by s), the exposed (denoted by e), the infected (denoted by i), and the recovered (denoted by r). individuals in the infected class have fully developed disease symptoms and can infect other people. individuals in the exposed class are in the incubation period; they do not show symptoms but are still capable of infecting others. thus, another interpretation of the e and i compartments in our model is that they contain asymptomatic infected and symptomatic infected individuals, respectively. we introduce the following model to describe the transmission dynamics of the covid-19 epidemic: dv dt = ξ 1 e + ξ 2 i − σv , (2.1) where v is the concentration of the coronavirus in the environmental reservoir. the parameter λ represents the population influx, μ is the natural death rate of human hosts, α −1 is the incubation period between the infection and the onset of symptoms, w is the diseaseinduced death rate, γ is the rate of recovery from infection, ξ 1 and ξ 2 are the respective rates of the exposed and infected individuals contributing the coronavirus to the environmental reservoir, and σ is the removal rate of the virus from the environment. the functions β e (e) and β i (i) represent the direct, human-to-human transmission rates between the exposed and susceptible individuals, and between the infected and susceptible individuals, respectively, and the function β v (v) represents the indirect, environment-to-human transmission rate. we assume that β e (e), β i (i) and β v (v) are all non-increasing functions, given that higher values of e, i and v would motivate stronger control measures that could reduce the transmission rates. specifically, we make the following assumptions: apparently, system (2.1) has a unique disease-free equilibrium (dfe) at the infection components in this model are e, i, and v. the new infection matrix f and the transition matrix v are given by where w 1 = w + γ + μ. the basic reproduction number of model (2.1) is then defined as the spectral radius of the next generation matrix fv −1 [21] ; i.e., which provides a quantification of the disease risk. the first two parts ℛ 1 and ℛ 2 measure the contributions from the human-to-human transmission routes (exposed-to-susceptible and infected-to-susceptible, respectively), and the third part ℛ 3 represents the contribution from the environment-to-human transmission route. these three transmission modes collectively shape the overall infection risk for the covid-19 outbreak. we now analyze the equilibria of the system (2.1) which will provide essential information regarding the long-term dynamics of the disease. let (s, e, i, r, v) be an equilibrium of model (2.1) and thereby satisfy the following equations it follows from the first two equations of (2.6) that s can be denoted by a function of i, namely, yang and wang page 5 math biosci eng. author manuscript; available in pmc 2020 july 23. meanwhile, in view of the second equation of (2.5) and eqs (2.6), we obtain let us now consider curves s = ϕ(i), i ≥ 0 and s = ψ(i), i ≥ 0. in particular, the intersections of these two curves in ℝ + 2 determine the non-dfe equilibria. clearly, ϕ(i) is strictly decreasing, whereas ψ(i) is increasing since β e , and thus, we conclude: if ℛ 0 > 1, these two curves have a unique intersection lying in the interior of ℝ + 2 , since ψ(0) < ϕ(0) and ψ(i 1 ) ≥ ψ(0) > 0 = ϕ(i 1 ). furthermore, at this intersection point, eq (2.6) yields a unique endemic equilibrium (ee) x * = s * , e * , i * , r * , v * . if ℛ 0 ≤ 1, the two curves have no intersection in the interior of ℝ + 2 as ψ(0) ≥ ϕ(0). therefore, by eq (2.6), we find that the model (2.1) admits a unique equilibrium, the dfe x 0 , if ℛ 0 ≤ 1; and it admits two equilibria, the dfe x 0 and the ee x * , if ℛ 0 > 1. in what follows, we perform a study on the global stability of the dfe. by a simple comparison principle, we find that 0 ≤ s + e + i + r ≤ s 0 and 0 ≤ v ≤ ξ 1 + ξ 2 s 0 σ . thus, it leads to a biologically feasible domain theorem 2.1. the following statements hold for the model (2.1). if ℛ 0 ≤ 1, the dfe of system (2.1) is globally asymptotically stable in ω. if ℛ 0 > 1, the dfe of system (2.1) is unstable and there exists a unique endemic equilibrium. moreover, the disease is uniformly persistent in the interior of ω, denoted by ω°; namely, lim inf t ∞ (e(t), i(t), v (t)) > (ε, ε, ε) for some ε > 0. proof. let x = (e, i, v) t . one can verify that where the matrices f and v are given in eq (2.3). by manipulating some algebraic computaion, we let u = (β e (0), β i (0), β v (0)). it then follows from the fact differentiating ℒ along the solutions of (2.1), we have if ℛ 0 < 1, the equality if ℛ 0 = 1, then the equality it is easy to see that yang and wang page 7 math biosci eng. author manuscript; available in pmc 2020 july 23. hence, we have either e = i = v = 0, or β e (e) = β e (0), β i (i) = β i (0), β v (v) = β v (0), and s = s 0 . as processed before, each of cases would indicate the def x 0 is the only invariant set on (s, e, i, r, v ) ∈ ω: dℒ 0 dt = 0 . therefore, when ℛ 0 < 1 or ℛ 0 = 1, the largest invariant set on which dℒ 0 dt = 0 always consists of the singleton x 0 = (s 0 , 0, 0, 0, 0). by lasalle's invariant principle [22] , the dfe is globally asymptotically stable in ω if ℛ 0 ≤ 1. in contrast, if ℛ 0 > 1, then it follows from the continuity of the vector fields that dℒ 0 dt > 0 in a neighborhood of the dfe in ω°. thus the dfe is unstable by the lyapunov stability theory. the last part of the theorem can be proved by the persistent theory [23] which is similar to the proof of theorem 2.5 in gao and ruan [24] . □ in addition, we have conducted an analysis on the global asymptotic stability of the endemic equilibrium [25, 26] , and the details are presented in the following theorem. essentially, these stability results establish ℛ 0 = 1 as a forward transcritical bifurcation point, or, a sharp threshold for disease dynamics, and indicate that reducing ℛ 0 to values at or below unity will be sufficient to eradicate the disease. in other words, our model (2.1) exhibits regular threshold dynamics. in order to simplify our notations, we will adopt the abbreviations hence, the last inequality follows from the assumptions that β p (p) and β p (p)p, where p can represent e, i, or v, are non-increasing and non-decreasing functions of p, respectively. this implies 1 − β p * β p ≤ 0 p * ≤ p β p p β p *p * − 1 ≥ 0. similarly, one can verify that therefore, x * is globally asymptotically stable in ω°. □ we now apply our model to study the covid-19 epidemic in the city of wuhan. we use the outbreak data published daily by who and other sources [7, [27] [28] [29] [30] . these data sets contain the daily reported new cases, cumulative cases, and disease-caused deaths for the city of wuhan, as well as each province in china and all other countries that have reported covid-19 infection. to conduct the numerical simulation, we consider the following functions for the three transmission rates in our model: we implement our model and conduct numerical simulation for an epidemic period starting from january 23, 2020, when the city of wuhan was placed in quarantine, to february 10, 2020. according to the estimate made by the chinese government, about 9 million people remain in wuhan after january 23 and they are not allowed to move out of the city. meanwhile, only a relatively small number of people (mainly public health professionals) travel into the city since its lockdown. thus, the influx rate λ in our model is only based on newborns in wuhan. the values of the transmission constants β e0 and β i0 can be found in a recent study [13] . the incubation period of the infection ranges between 2-14 days, with a mean of 5-7 days [31] , and we take the value of 7 days in our model. the average recovery period is about 15 days [31] , and so we set the disease recovery rate as γ = 1/15 per day. members of the coronavirus family can survive in the environment from a few hours to several days [19] , and we take the value of 1 day which results in a virus removal rate σ = 1 per day. additionally, since the chinese government has been implementing a very strict isolation policy and intense medical care for all the confirmed cases, represented by i in our model, the chance of those infected individuals spreading the coronavirus to the environment connected with the general public is very low, and so we assume the virus shedding rate from the infected individuals is zero; i.e., ξ 2 = 0. note that our results in theorem 2.1 and theorem 2.2 still hold in this case since the contribution of the coronavirus to the environmental reservoir remains a positive number w 1 ξ 1 . these and other parameters, their values and sources are provided in table 1 . there are three parameters, however, that remain to be determined: the environment-to-human transmission constant β v0 , the transmission adjustment coefficient c, and the virus shedding rate ξ 1 by the exposed individuals. the values of these parameters are not available in the literature because the models published thus far have not considered the environmental component for the covid-19 infection, and they have generally applied constant transmission rates which remain fixed in time. to estimate the values for these three parameters, similar to [32] , we fit our model to the daily reported infection data for wuhan from january 23 to february 10 by using the standard least squares method. based on reported data, the initial condition is set as (s(0), e(0), i(0), r(0), v(0)) = (89985051000, 475, 10, 10000) [33] . figure 1 shows the numbers of cumulative confirmed cases in wuhan during this period versus our fitting curve. the parameter values and their 95% confidence intervals are presented in table 2 . the normalized mean square error (nmse) for the data fitting is found as 0.0058. based on the parameter values from data fitting, we are able to evaluate the basic reproduction number ℛ 0 = 4.25. specifically, we find that ℛ 1 = 1.959, ℛ 2 = 0.789, ℛ 3 = 1.497, which quantify the infection risk from each of the three transmission routes. among these three components, the largest one ℛ 1 comes from the exposed-to-susceptible transmission, since exposed individuals show no symptoms and can easily spread the infection to other people with close contact, often in an unconscious manner. meanwhile, the smallest component ℛ 2 comes from the infected-to-susceptible transmission, possibly due to the strict isolation policy on the symptomatic infected individuals. in addition, we observe that ℛ 3 = 1.497, showing a significant contribution from the environmental reservoir toward the overall infection risk. figure 2 displays a short-term prediction for i (the infected individuals) and e (the exposed individuals) in wuhan using our model. it shows that the infection level, starting from january 23 (marked as day 0 in our simulation), would continue increasing for about 80 days, reach a peak value around 45,000 infections, and then gradually go down afterwards. meanwhile, the long-term behavior of the epidemic would be determined by the property of the endemic equlibrium of the system, which is found as x * = (2583683, 1353, 2735, 6528015, 3111). a phase portrait of i vs. e is provided in figure 3 , where all the solution orbits converge to the endemic equlibrium, illustrating its global asymptotical stability that is stated in theorem 2.2. in addition, we have performed a numerical test using simple, constant transmission rates in our model: β e (e) = β e0 , β i (i) = β i0 , β v (v ) = β v 0 , (3.2) equivalent to setting c = 0 in eq (3.1). this leaves two parameters, β v0 and ξ 1 , to be estimated by data fitting. using the same set of data, we find that ξ 1 ≈ 4.28 with the 95% confidence interval (0, 15.611), and β v0 ≈ 4.91 × 10 −10 with the 95% confidence interval (4.218 × 10 −10 , 5.603 × 10 −10 ). the normalized mean square error (nmse) for the data fitting is 0.0266, larger than that in the previous scenario, 0.0058. meanwhile, figure 4 shows a prediction of the wuhan coronavirus outbreak size in this setting. compared to figure 2 , we now clearly observe a significantly higher level of infection; particularly, the peak value appears at 2.8 × 10 6 , which is extremely large and clearly unrealistic. the result demonstrates that using fixed transmission rates, which do not take into account the strong disease control measures currently on-going in wuhan, may overestimate the epidemic severity and generate misguided information. we have proposed a mathematical model to investigate the on-going novel coronavirus epidemic in wuhan, china. there are two unique features in our model: (1) the incorporation of an environmental reservoir into the disease transmission dynamics, and (2) the use of non-constant transmission rates which change with the epidemiological status and environmental conditions and which reflect the impact of the disease control measures implemented in wuhan. we have conducted a detailed analysis of this model, and applied it to study the wuhan epidemic using publicly reported data. the basic reproduction number ℛ 0 of this model consists of three parts, representing the three different transmission routes; i.e., from the exposed individuals, the infected individuals, and the environmental reservoir, to the susceptible individuals. these three transmission modes collectively shape the overall disease risk of this epidemic, suggesting that intervention strategies should target all these three transmission routes. our equilibrium analysis of this model shows that the disease dynamics exhibit a regular threshold at ℛ 0 = 1. we have established the global asymptotic stability of the disease-free equilibrium when ℛ 0 < 1, and the global asymptotic stability of the endemic equilibrium when ℛ 0 > 1. our numerical simulation results demonstrate the application of our model to the covid-19 outbreak in wuhan. our model can fit the reported data well. through data fitting, we obtain an estimate of basic reproduction number, ℛ 0 = 4.25. in particular, we find that the contribution of the environmental reservoir (measured by ℛ 3 ) is significant in shaping the overall disease risk. our model predicts the appearance of an epidemic peak, after which the infection level would decrease and approach an endemic state in the long run. we also find that if we use constant transmission rates instead, the model would predict a much higher and unrealistic epidemic peak. this is caused by the fixed transmission rates that do not reflect the impact of on-going disease control measures. it is an indication that using epidemiologically and environmentally dependent transmission rates can potentially generate more practical simulation results. at present, many aspects regarding the pathology, ecology and epidemiology of the novel coronavirus remain unknown, which adds challenges to the mathematical modeling. particularly, in our current model, we have employed a bilinear incidence rate based on the law of mass action to represent the environment-to-human transmission route [34] . practically, though, a saturation based incidence rate might better characterize the environmental pathogen, and we hope to investigate it in our future modeling efforts. meanwhile, the transmission rates β e and β v in our model depend on e and v, respectively, while in reality the exposed population e and the environmental pathogen concentration v may be unknown. to better quantify these transmission rates, we could instead assume that they are functions of i; i.e., β e (i) and β v (i), since the infected population i can be easily calculated from the reported data. nevertheless, it is reasonable to assume that e and v are positively correlated to i, and so the qualitative properties of these transmission functions would remain the same under both formulations. given the current development of covid-19, it is widely speculated that this disease would persist in the human world and become endemic. our mathematical analysis and numerical simulation results support this speculation. the findings in this study imply that we should be prepared to fight the coronavirus infection for a much longer term than that of the current epidemic wave, in order to reduce the endemic burden and potentially eradicate the disease eventually. among other intervention strategies, new vaccines for the novel coronavirus, which are currently in research and development, could play an important role in achieving that goal. we emphasize that our data fitting is based on the reported confirmed cases in wuhan from january 23 to february 10 in 2020. these confirmed cases were determined by the method of nucleic acid testing kits. on february 12, 2020, the national health commission in china started including cases confirmed by another method; i.e, clinical diagnosis, which refers to using ct imaging scans to diagnose patients. this change of criteria led to a surge of confirmed cases on february 12 (with an increase of about 14,000 new cases for wuhan in a single day), and our current study does not take into account this factor. in this regard, our prediction of the epidemic duration and size should be interpreted as applicable only to the confirmed cases based on the previous, more strict, testing method. the issues regarding the accuracy, reliability and standard of reported data are complex and are beyond the scope of this work, which is more oriented on the mathematical modeling side. we plan to address the new development of the outbreak data in another piece of work in the near future. we also plan to expand our modeling efforts to the province and country levels beyond the epicenter, the city of wuhan, and study the spread of the novel coronavirus in larger spatial scales. cumulative confirmed cases for the city of wuhan from january 23, 2020 to february 10, 2020. circles (in blue) denote the reported cases and solid line (in red) denotes the simulation result. the basic reproduction number is ℛ 0 = 4.25 based on the parameters from a simulation result for the outbreak size in wuhan using the transmission rates formulated in eq (3.1), the parameters from table 1 , and the result of data fitting. a simulation result for the outbreak size in wuhan using the constant transmission rates given in eq (3.2), the parameters from table 1 , and the result of data fitting. yang definitions and values of model parameters. λ influx rate 271.23 per day [30] β e0 transmission constant between s and e 3.11 × 10 −8 /person/day [13] β i0 transmission constant between s and i 0.62 × 10 −8 /person/day [13] β v0 transmission constant between s and v fitting by data c transmission adjustment coefficient fitting by data μ natural death rate 3.01 × 10 −5 per day [30] 1/α incubation period 7 days [31] w disease-induced death rate 0.01 per day [30] γ recovery rate 1/15 per day [31] σ removal rate of virus 1 per day [19] ξ 1 virus shedding rate by exposed people fitting by data virus shedding rate by infected people 0 per person per day per ml -page 21 who statement regarding cluster of pneumonia cases in wuhan, china. 2020 available from early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin, biorxiv return of the coronavirus: 2019-ncov the new coronavirus: what we do-and don't-know centers for disease control and prevention: 2019 novel coronavirus 2019-ncov) situation reports a novel coronavirus emerging in china -key questions for impact assessment who statement regarding the outbreak of novel coronavirus (2019-ncov), 2020 available from transmission of 2019-ncov infection from an asymptomatic contact in germany nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study novel coronavirus 2019n-cov: early estimation of epidemiological parameters and epidemic predictions, medrxiv estimation of the transmission risk of 2019-ncov and its implication for public health interventions transmissibility of 2019-ncov, reference source host and infectivity prediction of wuhan 2019 novel coronavirus using deep learning algorithm, biorxiv a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster novel coronavirus: where we are and what we know novel coronavirus (covid-19) outbreak: a review of the current literature human coronaviruses: insights into environmental resistance and its influence on the development of new antiseptic strategies persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission the stability of dynamical systems persistence under relaxed point-dissipativity (with application to an endemic model) an sis patch model with variable transmission coefficients global stability of seirs models in epidemiology global stability of infectious disease models using lyapunov functions wikipedia on the timeline of the 2019-20 wuhan coronavirus outbreak sina news real-time reports on novel coronavirus the government of wuhan homepage epidemiological parameter review and comparative dynamics of influenza, respiratory syncytial virus, rhinovirus, human coronvirus, and adenovirus, medrxiv a cholera transmission model incorporating the impact of medical resources the health commission of hubei province multiple transmission pathways and disease dynamics in a waterborne pathogen model this work is partially supported by the national institutes of health under grant number 1r15gm131315. the authors are grateful to the handling editor and reviewers for their helpful comments that have improved the quality of the original manuscript. key: cord-299584-zpiaka80 authors: biscayart, cristian; angeleri, patricia; lloveras, susana; chaves, tânia do socorro souza; schlagenhauf, patricia; rodríguez-morales, alfonso j. title: the next big threat to global health? 2019 novel coronavirus (2019-ncov): what advice can we give to travellers? – interim recommendations january 2020, from the latin-american society for travel medicine (slamvi) date: 2020-02-29 journal: travel medicine and infectious disease doi: 10.1016/j.tmaid.2020.101567 sha: doc_id: 299584 cord_uid: zpiaka80 nan on december 12th, 2019, the wuhan municipal health commission (wmhc) in the people's republic of china reported 27 human cases of viral pneumonia, 7 of them seriously ill. all had a shared exposure in the huanan seafood wholesale market, where farm animals, bats, and snakes were also sold [1, 2] . the city of wuhan, in the province of hubei, has almost 11 million inhabitants. its airport, tianhe international, located 23 km from its center, is a hub for major chinese airlines [3] . in 2018 alone, 24,500,356 passengers arrived and departed. although it is mostly a domestic airport, code sharing with several european and north american airlines allows with a single stop, to fly in a few hours to the major capitals and main cities around the world. in latin america only ciudad de mexico international airport [4] , são paulo guarulhos international in brazil [5] , and el dorado international airport in bogotá, colombia [6] , outdo that level of passenger traffic. this fact alone accounts for a realistic possibility of the global dispersal of the causative agent from china since human to human transmission has already been demonstrated [7] . the culprit has been identified as a new coronavirus -known provisionally as 2019-ncov-from the findings of ongoing investigations and by genomic sequencing carried out in local laboratories [8] . coronaviruses (covs) belong to the coronavirinae subfamily in the family coronaviridae of the order nidovirales, and this subfamily includes four genera: alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus [9] . the cov genome is a singlestranded rna. these are important pathogens of humans and other vertebrates. they can infect the respiratory, gastrointestinal, hepatic and central nervous system tracts of man, cattle, birds, bats [2] , rodents and various wild animals [10] . coronaviruses, like influenza viruses, circulate in nature in various animal species. alphacoronaviruses and betacoronaviruses can infect mammals and gammacoronaviruses and deltacoronaviruses infect birds, but some of them can also be transmitted to mammals [2] . to date, seven coronaviruses that can infect humans have been described. common human coronaviruses betacoronavirus hcov-oc43 and hcov-hku1, as well as alphacoronavirus hcov-229e cause common cold and also severe lower respiratory tract infections in children and the elderly, while alphacoronavirus hcov-nl63 is considered to be an essential cause of (pseudo)croup and bronchiolitis in children [11] . the emergence of coronaviruses infections with high impact in public health began in 2002-2003 with the sars outbreak [12, 13] and in 2012, mers-cov, another highly-pathogenic coronavirus which still circulates in the middle east and causes severe respiratory disease [14, 15] was reported. regarding 2019-ncov investigations, to date, could already reveal that its genome (genbank accession mn908947) has the highest similarity (89%) to a sars-related member of the sarbecoviruses (genbank accession mg772933), a subgenus within the betacoronavirus genus [16] . this fact could perhaps be part of the explanation about the behavior of this novel coronavirus concerning human infection. preliminary genome sequencing suggested the snake as a likely wildlife reservoir responsible for the current outbreak of 2019-ncov infection and origin-unknown homologous recombination identified within the spike glycoprotein of the 2019-ncov may explain snake-to-human cross-species transmission [2] . however, this theory has now been largely discounted and some researchers point towards bats as a reservoir and doubt that the coronavirus could have originated in animals other than birds or mammals [2] ; they are skeptical that the animal host or hosts of 2019-ncov can be identified without further field and laboratory research. many hope that genetic tests of animals or environmental sources, such as cages and containers, from the wuhan market will reveal clues [17] regarding the definite origin of the virus. the outbreak of viral pneumonia in wuhan is associated with exposures at the huanan seafood wholesale market, suggesting a possible zoonosis. the incubation period is estimated between 7 and 14 days. symptoms are similar to those from other respiratory viruses, including https://doi.org/10.1016/j.tmaid.2020.101567 received 28 january 2020; accepted 28 january 2020 travel medicine and infectious disease 33 (2020) 101567 available online 30 january 2020 1477-8939/ © 2020 elsevier ltd. all rights reserved. t fever, cough, and shortness of breath with radiographs showing invasive lesions in the lungs. some cases need hospitalization due to the worsening of the clinical status and in several cases, the complications could lead to death [18] [19] [20] . who has constantly updating information on the outbreak and definitions under (https://www.who.int/healthtopics/coronavirus). as of january 29, 2020, a total of about 7780 confirmed cases have been reported for novel coronavirus (2019-ncov) globally (> 7670 from china) (https://gisanddata.maps.arcgis.com/apps/opsdashboard/ index.html#/bda7594740fd40299423467b48e9ecf6), with imported cases in countries outside china [21, 22] including seven confirmed cases in australia, five cases in the us, five cases in france, a cluster of four cases in germany, three in canada, one in finland, one in ivory coast (africa), and cases in several other asian countries. who reported an increase in the number of confirmed and suspected cases and affected provinces. the case fatality rate of the currently reported cases is less than 3% (170 deaths, including one case in a healthcare professional), which implies that so far, this novel coronavirus does not seem to cause the high fatality rates previously observed for sars and mers-cov, 10% and 37%, respectively [20] . of the confirmed cases, 25% are reported to be severe and underlying comorbidities were detected in many of them and elderly. the chinese government declared the death of the first health professional who provided assistance at wuhan hospital. remarkably, who has reported that in the last one week, less than 15% of new cases reported had visited the huanan market. health care workers have also been infected. fourth-generation cases in wuhan and second-generation cases outside wuhan, as well as some clusters outside hubei province, could be traced back [21] . these findings underscore the role of human-to-human transmission of 2019-ncov [21] . all these facts together have led chinese authorities to enforce drastic containment measures such as the closure of public-transportation systems in wuhan as well as in other cities in the country including wuhan international airport [23] . the who emergency committee met on january 23rd and although the situation at that time is not considered to be a public health emergency of international concern (pheic), who monitors the situation closely and can, under the global legal framework, the revised international health regulations (ihr), recommend travel and trade restrictions when these are deemed necessary. at the moment of proofs correction of this editorial, the committee was about to be convened again (jan. 30, 2020) in order to reassess the situation and if declare the pheic. an estimate of r 0 of 1.4-2.5 was presented [23] . other estimates, however, yield higher r 0 figures. as researchers are saying, sustained human-to-human transmission of 2019-ncov is one of the most important topics issues that could explain the scale of the wuhan outbreak. considering this, it is not only important to follow the progression of the epidemic closely but to also coordinate the countries' mechanisms to mitigate the impact in health care services and the community [23] . there are no known useful treatments for the disease caused by this new coronavirus; therefore, contact and respiratory precautions are the only effective measures to prevent this emerging coronavirus [23] . given this situation, there are some key considerations and recommendations for travelers to southeast asia, especially china (table 1) , and other affected areas that should be considered. similar to the 2003 sars outbreak in guangzhou, wuhan is also a rapidly flourishing capital city of the hubei province and the traffic hub of central china. moreover, both outbreaks were initially connected to "wet markets" where game animals and meat were sold [19] . in the case of sars, the person-to-person transmission was efficient and super-spreading events led to significant outbreaks in hotels and hospitals. learning from the sars outbreak, which started as animal-tohuman transmission during the first phase of the epidemic, all game meat trades should be optimally regulated to terminate this portal of transmission [19] . emerging and reemerging pathogens are global challenges for public health and a matter for concerns in travelers from all over the world. as in previous scenarios [24, 25] , the latin american society for travel medicine (slamvi), is concerned for travelers arriving from china and other affected locations that would bring the 2019-ncov but also given the potential exposure for travelers from this table 1 key considerations and recommendations for travelers in the context of the ongoing outbreak of 2019-ncov (as of jan. 27, 2020). • the outbreak is ongoing so that the control measures may vary according to the evolution in the different countries. • according to preliminary reports, the confirmed cases have a direct or indirect epidemiological relationship with china, and in particular, the city of wuhan. • the tourism industry in latin america is expanding and contribute in the fourth place to the world gdp after northeast asia, north america, and the european union. in that context, globalization implies that travelers to southeast asia could move in a few hours to countries where there are currently no suspicious cases. • since the clinical respiratory symptoms of 2019-ncov are similar to influenza, it is essential not to underestimate the symptomatology in order to identify eventual suspected cases in travelers. make sure to be up to date with your influenza vaccine to rule out this differential diagnosis • underlying comorbidities are present in many cases. however, to date, the mortality rate is under 3%. • human-to-human transmission is already confirmed, and it would be highly feasible that would lead to the progress of the current epidemiological situation. consult public health information websites such as https://www.who.int/health-topics/coronavirus. • avoid travel to the cities and areas mainly affected by the 2019-ncov. • an innovative, and useful real-time online map is available at https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6. this was developed by john hopkins researchers to track the spread of the ongoing outbreak (fig. 1 ). • avoid visiting wet markets, especially those in which live animals are traded. • the consumption of raw or undercooked animal products should be avoided. raw meat, milk or animal organs should be handled with care, to avoid cross-contamination with uncooked foods, as per good food safety practices. • avoid large concentrations of people in public spaces (public transport, theaters, cinemas, shopping centers, offices, educational establishments, restaurants). • in the event these other activities are unavoidable, refrain from touching objects such as handrails, doorknobs and bringing hands to nose or mouth. • avoid close contact with anyone who has fever and cough. • avoid contact with sick people. • avoid contact with animals (alive or dead), animal markets, and products that come from animals (i.e., raw or undercooked meat). • when coughing and sneezing cover mouth and nose with flexed elbow or tissue -dispose tissues immediately and wash hands • wash hands frequently with soap and water for at least 20 seconds. use an alcohol-based hand sanitizer if soap and water are not available. • seek prompt consultation in case of fever and respiratory symptoms during or after the trip (up to 14 days). use your local emergency numbers to find out how to seek care and use a face mask if you go to health care facilities. region to china and other attractive countries, that may hold mass gathering events in the upcoming weeks, such as the upcoming 2020 olympic games in tokyo, japan to be celebrated on july 24-august 9, 2020 [26] , even more, when up to date, this country has also confirmed china-imported cases (4). none. outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin wuhan airport aeronautica civil de colombia global health concern stirred by emerging viral infections recent advances in the detection of respiratory virus infection in humans the structure and functions of coronavirus genomic 3' and 5' ends emerging coronaviruses: genome structure, replication, and pathogenesis sars and other coronaviruses as causes of pneumonia travel implications of emerging coronaviruses: sars and mers-cov the severe acute respiratory syndrome: impact on travel and tourism asymptomatic middle east respiratory syndrome coronavirus (mers-cov) infection: extent and implications for infection control: a systematic review mers-cov as an emerging respiratory illness: a review of prevention methods preparedness and proactive infection control measures against the emerging wuhan coronavirus pneumonia in china why snakes probably aren't spreading the new china virus a novel coronavirus from patients with pneumonia in china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster clinical features of patients infected with 2019 novel coronavirus in wuhan novel coronavirus (2019-ncov) -situation report -4 -24 world health organization. novel coronavirus (2019-ncov) -situation report -7 -27 statement on the meeting of the international health regulations (2005) emergency committee regarding the outbreak of novel coronavirus fifa world cup: communicable disease risks and advice for visitors to brazila review from the latin american society for travel medicine (slamvi) pan american games: communicable disease risks and travel medicine advice for visitors to peru -recommendations from the latin american society for travel medicine (slamvi) risk assessment of dengue autochthonous infections in tokyo during summer, especially in the period of the 2020 olympic games panel of scientific publications and teaching, latin american society for travel medicine (slamvi) key: cord-280970-gy0kfhy6 authors: peng, fujun; tu, lei; yang, yongshi; hu, peng; wang, runsheng; hu, qinyong; cao, feng; jiang, taijiao; sun, jinlyu; xu, guogang; chang, christopher title: management and treatment of covid-19: the chinese experience date: 2020-04-17 journal: can j cardiol doi: 10.1016/j.cjca.2020.04.010 sha: doc_id: 280970 cord_uid: gy0kfhy6 with over 1,800,000 cases and 110,000 deaths globally, covid-19 is one of worst infectious disease outbreaks in history. the objective of this paper is to critically review the available evidence regarding the lessons learned from the chinese experience regarding covid-19 prevention and management. the steps that have led to a near disappearance of new cases in china included rapid sequencing of the virus to establish testing kits which allowed tracking of infected persons in and out of wuhan. in addition, aggressive quarantine measures included the complete isolation of wuhan and then later hebei and the rest of the country, as well as closure of all schools and non-essential businesses. other measures included the rapid construction of two new hospitals and the establishment of fangcang shelter hospitals. in the absence of a vaccine, the management of covid-19 included antivirals, high flow oxygen, mechanical ventilation, corticosteroids, hydroxychloroquine, tocilizumab, interferons, intravenous immunoglobulin and convalescent plasma infusions. these measures appeared to provide only moderate success. while some measures have been supported by weak descriptive data, their effectiveness is still unclear pending well-controlled clinical trials. in the end, it was the enforcement of drastic quarantine measures that stopped sars-cov-2 from spreading. the earlier the implementation, the less likely resources will be depleted. the most critical factors in stopping a pandemic are early recognition of infected individuals, carriers and contacts, and early implementation of quarantine measures with an organized, proactive and unified strategy at a national level. delays result in significantly higher death tolls. since mid-december 2019, there has been a worldwide outbreak of coronavirus disease 90 (covid)-19, caused by sars-cov-2 (formerly 2019-ncov or and first detected in 91 wuhan, china. the incubation period is 1 to 14 days (mean: 5-6 days) in most cases, but can be 92 as long as 24 days. 1 the most commonly seen characteristics of covid-19 are fever, cough and 93 abnormal chest computed tomography (ct). 2, 3 at present, the chinese chrysanthemum bat is 94 thought to be the origin of sars-cov-2 based on sequence homology of 96% between 95 sars-cov-2 and bat-cov-ratg13. 4 , 5 the pangolin has been proposed as an intermediate host, 96 but this has not been confirmed. 6, 7 human-to-human transmission of sars-cov-2 occurs 97 mainly via respiratory droplets, 1 direct contact, 1 asymptomatic transmission, 8, 9 and intrafamilial managing the spread of the epidemic 128 the most important strategy to combat a pandemic is to prevent it from even happening. this shortage of personal protection equipment (ppe), which was mitigated by using reserve 210 supplies, acquiring donations, and production increases (appendix 1 and figure s1 ). wuhan is shown in figure 2 . table s1 . 240 emergency staffing was arranged as needed within a half hour. do not require supplemental oxygen, and hyperoxemia may induce further respiratory 306 injury and even higher mortality. 29 the indications for supplemental oxygen should be pharmacologic agents 345 we summarize the treatment of 327 pooled cases of severe cases with covid-19 ( (table 3) . 10, 36 365 interferon-α2b inhalation, 17 (28%) patients received arbidol and lopinavir/ritonavir, and 8 (13%) 369 received interferon-α2b by inhalation. 37 chen et al reported that 75 of 99 confirmed patients in 370 wuhan received antiviral treatment, including oseltamivir, ganciclovir, and lopinavir and 371 ritonavir. 38 the duration of antiviral treatment was 3-14 days. 38 15 zhou et al proposed that hydroxychloroquine could serve as a better therapeutic agent than 400 chloroquine due to reduced toxicity, fewer side effects, lower cost and relative safety in 401 pregnancy. 47 yao et al used physiologically-based pharmacokinetic (pbpk) models and found 402 that hydroxychloroquine was more potent than chloroquine at inhibiting sars-cov-2 in vitro. 403 they recommended hydroxychloroquine sulfate 400 mg twice daily for 1 day, followed by 200 404 mg twice daily for 4 days to treat sars-cov-2 infection. 48 the efficacy and safety data of 405 chloroquine or hydroxychloroquine from high-quality clinical trials are urgently needed. a retrospective study found that low-to-moderate dose glucocorticoid therapy had no effect 419 on the time to viral clearance in patients with covid-19. glucocorticoids are not recommended 420 in mild cases because there was no improvement in the rate of radiographic recovery. 52 however, 421 a single-center in wuhan shared that early, low-dose and short-term (1-2mg/kg/d for 5-7 days) 422 corticosteroids was associated with a faster improvement of clinical symptoms and absorption of 423 focal lung lesions in severe cases of covid-19. 53 another study analyzed 15 critical cases and 424 suggested that a low dose and short duration of corticosteroids (methylprednisolone <1 mg/kg, 425 less than 7 days) may be beneficial for critically ill patients with covid-19. 54 vaccine development 489 the development of a vaccine for sars-cov-2 has been accelerated as a priority project. improve sample collection and the accuracy of sars-cov-2 nucleic acid detection. 77 the 513 patients' position should be assessed and changed regularly to avoid decubitus skin injury. due to the fact that cardiac insufficiency can lead to a coagulation disorder and that severe 533 covid-19 patients were reported to have increased level of d-dimer, low molecular weight 534 heparin was recommended to treat covid-19 patients in the early phase of disease. 81 as in 535 sars-cov, ace2 has similarly been identified as the receptor for sars-cov-2 to enter cells. 82 the use of angiotensin converting enzyme inhibitors (acei) may not be of any benefit because 537 it does not bind to the ace2 receptor. this also means that discontinuing acei in patients with 538 covid-19 is not necessary. with regard to angiotensin receptor blockers (arbs), there is 539 evidence that arbs could lead to increased expression of ace2, thus worsening disease, but this effectiveness and importance of public health interventions 562 the who-china joint mission report reported that china's vigorous public health measures 563 to prevent the covid-19 are the most "ambitious, agile and aggressive disease containment 564 effort in history". 86 the drastic measures taken are listed in table 4 . if not for a national strategy once it is recognized that there is a new, potentially lethal virus, the virus needs to be 587 isolated, the viral genome sequenced, and testing kits validated and released for rapid 588 distribution. infected individuals and their contacts need to be tracked and isolated. the earlier 589 this is done, the less impact there will be on the personal and professional lives of people and the 590 economy, and the less resources will be needed. when more people are infected, the drastic 591 measures including shutting down cities and restricting travel will need to be more widespread, 592 healthcare resources will be exhausted and the economy will take a bigger hit. adult who meet any of the following criteria: (i) respiratory distress (≥30 breaths/ min); (ii) oxygen saturation ≤93% at rest; (iii) arterial partial pressure of oxygen (pao2)/fraction of inspired oxygen (fio2)≤ 300mmhg (l mmhg = 0.133kpa) §, or whose chest imaging shows obvious lesion progression within 24-48 hours >50% child who meets any of the following criteria: (i) tachypnea|| independent of fever and crying; (ii) oxygen saturation ≤ 92% on finger pulse oximeter taken at rest; (iii) labored breathing ¶, cyanosis, and intermittent apnea; (iv) lethargy and convulsion; (v) difficulty feeding and signs of dehydration;(vi) hrct show infiltration in both lungs or multiple lobes, lesion progress in a short time or pleural effusion 90 same as above mild, and respiratory support (high-flow nasal oxygen and non-invasive ventilation or invasive mechanical ventilation) patients who meet any of the following criteria: (i) respiratory failure and requiring mechanical ventilation; (ii) shock; (iii) with other organ failure that requires icu care clinical characteristics of coronavirus disease 2019 in china clinical characteristics of 50466 hospitalized patients with 2019-ncov infection china-who new coronavirus pneumonia (covid-19) joint inspection report a pneumonia outbreak associated with a new coronavirus of probable bat origin genome composition and divergence of the novel coronavirus (2019-ncov) originating in china evolutionary history, potential intermediate animal host, and cross-species analyses of sars-cov-2 transmission of 2019-ncov infection from an asymptomatic contact in germany what to do next to control the 2019-ncov epidemic? new coronavirus pneumonia prevention and control program (seventh trial edition).(in chinese) organization wh. coronavirus disease (covid-19) outbreak novel coronavirus pneumonia emergency response epidemiology t. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in china. zhonghua liu xing bing xue za zhi a novel coronavirus genome identified in a cluster of pneumonia cases -wuhan caring frontline healthworks in epidemic prevention and control fangcang shelter hospitals: a novel concept for responding to public health emergencies. the lancet clinical characteristics and outcomes of patients undergoing surgeries during the incubation period of covid-19 infection diagnosis and treatment protocol for novel coronavirus pneumonia (trial version 7): who; 2020. 21. who. clinical management of severe acute respiratory infection (sari) when covid-19 disease is suspected2020 clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records clinical features of patients infected with 2019 novel coronavirus in wuhan clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan clinical characteristics of 140 patients infected with sars-cov-2 in wuhan clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical features and progression of acute respiratory distress syndrome in coronavirus disease 2019. medrxiv consequences of hyperoxia and the toxicity of oxygen in the lung a multicenter rct of noninvasive ventilation in pneumonia-induced early mild acute respiratory distress syndrome non-invasive ventilation in community-acquired pneumonia and severe acute respiratory failure mechanical ventilation in adults with acute respiratory distress syndrome. summary of the experimental evidence for the clinical practice guideline chinese research hospital association of critical care medicine ycocrhaoccm. chinese experts consensus on diagnosis and treatment of severe and critical new coronavirus pneumonia. chin crit care med acute respiratory distress syndrome: the berlin definition critical care management of adults with community-acquired severe respiratory viral infection tang lanfang, version) clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study a trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-ncov) in vitro drug treatment options for the 2019-new coronavirus (2019-ncov). biosci trends discovering drugs to treat coronavirus disease 2019 (covid-19) press conference of the joint prevention and control mechanism of the state council hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov-2 infection in vitro breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid-19 associated pneumonia in clinical studies guangdong province for chloroquine in the treatment of novel coronavirus p covid-19: a recommendation to examine the effect of hydroxychloroquine in preventing infection and progression in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) clinical evidence does not support corticosteroid treatment for 2019-ncov lung injury. the lancet on the use of corticosteroids for 2019-ncov pneumonia retrospective study of side effects of low-dose glucocorticoids in rheumatoid arthritis early, low-dose and short-term application of corticosteroid treatment in patients with severe covid-19 pneumonia: single-center experience from wuhan, china. medrxiv potential benefits of precise corticosteroids therapy for severe 2019-ncov pneumonia short-term moderate-dose corticosteroid plus immunoglobulin effectively reverses covid-19 patients who have failed low-dose therapy effectiveness of glucocorticoid therapy in patients with severe novel coronavirus pneumonia: protocol of a randomized controlled trial treatment of mers-cov: information for clinicians: public health england the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis commission cnh. the clinical guideline of convalescent plasma treatment(trial version 2) 32 recovered patients donate plasma to others with coronavirus infection clinical trial registration information analysis of covid-19 in china hypothesis for potential pathogenesis of sars-cov-2 infection-a review of immune changes in patients with viral pneumonia understanding sars-cov-2-mediated inflammatory responses: from mechanisms to potential therapeutic tools analysis of property and efficacy of traditional chinese medicine in staging prevention and treatment of corona virus disease 2019 discovery of anti-2019-ncov agents from chinese patent drugs toward respiratory diseases via docking screening2020 expert consensus on diagnosis and treatment of 2019 novel coronavirus (2019-ncov) 28 71. china has successfully developed recombination vaccines of sars-cov-2 prone positioning in severe acute respiratory distress syndrome a multicenter retrospective review of prone position ventilation (ppv) in treatment of severe human h7n9 avian flu holistic care for patients with severe coronavirus disease 2019: an expert consensus pulmonary pathology of early-phase journal of thoracic oncology : official publication of the international association for the study of lung cancer pathological findings of covid-19 associated with acute respiratory distress syndrome two cases of increased positive rate of sars-cov-2 nucleic acid test by aerosol inhalation to induce sputum excretion guidelines for the diagnosis and treatment of hospital-acquired pneumonia and ventilator-associated pneumonia in adult in china expert consensus on principal of clinical management of patients with severe emergent cardiovascular diseases during the epidemic period of covid-19 pharmacokinetics, metabolism, and excretion of the antiviral drug arbidol in humans hypothesis for potential pathogenesis of sars-cov-2 infection--a review of immune changes in patients with viral pneumonia cryo-em structure of the 2019-ncov spike in the prefusion conformation inhibition of sars-cov-2 infections in engineered human tissues using clinical-grade soluble human ace2 recommendations from the peking union medical college hospital for the management of acute myocardial infarction during the covid-19 outbreak experiences and lesson strategies for cardiology from the covid-19 outbreak in wuhan, china, by 'on the scene' cardiologists covid-19: too little, too late? the impact of transmission control measures during the first 50 days of the covid-19 epidemic in china. medrxiv abbreviations: na: not available; hrct: high-resolution computed tomography; ards: acute respiratory distress syndrome; icu: intensive care unit; map: mean arterial pressure; sbp: systolic blood pressure; sd: standard deviation; hr: heart rate; bpm: beats per minute; sec: second; *: the elderly and immunosuppressed may present with atypical symptoms. symptoms due to physiologic adaptations of pregnancy or adverse pregnancy events, such as dyspnea, fever, gastrointestinal symptoms or fatigue, may overlap with covid19.†: fast breathing (in breaths/min): < 2 months: ≥ 60; 2-11 months: ≥ 50; enforcement laws including <law of the people's republic of china on the prevention and treatment of infectious diseases>, <surveillance protocol for pneumonia cases from novel coronavirus (second edition)>, <preventive measures against infectious diseases in business and service business sites>, <provisions on the emergency handling of entry-exit inspection and quarantine for public health emergencies at border ports>, etc. temperature screening on the public occasions, such as hospitals, supermarket purchasing daily necessities on a regular schedule delivering food and disinfectants for every family real time disinfection of public areas. key: cord-287222-wojyisu0 authors: zhou, min; zhang, xinxin; qu, jieming title: coronavirus disease 2019 (covid-19): a clinical update date: 2020-04-02 journal: front med doi: 10.1007/s11684-020-0767-8 sha: doc_id: 287222 cord_uid: wojyisu0 coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus-2 (sars-cov-2) has posed a significant threat to global health. it caused a total of 80 868 confirmed cases and 3101 deaths in chinese mainland until march 8, 2020. this novel virus spread mainly through respiratory droplets and close contact. as disease progressed, a series of complications tend to develop, especially in critically ill patients. pathological findings showed representative features of acute respiratory distress syndrome and involvement of multiple organs. apart from supportive care, no specific treatment has been established for covid-19. the efficacy of some promising antivirals, convalescent plasma transfusion, and tocilizumab needs to be investigated by ongoing clinical trials. currently, coronavirus disease 2019 (covid-19) poses a significant threat to global health. world health organization (who) has declared this outbreak as a "public health emergency of international concern" on january 31, 2020. within the first two months of the outbreak, the epidemic spread rapidly around the country and the world. as of march 8, 2020, a total of 80 868 confirmed cases and 3101 deaths had been reported in chinese mainland by national health commission of china, and 90 other countries are affected. covid-19 as an emerging disease, has unique biological characteristics, clinical symptoms, and imaging manifestations, though considerable progress has been made on the clinical management. this article will summarize the epidemiological, etiological, clinical, pathological, and radiological characteristics of covid-19 and review the latest advancements in the treatment. epidemic curves reflect that this epidemic may be a mixed outbreak pattern, with early cases suggestive of a continuous common source, potentially at huanan seafood wholesale market (hswm), and later cases suggestive of a propagated source as the virus began to be transmitted from person to person [1] . a retrospective analysis on the first 425 patients with confirmed covid-19 showed that during the early stages of this outbreak, the basic reproduction number r 0 was estimated to be 2.2 [2] . another modeling study estimated that the r 0 for covid-19 was 2.68 [3] . considering the strict prevention and control measures implemented by the chinese government, a phase-adjusted estimation of epidemic dynamics assumed that the effective reproduction number r 0 was 3.1 at the early phase of the epidemic, and could be gradually decreased [4] . of the first 99 laboratory-confirmed patients, 49 (49%) had been exposed to hswm, which was reported to be the possible initial source of severe acute respiratory syndrome coronavirus-2 (sars-cov-2) [5] . a shenzhen family cluster without exposure history to wuhan markets or wild animals also proved the possibility of person-to-person transmission [6] . another family cluster of patients provided evidence that asymptomatic carriers may also be potential sources of sars-cov-2 infection [7] . evidence has recently been obtained to suggest transmission along a chain of 4 generations [8] . sars-cov-2 spread mainly through respiratory droplets or close contact. while in the later stage of infection, the virus is also detectable in anal swabs, suggesting the possibility of oral-fecal route transmission [9] . significant environmental contamination by patients carrying sars-cov-2 through respiratory droplets and fecal shedding suggests that the environment serves as a potential medium of transmission and supports the requirement for strict adherence to environmental and hand hygiene [10] . currently, there is no clear evidence of infection caused by vertical transmission or aerosol transmission. sars-cov-2 is the causative pathogen of covid-19, identified as the seventh type of coronavirus to infect humans [11] . six other kinds of coronaviruses are known to cause human disease, including severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) with high mortality rate [12] . according to the genome characteristics, coronavirus is separated into four genera: α-cov, β-cov, γ-cov, and δ-cov [12] . deep sequencing revealed that this novel coronavirus isolated from lower respiratory tract samples of patient with covid-19 belongs to β-cov [11] . coronavirus has the appearance of crown under electron microscopy. they are enveloped viruses with a singlestrand, positive-sense rna genome, which is the largest known genome for an rna virus [13] . all coronaviruses share the same genome organization and expression pattern, with two large overlapping reading frames (orf1a/b) which encode 16 nonstructural proteins, followed by orfs for four major structural proteins: spike (s), envelope (e), membrane (m), and nucleocapsid (n) [13] . the sars-cov-2 protein also contains eight accessory proteins [14] . spike protein plays an essential role in binding to receptors and is critical for determining host tropism and transmission capacity. it is functionally divided into s1 domain and s2 domain, responsible for receptor binding and cell membrane fusion respectively. the receptor binding domain (rbd) of β-cov is commonly located in the c-terminal domain of s1 [15] . a team analyzed the cryogenic electron microscopy (cryo-em) structure of the sars-cov-2 spike protein and found that it has 10 to 20-fold higher binding affinity to human angiotensin-converting enzyme 2 (ace2) than sars-cov does [16] . phylogenetic analysis of the evolution history showed that sars-cov-2 shared a closer sequence homology toward the genomes of sars-cov than to that of mers-cov [17] . sars-cov-2 is highly similar to a bat coronavirus ratg13, with an overall genome sequence identity of 96.2% [18] , indicating that bat, which was discovered to be the natural reservoir host of various sars-related coronaviruses [19] , may also be the original host of sars-cov-2. the intermediate host in the process of transmission remains uncertain. clinical manifestation covid-19 has an incubation period of 1-14 days, mostly ranging from 3 to 7 days [20] . the most common symptoms in mild to moderate patients are fever, fatigue, and dry cough, followed by other symptoms including headache, nasal congestion, sore throat, myalgia, and arthralgia [5, [21] [22] [23] . a minority of patients had gastrointestinal symptoms, such as nausea, vomiting, and diarrhea, especially in children. in the study of 1099 covid-19 patients, 43.8% cases presented fever at onset of illness and the percentage further increased to 88.7% during following hospitalization [24] . notably, fever may occasionally be absent from elderly persons or immunocompromised ones. a part of patients may progress to shortness of breath, usually in the second week of the illness, and might be accompanied by or progress to hypoxemia [25, 26] . for patients presenting tachypnea, chest indrawing, or inability to feed or drink, severe pneumonia should be considered. in 10% to 20% of severe patients, the respiratory injury will inevitably develop into acute respiratory distress syndrome (ards) during 8-14 days of the illness, defined as partial pressure of oxygen (pao 2 ) to fraction of inspired oxygen (fio 2 ) ratio lower than 300 mmhg, as well as resultant non-cardiogenic pulmonary edema and mechanical ventilation [24, 25, 27] . ards, as the main cause of respiratory failure, is associated with high morbidity and mortality. risk factors for developing into severe to critical cases include advanced age, underlying comorbidities such as hypertension, diabetes, cardiovascular disease, and cerebrovascular disease [23, 25, 26] . as disease progresses, a series of complications tend to occur, especially in critically ill patients admitted to icu, including shock, sepsis, acute cardiac injury, acute kidney injury, and even multi-organ dysfunction [23, 24, 26] . patients may manifest altered mental status, low oxygen saturation, reduced urine output, weak pulse, cold extremities, low blood pressure, and mottled skin. besides, patients with acute cardiac injury would present tachycardia or bradycardia. critically ill ones may also suffer acidosis and increased lactate [23] [24] [25] . current studies reported the peak value of temperature in non-survivors of covid-19 was significantly higher than that in survivals during hospitalization [23, 24] . thus, patients presenting hyperthermia and chill should exclude the possibilities of co-infection with bacteria or other pathogens. attentions should be paid to prevent hospital-acquired pneumonia (hap) in critical cases and ventilator-associated pneumonia (vap) in those receiving mechanical ventilation. coagulopathy and thrombocytopenia are also common complications for covid-19 infection, which increase the risk of hemorrhage and thrombosis. mottled skin, petechial or purpuric rash, appearance of black stool or hematuresis could be found in some cases. patients with the syndrome of persistent hypoxemia, chest pain, pre-syncope or syncope, and hemoptysis should be suspected of having pulmonary thromboembolism (pte) [28] . the manifestation of limb pain, swelling, erythema, and dilated superficial veins should be suspected of deep vein thrombosis (dvt). nearly 20% of patients had abnormal coagulation function, and most of severe and critical patients presented coagulation disorders and had the tendency to develop into disseminated intravascular coagulation (dic) [5, 25, 26] . in the early stage of infection, the involved lung lobe presented obvious alveolar edema, proteinaceous exudates, and reactive pneumocyte hyperplasia, accompanied by mild inflammatory infiltration [29] . on gross examination, the whole lung showed bronzing surface and diffuse congestive appearance, with partly hemorrhagic necrosis, as same as the cut surfaces. on histological examination, the typical manifestations were extensive proteinaceous and serous exudation in the alveolar, hyaline membrane formation, and inflammatory infiltration with multinucleated syncytial cells. type ii alveolar epithelial cells showed extensive hyperplasia, and some presented necrosis and desquamation. viral inclusions could be identified in epithelium and macrophage. besides, alveolar septal vessels manifested congestion with alveolar edema. the infiltration of monocytes and lymphocytes in alveolar cavity and microthrombosis were prominent. some parts showed alveolar exudate organization and pulmonary interstitial fibrosis. with a fraction of desquamation of mucosal epithelium, bronchi were covered by mucus even mucus plug [20, 30, 31] . in addition, other organs also suffered pathological damage to some extent [20] . the atrophic spleen showed significantly reduced lymphocytes, focal hemorrhage and necrosis, and macrophage hyperplasia. with degeneration and necrosis of cardiomyocytes, a small number of monocytes, lymphocytes, and/or neutrophils were infiltrated in the myocardial interstitium. protein exudation was seen in renal glomerulus and within hyaline cast, and renal tubular epithelium degenerated and desquamated. besides, hepatocytes degeneration, necrosis, and inflammatory infiltration also occurred. the brain presented congestion, edema, and degeneration of some neurons. meanwhile, microthrombosis could be found in multiple organs. radiological images play an important role in the diagnosis and providing guidance for treatment. guan et al. found that 86.2% of patients manifested abnormalities in chest ct images, of whom more than 75% had bilateral lung involvement, mainly with peripheral and diffused distribution [24] . patients of different severity presented significant different lesions on chest ct (fig. 1) . mild patients manifested unilateral and focal ground-glass opacity (ggo) which gradually develops to bilateral or multilobular lesions. as the disease progressed further, ggos evolved to consolidation lesions, presenting mixpattern or pure consolidation, with the latter being more common in critically ill patients admitted to icu [5, 25, 32] . consistent with the interstitial involvement in viral pneumonia, zhao et al. suggested that 48.5% of ct images manifested reticular patterns, and 28.7% presented interlobular septal thickening [33] . unlike influenza pneumonia, which usually exhibited unilateral ggo and significant solid nodules, only 6% of covid-19 patients had solid nodules [32, 34, 35] . moreover, other lesions included adjacent pleura thickening, vascular enlargement, bronchial wall thickening, traction bronchiectasis, air bronchogram, pericardial effusion, etc. [32, 33, 36] . follow-up of ct scan could help to monitor disease changes and evaluate therapeutic effects [32] . some dynamic images fluctuate repeatedly, and showed coexistence of absorption of primary lesions and emergence of new ones. during disease deterioration, increased number of or enlarged lesions could be observed in radiological imaging, and part of them even developed into a "white lung" with diffusely involved lung [37] . a majority of covid-19 patients showed normal leucocyte count, and nearly one third had leucopenia [21, 24] . lymphocytopenia, as one of the most typical laboratory abnormalities, was present in 83.2% of patients, with an even higher proportion in severe ones [24, 26] . in addition, previous studies also revealed that increased ddimer level and prolonged prothrombin time were also common features of covid-19, especially for severe patients [24] [25] [26] . meanwhile, sars-cov-2 might damage liver and myocardium to some extent, showing elevated levels of aminotransferase, creatine kinase, and myoglobin with diverse degrees, as well as increased troponin in critical patients [5, 23, 25] . a few patients had renal dysfunction, presenting increased serum creatinine or blood urea nitrogen [5] . as for infection-related serum biomarkers, our studies have reported that most of patients had increased concentration of c-reactive protein, interleukin-6 (il-6), and erythrocyte sedimentation rate [5] . likewise, huang et al. observed similar phenomenon and proposed that icu patients might suffer severe cytokine storms, with a overproduction of il-7, il-10, gcsf, ip10, mcp1, mip1a, and tnf-α, etc. [25] . multi-drug resistant acinetobacter baumannii and klebsiella pneumoniae have been isolated in covid-19 patients [5, 23] . other identified microorganisms included pseudomonas aeruginosa, aspergillus flavus, aspergillus fumigatus, candida albicans, and candida glabrata [5, 23] . laboratory confirmed covid-19 patients had positive results on real-time reverse transcriptase polymerase chain reaction (rt-pcr) of nasal and pharyngeal swab, sputum, blood, faeces, and urine specimens [25] . the collected clinical specimens need to be transported to designated laboratories promptly, and extracted for rna correctly, followed by rt-pcr detection with primers and probes of appropriate sequences [25] . the value of cycle threshold (ct) was the criterion to determine the detection result, with less than 37 being defined as negative, above 40 as positive and a medium load (37) (38) (39) (40) calling for confirmation by retesting [2] . the detection of sars-cov-2 specific igm and igg antibodies can also be used for diagnosis [20] . covid-19 infection could be determined with one of the following criteria: positive specific igm, the transformation of specific igg from negative to positive, a 4-fold increase in igg titer during recovery period compared with the result of acute phase. although antibody detection was simple, rapid, and inexpensive, it is still not widely used due to inherent limitations, for example, false-negativity resulted from the existence of window period, noncomparable sensitivity and specificity with pt-pcr, absence of exclusion criteria making it a diagnosis tool only. these is no specific antiviral treatment which has been proven to be effective for covid-19. combinations of over three antivirals are not suggested. current treatment options are mainly based on previous experience showing clinical benefits in treating influenza, ebola, mers, sars, and other viral infections. it is reported that most of covid-19 patients received antiviral therapy in china [5, 21, 25] , and here we will introduce some commonly used drugs. ribavirin is representative of nucleoside analogs. the combination of ribavirin and recombinant interferon, a broad spectrum antiviral agent, showed augmentation effect in inhibiting mers-cov replication and reduced doses of both ribavirin and interferon [38] . however, most of clinical experiences in mers patients come from limited case reports and observational studies, making the quality of evidence for ribavirin and interferon treatment efficacy very low [39] . it is recommended to administer ribavirin by intravenous infusion in combination with inhaled interferon-α or oral lopinavir/ritonavir in the 5th version guideline on covid-19 diagnosis and treatment issued by chinese national health commission [20] . notably, ribavirin is not suggested by military medical team coming to hubei [40] and interferon-α inhalation is worried to increase the risk of virus-containing aerosol production and airway stimulation. lopinavir/ritonavir is a combination of a protease inhibitor and a booster used for the treatment of human immunodeficiency virus (hiv) infection. currently, randomized controlled trials for the efficacy of a combination of lopinavir/ritonavir with interferon-α in mild to moderate patients (chictr2000029387) and severe to critical patients with covid-19 (chictr2000029308) are in progress. remdesivir, a novel nucleotide analog rna polymerase inhibitor, is considered as the most promising antiviral drug for the treatment of covid-19. it showed broad spectrum antiviral activities, from inhibition of human and zoonotic coronavirus (including sars-cov-2 [41] as well ebola virus) in vitro, to prophylactic and therapeutic effects in animal model of mers-cov and sars-cov infection [42, 43] . the first covid-19 patient identified in the united states was given remdesivir without obvious adverse reactions. two trials on efficacy of remdesivir have been launched in china among mild to moderate patients (nct04252664) and severe to critical patients (nct04257656) infected with sars-cov-2. neuraminidase inhibitors (nais), such as oral oseltamivir and intravenous peramivir, showed substantial clinical improvement in treating influenza patients [44] . oseltamivir was widely used for suspected and confirmed covid-19 patients in china [26] , however, there is no exact evidence that supports its application. a research team from zhejiang university reported that abidol has the potential to inhibit sars-cov-2, which was previously used for influenza. there is a multicenter, randomized, and controlled trial (chictr2000029573) to evaluate the efficacy of abidol and lopinavir/litonavir, either alone or in combination with a new type of interferon, novaferon. according to current who interim guidance on covid-19 management [27] , corticosteroids were not recommended as routine therapy unless indicated for another reason, because possible harms and higher risk of mortality attributed to corticosteroids therapy have been identified by studies on other coronaviruses and influenza. an epidemiological study conducted in wuhan observed a larger percentage of patients receiving corticosteroids in icu groups when compared with non-icu groups (6 (46%) vs. 3 (11%); p = 0.013), while we still cannot determine the effects of corticosteroids due to the limited sample size [25] . according to the latest guidelines issued by national health commission of china (version 7) [20] and the interim guidance of who [27] , when sars-cov-2 infection is suspected, corticosteroids should be recommended to use with caution. new coronavirus infection diagnosis and treatment scheme (trial version) published by military support hubei medical team also put forward that for mild to moderate covid-19 patients, corticosteroids should not be given principally and highdose corticosteroid pulse therapy was not recommended. only patients presenting ongoing deterioration in oxygenation index, or rapid progression of radiological findings, or excessive activation of immune responses, will be considered to use short-term corticosteroid therapy within 10 days of illness onset. seven designated hospitals in zhejiang province gave patients corticosteroids when they showed increased resting respiratory rate ( > 30 breaths/ minute), drop in oxygen saturation ( < 93%) on room air, or multi-lobular progression ( > 50%) on imaging within 48 h [21] . timely and appropriate use of corticosteroids combined with ventilator support should be considered for severe patients to prevent progression to ards [30] . the pharmacologic use of corticosteroids in covid-19 treatment should vary with severity [20, 40] . for severe cases, it is suggested to start at a dose of 40 to 80 mg/day methylprednisolone and slowly taper over 7 to 10 days, and some suggested for a shorter period of 3 to 5 days. for critically ill cases, a starting dose of 80 to 160 mg/day methylprednisolone, following a slow withdrawal within 7 to 10 days is considered. it is widely recognized that many patients, especially critically ill patients were susceptible to secondary infections. patients receiving corticosteroids had increased risks of developing hap due to the immunosuppression effects, and those who received mechanical ventilation were susceptible to vap. the latest guidelines issued by national health commission of china for the diagnosis and treatment of covid-19 infection (version 7) [20] advise against inappropriate and unnecessary use of antimicrobial therapy, especially combination of broadspectrum antibiotics. if the sputum or blood specimens showed a clear evidence of etiology or the pct levels increased, administration of antimicrobial agents should be considered. as shown in a study of 99 patients with covid-19, acinetobacter baumannii, klebsiella pneumoniae, and aspergillus flavus were simultaneously cultured in one patient. meanwhile, one case of fungal infection was attributed to candida glabrata and three cases of fungal infection were caused by candida albicans [5] . when selecting antimicrobial agents for initial empiric treatment, in addition to the local epidemiological data of hap/vap pathogens, imaging features of pulmonary lesions should also be taken into account [45] . as for fungal infections, voriconazole is recommended for the treatment of aspergillus infections, while fluconazole is more suitable for candida spp. infections. when patients are suspected with pneumocystis pneumonia, sulfamethoxazole and caspofungin should be promptly administrated [45] . in clinical practice, nearly 20% of patients with covid-19 are found to have abnormal coagulation function, and almost all severely and critically ill patients presented coagulation disorders [5, 25, 26] . in view of no relevant experience for reference, anticoagulation should be given with great caution in patients with dic though microthrombosis was observed in lung, liver, and other organs by autopsy. when patients exhibit a bleeding tendency or when surgical treatment is needed, platelet transfusion or administration of fresh-frozen plasma is recommended to correct coagulopathies analogs [46] . low molecular weight heparin (lmwh) can be used for drug prevention. as for subjects with clinical manifestations, clinicians need to be alert to the occurrence of pte, initiate the diagnostic procedures, and develop corresponding treatment strategies based on risk stratification. considering the risk of disease transmission and the false positive results caused by the presence of lung lesions, the diagnosis of pte by pulmonary ventilation-perfusion imaging is not recommended. if the critically ill patients cannot take examination due to specific conditions and the infectivity of covid-19, it is recommended to perform anticoagulant therapy for patients without contraindications. if the condition is lifethreatening and bedside echocardiography indicates new onset of right ventricular volume overload or pulmonary hypertension, thrombolytic therapy or other cardiopulmonary support treatments, such as extracorporeal membrane oxygenation (ecmo) can be initiated with the patient's full informed consent. for mild to moderate patients with hypoxemia, nasal catheters and masks and even high-flow nasal cannula oxygen therapy (hfnc) are advised. while for severe and critical patients with respiratory distress, hfnc, noninvasive mechanical ventilation (niv) or invasive mechanical ventilation, and even ecmo should be considered. hfnc can provide accurate oxygen concentration and a certain positive airway pressure to promote alveolar expansion to improve oxygenation and respiratory distress [47] . however, according to expert consensus on the use of hfnc for covid-19, patients with cardiac arrest, weak spontaneous breathing, pao 2 /fio 2 < 100 mmhg, paco 2 > 45 mmhg and ph < 7.25 and upper airway obstruction are contraindicated. for severe patients with respiratory distress or hypoxemia that cannot be alleviated after standard oxygen therapy, niv can also be considered with close surveillance [24, 26] . dangers et al. considered that changes in dyspnea could be used as a variable to predict the failure of noninvasive ventilation [48] . if the patient continuously deteriorates or the respiratory rate cannot be improved after a short time (about 1-2 h), timely tracheal intubation and invasive ventilation are required [49] . notably, patients with hemodynamic instability, multiple organ failure or abnormal mental status should not receive noninvasive ventilation. lung protection ventilation strategies (small tidal volume, limited plateau pressure, and permissive hypercapnia) are suggested to be adopted in invasive mechanical ventilation to reduce ventilator-related lung injury [50] . compared with niv, invasive mechanical ventilation can more effectively improve the pulmonary ventilation function and respiratory mechanics of patients with acute respiratory failure. it can effectively increase the sao 2 level and is more conducive to lower the plasma bnp level [51] . however, invasive mechanical ventilation requires tracheotomy, or oral/nasal tracheal intubation to establish an artificial airway, which is very likely to cause damage to patients, such as mediastinal emphysema, ventilatorrelated lung injury, and other related complications, such as reduced swallowing function, gastresophageal reflux, infections, etc. what's more, invasive mechanical ventilation also increases the risk of secondary infections transmitted by aerosol particles [52] . for critical patients, crrt can support organ function, reduce cytokine storms and maintain internal environment stability [53] . three clinical studies showed that the incidence of aki in patients with covid-19 was 3% to 7%, and 7% to 9.0% were treated with crrt. in icu, the rate of crrt application was 5.6% to 23.0% and reached as high as 66.7% to 100% in patients with aki [5, 26, 54] . crrt is recommended for patients who exhibit aki indications (hyperkalemia, acidosis, pulmonary edema, severe sodium ion disorders) or patients with ckd who have not undergone hemodialysis. during septic shock, crrt can effectively remove inflammatory mediators and significantly improve hemodynamics. when ards appears in combination with multiple organ dysfunction syndrome (mods), early crrt is recommended [55] . crrt combined with the treatment of ecmo may remove cytokines, reduce the activity of macrophages and monocytes, and better preserve lung parenchyma. some studies reported that early convalescent plasma treatment for influenza and sars-cov infection is associated with decreased viral load and reduction in mortality [56] , however, the studies were heterogeneous and of low quality. the who deemed convalescent plasma transfusion as the most promising therapy for mers-cov infection, while the efficacy remained inconclusive, with a lack of adequate clinical trials [56] [57] [58] . since the virological and clinical characteristics among sars, mers, and covid-19 were comparable [59] , convalescent plasma could have immunotherapeutic potential in covid-19 treatment and further investigations are needed to prove its safety and efficacy. one possible explanation for the efficacy of convalescent plasma therapy is that the neutralizing antibodies from convalescent plasma might suppress viremia [60] , so understanding the antibody response during the course of sars-cov-2 infection could provide strong empirical support for the application of convalescent plasma therapy. a study reported that on day 5 after treatment, an increase of viral antibodies can be seen in nearly all patients, igm positive rate increased to 81%, whereas igg positive rate increased to 100%, which was considered as a transition from earlier to later period of infection [9] . preliminary study has showed that patients who have recovered from covid-19 with a high neutralizing antibody titer and could provide a valuable source of the convalescent plasma. plasma transfusion may cause adverse effects, so convalescent plasma therapy is recommended as a last resort to improve the survival rate of severe patients with covid-19. the optimal dose and treatment time point, as well as the therapeutic indications of convalescent blood products in covid-19 remain uncertain, which need to be further investigated in randomized clinical studies. tocilizumab is a humanized igg1k monoclonal antibody which can specifically bind soluble or membrane-type il-6 receptors (sil-6r and mil-6r), and has been widely used in the treatment of autoimmune diseases such as rheumatoid arthritis [61] , adult-onset still's disease [62] , and large vessel vasculitis [63] . for covid-19 infection, clinical studies have shown that serum levels of inflammatory mediators in severe patients are significantly higher than those in common patients [25] . excessive immune responses can trigger cytokine storms and cause damage to multiple target organs. recent guidelines also point that a progressive rise in il-6 may be a clinical warning indicator for the deterioration of covid-19. a domestic research team found that tocilizumab can block the signaling pathways of two key inflammatory factors, il-6 and gm-csf, and reduce the inflammatory response. a multicenter, randomized, controlled clinical study has been coducted to evaluate the efficacy and safety of tocilizumab in the treatment of moderate patients at high risk to develop into severe and critical patients (registration number: chictr2000029765). for patients with elevated il-6 levels, the efficacy of tocilizumab can be expected. in this review, we gave an overview of epidemiological, etiological, clinical, pathological, and imaging characteristics of 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in part by a grant from innovative research team of high-level local universities in shanghai. min zhou, xinxin zhang, and jieming qu declare that they have no conflict of interest. this manuscript is a review article that does not involve a research protocol requiring approval by the relevant institutional review board or ethics committee. key: cord-281102-ohbm78it authors: gutzeit, andreas; li, qiubai; matoori, simon; li, basen; wang, liang title: what can european radiologists learn from the outbreak of covid-19 in china? a discussion with a radiologist from wuhan date: 2020-04-08 journal: eur radiol doi: 10.1007/s00330-020-06841-6 sha: doc_id: 281102 cord_uid: ohbm78it nan communication is to determine what we can learn from the chinese experience and how hospitals and radiology departments all around the world can prepare for a widespread outbreak of this disease. on 31 december 2019, the world health organization (who) documented an outbreak of pneumonia of unknown etiology in the city of wuhan, china [1] [2] [3] . few days later, chinese researchers identified a novel coronavirus (2019-ncov) as the causative agent of the outbreak and the resulting disease was subsequently named covid-19 [2] . the outbreak appears to be linked to a single or multiple zoonotic transmission events at a wet market in wuhan where animals were sold [4] . on 31 march 2020, more than 750,890 people have been infected with the coronavirus and more than 36,405 people have died. while in many countries the numbers of new infections are increasing, the numbers in different asian countries, namely china, seem to be stable or decreasing according to the covid-19 situation report of the who on 31 march 2020. this article is not about telling radiology departments how to behave. we just want to show what has worked in the crisis situation in wuhan. if there is one positive thing about the covid-19 outbreak, it is the insight that humanity can only solve today's complex problems through international collaboration. scientists are particularly important participants of such discussions as they find solutions collaboratively based on scientific evidence and rational thinking. when did the first disaster trainings start within the hospital in wuhan after the covid-19 outbreak? wuhan hospitals started with comprehensive training for the whole hospital staff immediately after the covid-19 electronic supplementary material the online version of this article (https://doi.org/10.1007/s00330-020-06841-6) contains supplementary material, which is available to authorized users. * andreas gutzeit andreas.gutzeit@hirslanden.ch * liang wang wang6@tjh.tjmu.edu.cn outbreak. the entire staff of the hospitals were trained, including medical staff, administrative staff, and service departments (cleaning service, security, and others). the training content was standard prevention, personal protection, correct use of protective equipment, procedures to optimize putting on and removing protective equipment, hand hygiene, isolation measures, medical waste management, and air and environmental surface cleaning and disinfection. the training methods were on-site training and the recording of sample videos for elearning purposes. what kind of hospital management was in place in wuhan during the crisis? the director of the clinical and medical technology department in wuhan was the most important person during the coronavirus crisis. this person supervised prevention and control in the department, effectively played the leading role in the infection control group in each department, carried out critical self-assessment and self-correction, and timely identified problems and communicated them along with suggestions for improvement. basically, there is no need for a director, but there is a need for a person or management team with medical and management experience to take responsibility and take decisions in difficult times. the hospital infection management established an inspection system to strengthen the guidance and supervision of the implementation of the clinical department's control measures and the correct wearing of protective equipment. what were the management processes in radiology departments during the crisis? it was essential to avoid cross-infections. every technician and radiologist in wuhan was familiarized with the knowledge about prevention and infection control of the coronavirus situation. the workplaces were divided into clear different zones to prevent transmissions. leaving the critical zone with potentially infected patients was only allowed after standardized cleaning procedures and the removal of protective clothing and disinfection. despite possible impairment of scan and image quality, xray technicians required patients to wear protective equipment such as face masks during the examination. the stay in the waiting room was reduced to a minimum. patient crossing was reduced as much as possible and the distance between patients was more than 2 m. special times were reserved in the radiology departments for possible and confirmed covid-19 patients, if the patients could not be separated due to lack of equipment or space. in cases with enough radiology equipment and enough space, special imaging modalities were reserved for the patients with covid-19 positive or unclear status. the examination room had to be temporarily vacated before the examination. after the examination, all the surfaces which the patient had been in contact with (including the floor) were disinfected. after training, the cleaning staff needed about 10 min for the standardized cleaning procedures. in these areas, only patients with a negative covid-19 test were examined, and only employees without any potential covid-19 symptoms were allowed to enter these areas. during the crisis in wuhan, technicians, nurses, radiologists, and all other persons had to pay close attention to regular hand hygiene, wearing face masks (ffp2/filtering facepiece 2 respirator), protective clothing according to the protection requirements of class ii environments, and removal of protective equipment after work. this was necessary in order to prevent the staff from getting infected in the course of the crisis and to avoid additional absences and shortage of staff. in wuhan, desktop, computer, and intercom systems in the radiology departments were regularly cleaned after use with 250-500 mg/l chlorinated disinfectant or 75% (v/v) medical ethanol. the use of spraying devices was avoided to reduce the risk of damage to electronic equipment or provoking a fire hazard. this applied to the covid-19-positive sections and the covid-19-negative sections. for more information on the disinfection protocol, the readers are referred to the appendix. these are the experiences from tongji university hospital in wuhan and not evidence-based. how did wuhan deal with the enormous quantities of potentially contaminated protective suits and equipment during the covid-19 epidemic in the radiology departments? all wastes generated in the imaging procedures planned for covid-19 were treated as medical waste. these were packed in double yellow medical waste bags, sealed, and removed from the examination room. the packaging bag was specially marked with infectious covid-19 waste. the bags were sprayed from the outside with 2000 mg/l chlorine-containing disinfectant and cleaned. the waste was then transported away by a transport vehicle and incinerated in a plant. the waste was not mixed with general medical waste and household waste. wuhan and china cannot be compared with europe in terms of society and infrastructure. the management processes during the covid-19 outbreak, which are described here, were possible in wuhan. we cannot judge whether this can be implemented in every hospital in europe. we expect an enormous increase of covid-19 patients in the next weeks and months all over the world and also in europe. if radiology departments want to think about whether their own plans are sufficient, they can compare them with the procedures in wuhan. we hope this will give our european colleagues the opportunity to learn how a national crisis has been successfully managed. clinical features of patients infected with 2019 novel coronavirus in wuhan pattern of early human-to-human transmission of wuhan a pneumonia outbreak associated with a new coronavirus of probable bat origin a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating personto-person transmission: a study of a family cluster publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations institute of radiology and nuclear medicine and breast center st.acknowledgments we thank prof. liang wang and his radiology teams and all our medical colleagues in china for the exchange of knowledge.prof. liang wang kindly offered his support to the radiology community and can be contacted via email (wang6@tjh.tjmu.edu.cn).funding information ag, ql, sm, and bl did not receive any funding for this work. lw received funding from the national natural science foundation of china (#81171307, 81671656). guarantor the scientific guarantor of this publication is andreas gutzeit. conflict of interest the authors of this manuscript declare no relationships with any companies, whose products or services may be related to the subject matter of the article.statistics and biometry one of the authors has significant statistical expertise.no complex statistical methods were necessary for this paper.informed consent written informed consent was not required for this study because there are no patients included.ethical approval institutional review board approval was not required because there are no patients included. • rapid communication key: cord-297168-t6zf5k99 authors: brüssow, harald title: the novel coronavirus – a snapshot of current knowledge date: 2020-03-06 journal: microb biotechnol doi: 10.1111/1751-7915.13557 sha: doc_id: 297168 cord_uid: t6zf5k99 another animal to human transmission of a coronavirus occurred in december 2019 on a live animal market in the chinese city of wuhan causing an epidemic in china, reaching now different continents. this minireview summarizes the research literature on the virological, clinical and epidemiological aspects of this epidemic published until end of february 2020. in late december 2019, chinese physicians identified a series of pneumonia cases in wuhan, an 11-million inhabitant megacity and traffic hub in central china. the infections were epidemiologically associated with a seafood 'wet' market in the city. 'wet' market means that live and dead animals are sold, raising the suspicion of another zoonotic virus infection that had spilled over into the human population similar to the severe acute respiratory syndrome (sars) epidemic in 2002, which also started from a live animal market. in sars, the viral source was traced back to a bat coronavirus with civets as potential intermediate host. the novel wuhan virus figures under different names (2019-ncov for novel coronavirus in the research literature, sars-cov-2 by the international committee on taxonomy of viruses, covid-19 as disease denominator by who), all names indicating that it represents a coronavirus. one might argue whether 'new' instead of 'novel' coronavirus is not a better term since it is not completely different, but related to the sars coronavirus, while others find that sars-cov-2 suggests a too close relations with the sars virus possibly leading to some confusion (jiang et al., 2020) . as the wuhan virus name changed, so changed the character of the epidemic and this overview can only provide a snapshot of the scientific research literature on this topic at the moment of this writing (29 february 2020). within a record time of less than a month, the novel coronavirus was identified, isolated and sequenced by three groups of chinese scientists. a large consortium coordinated by w. tan from the chinese centers for disease control and prevention (chinese cdc) obtained eight complete viral genome sequences from nine patients either by direct rna isolation and sequencing from bronchoalveolar lavage fluid (balf) or from classical virus isolation on human airway epithelial cells (lu et al., 2020) . the eight genomes showed sequence identity of 99.98%, i.e. only four nucleotides differed out of the 30 000 nucleotide-long single-stranded rna genomes. this level of viral genomic identity isolated from different human subjects is unusual for an rna virus that has been circulating for a long time in the human population. this observation suggests a recent single spill-over event from an animal source into humans. geneticists estimated that this event might have occurred in november 2019. the closest relatives of the new virus are coronaviruses isolated from bats in eastern china, but they shared only 87.6% sequence identity with the new isolates. therefore, viral taxonomists consider the novel coronavirus as a new viral species belonging to clade 2 of the sarbecovirus group, acronym for sars comprising betacoronaviruses. with the sars virus, the new isolates shared even less, namely 79% sequence identity. while bats are still considered the most likely source for this novel coronavirus, bats were already hibernating at the time of onset of this epidemic and no bats were sold at the huanan food market in wuhan, suggesting an intermediate animal host where adaptation to human transmission might have occurred. live hedgehogs, badgers, snakes and turtledoves were sold at the huanan market. claims were made, but were not (yet) substantiated that snakes or pangolins were intermediate hosts for creating the coronavirus by recombination events. w. tan and colleagues, who now constitute the china novel coronavirus investigating and research team, described subsequently the isolation of further coronaviruses from three patients in wuhan who tested negative for 18 viral and four bacterial respiratory pathogens. these viruses were closely related to those of the earlier nine patients. in human airway epithelial cells, the cytopathic effect of this virus was a lack of cilium beating . another group led by y.-z. zhang from the zoonosis group of the chinese cdc in beijing determined the genome of a closely related coronavirus by deep metatranscriptomic sequencing of the bronchoalveolar fluid of a patient working at the seafood market of wuhan (wu et al., 2020c) . analysis of the cell receptor interacting viral s (spike) gene showed indications of a recombination event. protein modelling suggested the human angiotensin-converting enzyme ii (ace2) protein as receptor. z.-l. shi from the wuhan institute of virology, and collaborators, presented a detailed characterization of the viruses detected in seven patients from wuhan suffering from severe pneumonia. six of them were professionally associated with the local food market . metagenomics of balf yielded coronaviruses that shared 99.9% sequence identity between the patients and the other coronavirus isolates from wuhan. using primers corresponding to a region in the s gene, these scientists developed a sensitive and outbreakspecific pcr test providing a diagnostic tool for the virus detection in balf or alternatively oral swabs of patients. for one patient, the researchers demonstrated an igm seroconversion followed by an igg seroconversion when using elisa technique with the viral nucleocapsid as target antigen. three patients showed specific igm responses indicating an acute infection. this serological evidence is important since the full set of koch's postulates for the identification of a new pathogen has not yet been fulfilled. from one patient, they isolated a virus that caused cytopathic effects on the established vero cell line after 3 days of incubation. the virus-infected cells were stained with specific antibodies and were observed by fluorescence microscopy, allowing the establishment of a virus neutralization test. all patients developed neutralizing serum antibodies. while hela cells could not be infected with the novel coronavirus, this cell line became susceptible when expressing the ace2 protein of human, bat and civet (but not of mouse) origin indicating that this novel coronavirus uses this protein as a cell receptor, as did the sars coronavirus from the 2002 epidemic. zhang et al. (2020a) compared 27 novel coronavirus genomes isolated from patients in three chinese cities (wuhan, zhejiang and guangdong) and thailand, all of whom had contact to wuhan. the genomes were very similar but could still be classified into six genogroups, suggesting that mutations had accumulated within patients during the current outbreak. curiously, the most basal genogroups were detected in guangdong, and not wuhan, isolates. another group did an in-depth annotation of the genomes of the novel coronaviruses with sars virus and identified 380 amino acid substitutions affecting all predicted proteins of the viral genome (wu, peng et al., 2020b) . one study focused on the cases of 41 patients hospitalized in wuhan before january 2, all of whom had laboratory-confirmed 2019-ncov infection (huanget al., 2020) . at this earliest phase of the outbreak, patients were mostly males (73%), half of whom had underlying diseases and 66% of whom were exposed to the huanan seafood market. common presenting symptoms were fever (98%), cough (76%) and myalgia or fatigue (44%). dyspnoea (laboured or difficult breathing) developed in 55%; acute respiratory distress syndrome (ards) was seen in 29%; 32% of patients needed to be transferred to an intensive care unit (icu); and 15% died. the patients showed lymphopenia (a reduction of lymphocytes in the circulating blood) and signs of a 'cytokine storm'. a follow-up study investigated 99 patients at jinyintan hospital in wuhan between january 1 and january 20. all 99 patients had pcr-confirmed 2019-ncov infection (chen et al., 2020) . during this next phase of the epidemic, fewer patients had had an exposure to the huanan seafood market (49%), but they were still predominantly male (67%). the average age was 55 years, and again, half of them suffered from chronic diseases. the predominant clinical manifestations in these patients were fever (83%), cough (82%) and shortness of breath (31%). imaging techniques showed bilateral pneumonia in 75% of the cases. seventeen per cent developed ards, which worsened in 11%, leading to death from multiple organ failure. in a third report, 138 patients with confirmed novel coronavirus infection were admitted between january 1 and 28 at zhongnan hospital of wuhan . this report differed from the previous two in important respects. in this cohort, only 9% of the patients reported having had an exposure to the huanan seafood market, and the gender ratio was not significantly biased. the presenting symptoms were fever (99%), fatigue (70%) and dry cough (59%), followed by anorexia, myalgia and dyspnoea. bilateral shadows, or ground glass opacities, were revealed by imaging techniques in the lungs of all patients. overall, 26% of the patients needed a transfer to icu and 4% died. half of the patients showed comorbidities (hypertension, cardiovascular disease and diabetes). most notably, 41% were possibly infected in the hospital, including 40 healthcare workers. until february 9, only nine cases of 2019-ncov infections were reported in infants under 1 year in china, all of whom had had infected family members. all infants had a mild form of disease (wei et al., 2020) . for planning public health measures, basic transmission data for the novel coronavirus are essential. the first 425 confirmed cases from wuhan provided data for a first epidemiological analysis (li et al., 2020a) , but it should be kept in mind that the virus might evolve during the epidemic and change its properties. over the three early phases of the infection (< jan1, jan1-11, jan 12-22), no change in average age was seen (56-61 years); no cases < 15 years of age were observed. male dominance among the patients disappeared, and the degree of 'wet' market exposure in the patients dropped over time. in addition, patient contact with persons showing respiratory symptoms was reported in fewer than 30% of the cases. these scientists calculated a mean incubation period of 5.2 days displaying a long tail (95th percentile: 12.5 days). comparisons of index cases and secondary cases in five clusters yielded a 'serial interval' of 7 days. from onset of illness to a medical visit, and then to hospital admission, 5 and 12 days elapsed respectively. the wuhan epidemic showed a doubling time of 7 days. from the cluster analysis, a basic reproduction number of 2.2 was estimated, i.e. each case led on average to 2.2 new infections. another report investigated a case of a family from shenzhen visiting relatives in wuhan . one wuhan relative had developed fever, cough and dyspnoea four days before the arrival of family members from shenzhen. four further relatives developed respiratory symptoms which led to hospitalization in two. from the six shenzhen family visitors, the four adults developed symptoms (fever, cough, weakness and diarrhoea) during the 5 days of their wuhan visit, while two children remained unaffected. notably, a family member who remained in shenzhen contracted the disease four days after the return of the visitors from wuhan to shenzhen. the data are evidence for efficient human-to-human virus transmission. the virus was detected in most nasopharyngeal and half of the throat swabs, a single serum sample, but no urine or stool sample of this family cluster. of importance for easy sampling and virus diagnostics, 90% of hospitalized patients from hongkong were positive for pcr virus detection in self-collected saliva (te et al., 2020) . the viral load ranged from 10 3 to 10 8 viral copies per ml saliva and decreased over the duration of hospitalization, but in one patient, it was still detectable 11 days after hospitalization. another study extended the epidemiological analysis to 88 infected patients living outside of wuhan, but who had a recent travel history to wuhan (backer et al., 2020) . this cohort allowed an estimation of the mean incubation period to 6.4 days. upper estimates range up to 11 days, which is important to determine the appropriate duration of quarantine. the novel coronavirus is spreading rapidly. on january 19, the first patient was reported on the west coast of the united states. the patient developed respiratory symptoms after a family visit to wuhan (holshue et al., 2020) . during hospitalization, the patient developed diarrhoea and the stool was weakly virus-positive. this observation is important since it could indicate a gut tropism in addition to lung tropism, not unusual for coronavirus. one might therefore count on a changing symptomatology in the unfolding of the current epidemic, necessitating public health measures against faecal-oral transmission (danchin et al., 2020) . this scenario is not unlikely, since the ace2 host receptor for the novel coronavirus is highly expressed on gut enterocytes (liang et al., 2020) . some change in symptomatology was already seen for chinese patients outside of wuhan. among the first 2019-ncov patients from beijing, upper airway congestion was the dominant finding (chang et al., 2020a) . disease in 62 laboratory-confirmed patients from zhejiang province showed mostly mild to moderate disease; 9% had diarrhoea, and only one patient needed icu (xu et al., 2020) . when analysing 72 314 cases, an overall case fatality rate (cfr) of 2.3% was calculated. however, when the analysis was limited to cases outside of the hubei province (where wuhan is located), the cfr was only 0.4% (wu and mcgoogan, 2020) , possibly suggesting change of the epidemic to milder diseases with larger chains of transmission (vetter et al., 2020) . on january 24, two citizens of germany developed symptoms and became 2019-ncov-positive after meeting a chinese business partner, who only became ill on the flight back to china. two further subjects developed symptoms who had contact with one of the infected germans notably before this person developed symptoms. this report suggests that infected persons can infect contact persons during the incubation period (rothe et al, 2020) . wu and leung (2020a) estimated the national and global spread of the novel coronavirus on the basis of the air and train traffic data from and to wuhan, accounting for the strict metropolitan-wide quarantine measure imposed on wuhan on january 24 by using an infection metapopulation model. according to this calculation, sufficient numbers of infected subjects had already been exported to major chinese cities (900 infected subjects to five cities) to start secondary local epidemics. the peak of the wuhan epidemic was predicted for april 2020 and that of local epidemics peaks in other chinese cities would lag by 1-2 weeks. if transmissibility could be reduced by 25% through restrictions of people's mobility, then the magnitude of the epidemic could be reduced by 50% and the peak of the epidemic would be delayed by one month. one major unknown factor of this model is the seasonality of the novel coronavirus infections, respiratory infections being typical winter infections declining with the warming of the seasons. research, available only as preprint (lai et al., 2020) , estimated that more than 800 infected subjects from wuhan travelled to international destinations, with thailand and japan leading the list. public health measures must therefore also be taken in these countries to contain the international spread of the epidemic. the epidemic has also reached europe with an unexplained focus in northern italy. particularly, worrisome will be the spread of infections to african countries where many regions have close economic connections with china, but insufficient hospital and public health resources to assure efficient containment measures (gilbert et al., 2020) . risk of transmission to africa and south america is, however, by some epidemiologists considered to be low (haider et al., 2020) . it is currently unclear whether transmission will be muted in agro-economies with lower population densities. so far, chinese physicians have developed an empirical treatment and triage algorithm based on their experience with patients from wuhan (zhang, et al., 2020b) . this triage scheme proposes a separation of patients into those receiving home treatment and those receiving treatments for regular community acquired pneumonia. suspected viral pneumonia cases are tested for the novel coronavirus under isolated observation; in case of dyspnoea and hypoxia development, supplemental oxygen supply will be given. the viral pneumonia patients were treated with arbidol, approved in russia and china for influenza treatment. when the diagnosis of the novel coronavirus has been confirmed, a patient has been transferred to a specially designated hospital. the efficacy of arbidol against coronavirus is not, however, well substantiated scientifically or clinically. emergency conditions call for a need for speed in drug development. a promising approach is the repurposing of drugs tried against coronaviruses from previous outbreaks with sars or middle east respiratory syndrome (mers) coronavirus (li and de clercq, 2020) . mers, in contrast with sars, is a coronavirus zoonosis of likely bat origin with camels as intermediate hosts that is still circulating. the four non-structural proteins that were preclinically explored as antiviral targets against sars and mers coronaviruses are reasonably well conserved in the novel coronavirus, raising hopes for this approach. however, patient enrolment for a mers treatment trial with lopinavir (an antiretroviral proteinase inhibitor)/ritonavir (cytochrome p450 inhibitor to prolong the half-life of lopinavir) and interferon-b1b (miracle) is still ongoing. numerous clinical trials have been registered in china to test different compounds or combinations of compounds against the new coronavirus infection. test drugs range from antiviral nucleotide analogs over viral protease inhibitors to traditional chinese herbal medicine (e.g. forsythia derivative lian qiao) (maxmen, 2020) . it is important to start the tests now to get the informative patients enrolled and tested before the current epidemic stops. who suggests a shared standard clinical protocol for these trials to make the outcomes comparable. with virus neutralization tests now at hand, chinese researchers have already done in vitro efficacity tests against the novel coronavirus . the most promising effects were observed with the nucleotide analog remdesivir and the anti-malaria compound chloroquine. both showed inhibition of the novel coronavirus in the low micromolar concentration range. remdesivir acts on viral rna transcription at the postviral entry level, while chloroquine needs to be applied at the beginning of the infection; chloroquine's action on lysosome membranes might interfere with the viral entry-fusion events. it is of note that the nucleotide analog remdesivir had a better activity against mers coronavirus than the protease inhibitor lopinavir combined with ritonavir, and this both in cell culture and in mouse infections. in the mouse mers infection model remdesivir improved pulmonary function, reduced lung viral loads and decreased severe lung pathology (sheahan et al., 2020) . in addition, remdesivir given prophylactically to mers virus-challenged rhesus monkeys significantly reduced viral titres in the lung and prevented lung pathology as assessed by histology or by x-ray radiographs when compared to control animals (de wit et al., 2020) . treatment with remdesivir 12 h after viral challenge had a more limited protective effect in rhesus monkeys. in early february, two randomized, placebocontrolled clinical trials testing the therapeutic efficacy of remdesivir were started in china. one trial will enrol 308 patients with mild or moderate novel coronavirus disease (clinicaltrials.gov: nct04252664) and the other 453 patients with severe disease (clinicaltrials.gov: nct04257656). the enrolment is planned to be completed by end of april and may 2020 respectively. the importance of evidence-based treatments proven in controlled clinical trials must be stressed since in the sars epidemic untested drug treatment seems to have done more harm than no treatment (a. danchin, personal communication) . therapeutics directed against immunopathological host responses might have a treatment value in view of the 'cytokine storm' seen in some patients with novel coronavirus infections. vaccines against mers and sars are currently not available. as in the case of the sars epidemic, the current epidemic must be fought with public health measures. as a first measure, the chinese authorities have closed the 'wet' seafood market in wuhan. due to the close contact of live animals with humans, these markets offer ideal conditions for the transmission of zoonotic infections. after two coronavirus infections having emerged from chinese 'wet' food markets, strict hygiene measures are clearly warranted. however, consuming meat and other products of wild animals has a long tradition in china. there is a philosophy of medicine food homology, ('eaten when hungry is food, eaten when ill is medicine') such that in china pangolin products, for example are reputed to help against rheumatism; 'meridian obstruction'; liver disease; and to improve eyesight (li and li, 2020b) . more recently, consumption of meat of wild animals has become a sign of social status. it will not be easy to eradicate these false medical beliefs. interdiction might create black markets; therefore, some scientists recommend strictly controlling, instead of forbidding, this market. protecting the healthcare workers against nosocomial infection is another urgent need, since patient care will already represent a heavy burden to the health system and any reduction in health personnel would cause further problems. face masks are insufficient protection for them; n95 masks, goggles and protective gowns are needed for medical personnel (chang et al., 2020b) . for the general public, frequent hand washing, cough and sneezing etiquette and wearing masks when visiting public places are recommended . however, scientific evidence is lacking for the effectiveness of wearing masks by the uninfected person in contrast to the proven effectiveness of hand washing against respiratory infections. the sars epidemic was contained by means of syndromic surveillance; isolation of patients; and quarantine of contacts. these measures will also play an important role in the current epidemic which, due to its sheer size, will necessitate more draconian measures such as limiting the movement of persons to and from hotspots of infection, resulting in the lockdown of wuhan and of particular small cities in italy and germany. who has declared the novel coronavirus epidemic as a public health emergency. this expanding epidemic will be a stress test for existing health systems, including those of industrialized countries. it should also be a further motivation to strengthen fundamental research in trans-species viral infections and on potential zoonosis impacts, particularly from bats, under changing environmental conditions. from the viewpoint of citizens, when it comes to the protection of lives, one might ask whether one should not put the same spending on public health and preventive research as on the spending on defence budgets. incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan, china protecting health-care workers from subclinical coronavirus infection epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study a new transmission route for the propagation of the sars-cov-2 coronavirus. medrxiv preprint preparedness and 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to progress in patient-level and population-level decision-making. we need to build on prior experience and identify similarities versus differences. in this sense, the pandemic influenza surge in 2009 can be of help. our colleagues in wuhan, who placed their lives at risk by treating patients with covid-19, recently reported their experience in a scenario of crisis management with limited resources [1] . interpretation of these findings in comparison with first reports of pandemic influenza in european icus would help to better confront the current challenge [2] . some intensivists are extrapolating influenza a (h1n1)pdm2009 data and applying it to covid-19, but there is a huge difference between the coronavirus and influenza, with respect to the impact of their viral shedding. in influenza a (h1n1)pdm2009, death was not as frequent in the medical and nursing staff than in patients. in sars and mers this was the case, and it appears that hospital staff are also particularly vulnerable in covid-19 [3] . it is likely that some ''sick'' coronavirus patients shed very large amounts of virus, whereas in influenza that is not necessarily the case. if a healthcare worker is exposed to a large initial inoculum of coronavirus, ards can develop rapidly. to provide useful insight, table 1 compares the wuhan report with our experience with the first icu admissions caused by influenza a (h1n1)pdm2009 [2] . among 37 ventilated patients in the wuhan cohort [1] , only 4 (10.8%) were alive and free of mechanical ventilation 28-days after icu admission. in contrast, a first look suggests that 28-day survival rate in the european influenza cohort was more than doubled. this can be due to the delayed intubation (patients admitted in icu when already under mechanical ventilation or requiring a fraction of inspired oxygen (fio2) 60%) associated with the extreme working conditions and the limited resources in wuhan. indeed, data from a detailed surveillance study from the china cdc indicates that mortality rates in critically ill patients from other chinese provinces were lower than 50% [3] . this analysis reports that overall, 80% of confirmed cases were mild, 15% of severe cases required hospitalisation and 5% were critically ill. however, as many patients can remain asymptomatic or with very low symptomatology and because criteria of hospital admission were not standardised, the proportion of patients requiring supportive techniques for hypoxemia is probably lower. covid-19 is showing respiratory deterioration 7-9 days after onset, which is double the 3-5 days period documented in influenza pandemic, suggesting that it cannot be related to the viral load. this interpretation may justify the high rate of use of steroids in the wuhan report [1] . despite some controversies, steroids, alpha-interferon and macrolides are not beneficial [4] . prior experience with viral pneumonia, including influenza and mers-coronavirus, suggest that steroids can contribute to higher mortality, increase viral replication with longer periods of viral clearance and more superinfections (including invasive pulmonary aspergillosis, as already reported in the wuhan cohort) [5, 6] . another difference is that most covid-19 infected patients were diagnosed with viral pneumonia, whereas acute exacerbations of copd or bronchospasm or myocarditis were more common in influenza. the effect on epidemiology and presentation is unknown due to its coexistence within the epidemic season of influenza. because presentation is overlapping, tests for sars-cov-2 should be conducted in patients with severe pneumonia of unknown aetiology, concomitantly with the search for other respiratory viruses. a common aspect with the influenza virus is the tropism for lower respiratory tract and its impact on the interpretation of diagnostic tests [7] . rt-pcr tests can be affected by sampling errors and viral load, with prior studies in sars demonstrating low sensitivity during the first days after onset. moreover, multiple rt-pcr tests of throat or nasopharyngeal swabs have been reported as false negative when compared with bal tests. its consequent impact on screening of potential organ or tissue donors is the reason why a definition of clinically ''suspected cases'' of acute respiratory disease was introduced for recording cases in hubei, and why chest ct for covid-19 screening is currently conducted in specimen should be obtained (rather than a ct scan) in cases with negative rt-pcr upper respiratory tract swabs. thin-slice chest ct findings have been recommended in hubei, china as a major evidence for clinical diagnosis of covid-19. typical ct findings of covid-19 include peripherally distributed multifocal ground-glass opacities with patchy consolidations and posterior part of lower lobe involvement predilection. serial ct scans have been used to monitor evolution. extent and densities of ground-glass opacities indicate disease progression [8] . it is not clear that it would provide better information than monitoring hypoxemia, as a surrogate of severity. protecting health care workers and preparedness of icus to confront an epidemic cluster should be the main priority, based on experiences learnt from mers-coronavirus and 2003 sars coronavirus [8] . recently, antiseptic hand rubbing using ethanol-based disinfectants was found to be less effective than hand washing in inactivating influenza virus under experimental conditions [9] . for patients with coronavirus suspicion in the icu, airborne plus contact precautions and eye protection should be implemented. during aerosol-generation procedures, wearing a fit-tested n95 mask in addition to gloves, gown and face/eye protection is recommended. open suctioning of the respiratory tract, manual ventilation before intubation, nebuliser treatment, and chest compressions were identified as risk procedures during the sars outbreak [10] . close-circuit suctioning may reduce exposure to aerosols in intubated patients. thus, support with early diagnosis, implementation of effective infection control measures, and limitation of procedures associated with risk of environmental and personal contamination, such as aerosolisation, bronchoscopies or transfers for ct scans should be implemented. ventilator strategies favouring aerosolisation, such as noninvasive mechanical ventilation (niv), which may quite delay but not avoid intubation, should be limited, and hypoxemia rescue therapies such as nitric oxide should be implemented. use of noninvasive ventilation is controversial, showing limited efficacy in mers and is associated with very high levels of aerosol spread, exposing staff at much greater risk of infection [11, 12] . however, niv can avoid the need for ventilation, at least in sars. there is therefore an argument that it may be appropriate only if adequate levels of staff protective equipment are available [13] . in influenza, a small cohort of patients showed that high-flow nasal cannula was associated with avoidance of intubation in 45% of patients, although those with shock or high severity of illness required intubation [14] . thus, efforts should be done not to delay intubation in patients with viral pneumonia and acute respiratory failure. in summary, it is necessary to go beyond china, as some results and practices may not be generalisable elsewhere. a priority should be to protect healthcare workers from exposure. icu doctors should participate in early identification and lead the management of these patients. the authors declare that they have no competing interest. clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a singlecentered, retrospective, observational study intensive care adult patients with severe respiratory failure caused by influenza a (h1n1)v in spain novel coronavirus pneumonia emergency response epidemiology team.. [the epidemiological characteristics of an outbreak of on the use of corticosteroids for 2019-ncov pneumonia corticosteroid therapy in patients with primary viral pneumonia due to pandemic (h1n1) 2009 influenza corticosteroid therapy for critically ill patients with middle east respiratory syndrome strengthening icu health security for a coronavirus epidemic sensitivity of chest ct for covid-19: comparison to rt-pcr situations leading to reduced effectiveness of current hand hygiene against infectious mucus from influenza virus-infected patients critical care management of adults with community-acquired severe respiratory viral infection noninvasive ventilation in critically ill patients with the middle east respiratory syndrome the effects of azithromycin on patients with diffuse panbronchiolitis: a retrospective study of 29 cases should noninvasive ventilation be considered a high-risk procedure during an epidemic? high-flow nasal therapy in adults with severe acute respiratory infection: a cohort study in patients with 2009 influenza a/h1n1 v key: cord-294810-mq9vjnro authors: huang, qiong; deng, xuanyu; li, yongzhong; sun, xuexiong; chen, qiong; xie, mingxuan; liu, shao; qu, hui; liu, shouxian; wang, ling; he, gefei; gong, zhicheng title: clinical characteristics and drug therapies in patients with the common-type coronavirus disease 2019 in hunan, china date: 2020-05-14 journal: int j clin pharm doi: 10.1007/s11096-020-01031-2 sha: doc_id: 294810 cord_uid: mq9vjnro background clinical characteristics of patients with the coronavirus disease 2019 (covid-19) may present differently within and outside the epicenter of wuhan, china. more clinical investigations are needed. objective the study was aimed to describe the clinical characteristics, laboratory parameters, and therapeutic methods of covid-19 patients in hunan, china. setting the first hospital of changsha, first people’s hospital of huaihua, and the central hospital of loudi, hunan province, china. methods this was a retrospective multi-center case-series analysis. patients with confirmed covid-19 diagnosis hospitalized at the study centers from january 17 to february 10, 2020, were included. the following data were obtained from electronic medical records: demographics, medical history, exposure history, underlying comorbidities, symptoms, signs, laboratory findings, computer tomography scans, and treatment measures. main outcome measure epidemiological, clinical, laboratory, and radiological characteristics and treatments. results a total of 54 patients were included (51 had the common-type covid-19, three had the severe-type), the median age was 41, and 52% of them were men. the median time from the first symptoms to hospital admission was seven days. among patients with the common-type covid-19, the median length of stay was nine days, and 21 days among patients with severe covid-19. the most common symptoms at the onset of illness were fever (74.5%), cough (56.9%), and fatigue (43.1%) among patients in the common-type group. fourteen patients (37.8%) had a reduced wbc count, 23 (62.2%) had reduced eosinophil ratio, and 21 (56.76%) had decreased eosinophil count. the most common patterns on chest-computed tomography were ground-glass opacity (52.2%) and patchy bilateral shadowing (73.9%). pharmacotherapy included recombinant human interferon α2b, lopinavir/ritonavir, novaferon, antibiotics, systematic corticosteroids and traditional chinese medicine prescription. the outcome of treatment indicated that in patients with the common-type covid-19, interferon-α2b, but not novaferon, had some benefits, antibiotics treatment was not needed, and corticosteroids should be used cautiously. conclusion as of february 10, 2020, the symptoms of covid-19 patients in hunan province were relatively mild comparing to patients in wuhan, the epicenter. we observed some treatment benefits with interferon-α2b and corticosteroid therapies but not with novaferon and antibiotic treatment in our study population. electronic supplementary material: the online version of this article (10.1007/s11096-020-01031-2) contains supplementary material, which is available to authorized users. severe acute respiratory syndrome coronavirus 2 (sars-cov-2), a novel coronavirus which caused an outbreak of an infectious disease that originated in wuhan, china [1] [2] [3] , is now a world pandemic. the genetic characteristics of this virus proved to be significantly different from human sars-cov and the middle eastern respiratory syndrome (mers) cov [4] . considering the homology of the pathogen, it has been speculated that bats are the primary source of this virus [5] . the recovery rate of sars-cov-2 infection is about 92.7% in china, and the mortality is 5.1% globally [6] . the virus is highly infectious, spreading rapidly in human-tohuman transmission, posing a dangerous threat to global public health [7, 8] . coronavirus disease 2019 refers to the disease caused by the infection of sars-cov-2. the clinical characteristics of this disease were described [9, 10] , but lacked the pathogenesis explanation and pharmacological therapies. the clinical syndrome, such as fever, cough, dyspnea, myalgia, fatigue, and radiographic evidence of pneumonia, were recorded. severe patients developed shock, acute respiratory distress syndrome (ards), acute cardiac injury, acute kidney injury, and even death [10] . according to the clinical manifestations, the confirmed covid-19 patients can be divided into mild, common, severe, and critical type groups based on the china national health commission diagnosis and treatment plan of novel coronavirus pneumonia (trial version 6) [7] . the mild group refers to mild clinical symptoms, and no sign of pneumonia is found in chest computed tomography (ct) imaging. the common type refers to patients with fever, respiratory symptoms, and the sign of pneumonia in ct scanning. severe covid-19 patients present with any of the following: (1) shortness of breath, plus respiratory rate ≥ 30 breaths/min, (2) in resting state, oxygen saturation (spo2) ≤ 93%, and 3) arterial partial pressure of oxygen (pao2)/fraction of inspiration oxygen (fio2) ≤ 300 mmhg. critical covid-19 patients are diagnosed by any of the following: (1) respiratory failure requiring mechanical ventilation, (2) shock, and (3) organ failures requiring intensive care unit admission and treatment. the first confirmed cases in china were concentrated in wuhan, and nearly all associated with huanan seafood market [10] . sars-cov-2 was possibly derived from the animal transmission, then spreading from person to person, and eventually into other communities. the recovery rate in hunan province is about 94.2%. reports have shown that the clinical characteristics of patients are different between those infected in wuhan and those infected outside of wuhan [11, 12] . the clinical investigation of patients, especially outside of wuhan, is warranted. this multi-center study was aimed to describe the clinical characteristics, laboratory parameters, and therapeutic methods of covid-19 patients in hunan, china. this retrospective case series was approved by the institutional ethics board of xiangya hospital of central south university (no. 20200123). our study included patients with covid-19 diagnosed according to the world health organization's interim guidance [6] . patients were admitted to the first hospital of changsha, first people's hospital of huaihua, and the central hospital of loudi, from january 17 to february 10, 2020. epidemiological, clinical, laboratory, and radiological characteristics, as well as treatment and outcome data, were obtained with data collection forms from electronic medical records. data were reviewed by a trained team of physicians. the information recorded included demographic data, medical history, exposure history, underlying comorbidities, symptoms, signs, laboratory findings, ct scans, and treatment measures. only 37 patients with the common-type covid-19 and the three patients with the severe-type had complete laboratory test data. the specific conserved sequences of ncov-open reading frame1ab (orf1ab) and nucleocapsid protein n gene were used as target regions, and the expression of rna in each sample was detected by real-time reverse transcription-polymerase chain reaction assay (rt-rcr). specific steps are as follows. throat swab samples were collected from patients suspected of having sars-cov-2. after collection, samples were placed into a collection tube with 150 µl of virus preservation solution, and total rna was extracted within 2 h using a respiratory sample rna isolation kit. then, a pcr reaction mixture containing 26 µl of pcr action buffer and 4 µl enzyme solution was added to 4 µl of the sample to perform rt-rcr. fam (orf-1ab region) and rox (n gene) channels were selected to detect sars-cov-2, and the hex channel was used for the internal standard. rt-pcr assay was performed under following conditions: incubation at 50 °c for 30 min and 95 °c for 1 min, 45 cycles of denaturation at 95 °c for 15 s, and extending and collecting fluorescence signal at 60 °c for 30 s. a cycle threshold value (ct-value) of 40 or less for fam or rox channel was defined as a positive test result. ct-values more than 40 for fam and rox channels and ct-value of 40 or less for hex channel were defined as a negative test. also, ct-values for fam, rox, and hex more than 40 were defined as an invalid test result. categorical variables were described as frequencies and percentages, and continuous variables were described using the median and interquartile range (iqr). paired student's t test was used to compare the differences in plasma concentrations between admission and discharge groups. normally distributed data were analyzed by a two-sample t-test. means for continuous variables were compared using the mann-whitney test when data were not normally distributed. all statistical analyses were performed using spss version 17.0 software (spss inc). for unadjusted comparisons, a two-sided α < 0.05 was considered statistically significant. a total of 54 patients were analyzed: 51 had the commontype covid-19, and three patients had severe covid-19. in the common type group, the median age was 41 years (iqr 31-51; range 10-76 years), 26 (51.0%) were males ( table 1 ). the age of patients with severe covid-19 also had a wide range; they were 18, 37, and 74 years old, respectively. all patients had no history of exposure to the huanan seafood market. sixteen patients lived in wuhan for more than 6 months, 13 traveled to wuhan recently, 14 patients had close contact with individuals diagnosed with sars-cov-2 infection, one patient was a nurse worked in a hospital, and 10 patients were unable to identify the source of infection. the median time from the first symptom to hospital admission was 7 days (iqr 5-9), and the median length of stay was 9 days (iqr 7-12) among patients with the common-type covid-19. patients with the severe-type took a longer time to be admitted from their first symptom (median, nine days; iqr 7.5-10.5) and had a more extended hospital stay (median, 21 days; iqr 20-24). among the 51 patients with the common-type covid-19, 16 (31.4%) had one or more coexisting medical conditions. the most common comorbidities were hypertension (7 patients), cardiovascular disease (7), chronic liver disease (4), and diabetes (3) . two patients had cerebrovascular disease. two patients had chronic bronchitis. among patients who had the severe-type covid-19, one had hypertension, cardiovascular disease, diabetes, and cerebrovascular disease, one had diabetes, and the other patient had no coexisting condition. the most common symptoms at the onset of illness in the common-type group were fever ( less common symptoms were shortness of breath, pharyngalgia, headache, chest distress, dizziness, and diarrhea ( table 1 ). all patients with the severe-type covid-19 had fever, cough, fatigue, expectoration, and muscle soreness as well as ards. all 54 patients were discharged without death occurrence. the results of blood analysis showed some typical characteristics in patients with virus infection; however, there were limited findings that presented consistently across all patients. all the severe patients showed decreased platelet count and eosinophil ratio. the blood test also showed that in general, patients with severe covid-19 had worse results such as electrolyte and inflammatory biomarker abnormalities than those in patients with the common-type infection. all severe covid-19 patients had increased ca 2+ , ck, ck-mb, ldh, and hs-crp concentrations ( table 2) . more detailed blood test results can be found in figure s1 . among the 51 common-type covid-19 patients who underwent chest ct on admission, 46 (90.2%) had imaging findings of viral pneumonia. the most common patterns were ground-glass opacity (52.2%) and patchy bilateral shadowing (73.9%) ( table 3 ). figure 1 demonstrates the representative radiologic findings of two patients with covid-19. in the early stage, covid-19 pneumonia patients with initial lung findings were small subpleural ground-glass opacities that grew larger with crazy-paving pattern and consolidation. lung involvement increased to consolidation up to 2 weeks after the initial disease onset. in the later stage, the lesions were gradually absorbed, leaving extensive ground-glass opacities and subpleural parenchymal bands. all the severe patients had ground-glass opacity in their ct results. all 54 patients were admitted to isolation wards and received oxygen therapy and ventilatory support. we analyzed 37 patients (common-type) and three severe patients who had complete laboratory tests record. among 37 common type patients, 36 patients (97.3%) received antiviral treatment, 29 patients (78.5%) were given probiotics (lactobacillus bifidus triple live bacteria tablets), 28 patients (75.7%) were treated with traditional chinese medicines (tcms), 22 patients (59.5%) received antibiotics (fluoroquinolone or β-lactams), 11 patients (29.7%) were given systematic corticosteroids, 18 patients (48.6%) were treated with recombinant human interferon α2b injection (ifn-α2b), and 13 patients (35.1%) received recombinant cytokine gene-derived protein injection (novaferon). ifn-α2b (5 million units diluted with 2 ml sterile water) was administered twice a day via inhalation by high-pressure oxygen atomization. the three severe covid-19 patients were treated with antivirals, antibiotics, novaferon, and systematic corticosteroids. all 54 discharged patients were based on a reduction of fever for at least 3 days, with improved evidence on ct and respiratory symptoms. also, nucleic acid tests were negative at a minimum of two times. at the point of discharge, many clinical indicators of covid-19 patients were improved. among them, the ck and hs-crp values were significantly decreased. the number of platelets, eosinophil ratio, lymphocyte, monocyte, neutrophil, eosinophil, and plateletocrit was increased significantly (table 4 ). we analyzed different subgroups of patients with covid-19 based on types of the pharmacotherapies they received. the findings showed that ifn-α2b therapy increased k + (p < 0.01) and ca 2+ (p < 0.05) concentration and decreased total bilirubin value (p < 0.05). the ck value was significantly reduced (p < 0.05) in patients who received corticosteroid therapy. patients who received corticosteroid treatment had increased total bile acid (p < 0.05) and blood urea nitrogen (bun) (p < 0.01). novaferon treatment did not lower ck values (p < 0.05), but decreased bun (p < 0.01) compared to patients who did not receive the therapy. we also found that patients who received antibiotic treatment had decreased creatinine (p < 0.05), platelets (p < 0.05), and plateletocrit (p < 0.05) values, but increased total bilirubin (p < 0.05), indirect bilirubin (p < 0.01) and total bile acid (p < 0.05) concentrations (table 5, figure s2 ). in this study, we reported the clinical characteristics of patients with covid-19 as well as therapies they received during hospitalization in hunan province, china. none of the 54 infected patients had been exposed to the huanan seafood market, suggesting human to human transmission, as previously reported [7, 11] . in this study, 51 out of the 54 patients fell into the common-type group. most of these patients had mild to moderate symptoms. the median age of this group of patients was 41 years, and the median length of hospital stay was 9 days. the common clinical manifestations were fever, cough, and fatigue. a few patients had pharyngeal pain and muscle pain. these cases usually have a long incubation period and may present atypical symptoms as the first symptoms, thus becoming a potential source of infection. ground-glass opacity and patchy bilateral shadowing were hallmarks of ct scans. for the three cases with a severe-type of covid-19, the median age was 37 years, and the median hospitalization was 21 days. the median duration from the first symptoms to hospital admission was 9 days. all of them had fever, cough, fatigue, expectoration, and muscle soreness, as well as adrs. only 37 (common-type) and three severe covid-19 patients had complete laboratory test data. the laboratory test results showed that the patients with the common-type of covid-19 experienced mild illness. for example, only some of these patients had decreased wbc count, decreased platelet count, decreased hematocrit, decreased lymphocyte ratio, decreased eosinophil ratio, decreased lymphocyte, decreased neutrophil, decreased eosinophil and increased basophil values. about 27.0% of these patients had increased ldh, and 70.3% of them had increased hs-crp concentrations. whereas, the patients with the severe-type covid-19 had more severe symptoms such as ards. showing ground glass opacity and crazy-paving pattern and consolidation on day 1 after symptom onset, the lesions were gradually absorbed leaving extensive ground glass opacities and subpleural parenchymal bands in this study, all patients were treated in isolation with a high nasal flow of oxygen. when discharged, many clinical parameters were back to normal, including ck (p < 0.0.000), hs-crp (p < 0.0.01), platelets (p < 0.0.01, eosinophil ratio (p < 0.0.01), lymphocyte (p < 0.0.01) and eosinophil count (p < 0.0.01). we also found that the common-type of covid-19 patients had a better overall recovery, which may be related to their fewer complications. older age patients admitted had a good prognosis, but follow-up attention should be paid to monitor for long-term complications (particularly pulmonary changes, such as pulmonary fibrosis). among patients with common-type covid-19, 97.3% of them received antiviral treatment, lopinavir/ritonavir (lpv/r). lpv/r is a new proteinase inhibitor used in antiretroviral therapy for hiv infected disease [13] . lpv/r was recently used to treat covid-19 infection, however, the study did not show any treatment benefit beyond the standard of care for severe-type adult covid-19 patients [14] . due to lack of control cases, we were not able to analyze the treatment benefit of lpv/r in our study as well. about 49% of the patients were treated with ifn-α2b, which increased patients' serum k + and ca 2+ and decreased the total bilirubin concentrations. it has been reported that ifn-α2b showed a therapeutic effect on sars-cov infection in rhesus macaques [15] and hand, foot, and mouth disease in humans [16] . patients who received systematic corticosteroids showed a significant decrease in ck concentration. elevated ck is present in the serum when there is cell injury, fever, and stress [17] . glucocorticoids also have anti-inflammatory and antiviral effects and can be used for a short time. meanwhile, 35.1% of patients received novaferon, a new type of interferon possessing anti-tumor and antiviral activities [18] . however, there was no treatment effect on patients with covid-19 infection. almost 60% of the patients received antibiotic treatment. no treatment effects were observed, yet adverse effects on liver and kidney function were found, suggesting antibiotics treatment was not recommended among patients with the common-type covid-19 infection. patients with severe covid-19 received antiviral treatment, probiotics, antibiotics, and systematic corticosteroids. antiviral treatment ifn-α2b and corticosteroids to these patients in our study showed a benefit for patients with covid-19. it is worth to point out the role of pharmacists in the care of covid-19 patients. many drugs are used off-label, and pharmacists can assist in evaluating the efficacy and safety of these drugs and to monitor adverse drug reactions. pharmacists should warn physicians about any interactions between tcms and western medicines when these drugs are prescribed [19, 20] . the limitation of our study was the small sample size. therefore, the generalizability of the study findings might be limited. the symptoms of patients in this study are relatively mild compared to the patients initially infected in wuhan. we observed some treatment benefits with ifn-α2b and corticosteroid therapies but not with novaferon and antibiotic treatment in our study population. larger sample size studies are needed to validate these findings in future studies. outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle the continuing 2019-ncov epidemic threat of novel coronaviruses to global health: the latest 2019 novel coronavirus outbreak in wuhan, china the emergence of a novel coronavirus (sars-cov-2), their biology and therapeutic options a novel coronavirus from patients with pneumonia in china a pneumonia outbreak associated with new coronavirus of probable bat origin who. coronavirus disease 2019 (covid-19) situation report-73. 2th clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series xuebijing injection versus placebo for critically ill patients with severe community-acquired pneumonia: a randomized controlled trial clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan clinical features of patients infected with 2019 novel coronavirus in wuhan a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan lopinavir/ritonavir (abt-378/r) a trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 treatment with interferon-alpha2b and ribavirin improves outcome in mers-cov-infected rhesus macaques efficacy and safety of interferon-alpha2b spray in the treatment of hand, foot, and mouth disease: a multicenter, randomized, double-blind trial creatine kinase in cell cycle regulation and cancer novaferon, a novel recombinant protein produced by dna-shuffling of ifnalpha, shows antitumor effect in vitro and in vivo providing pharmacy services during the coronavirus pandemic providing pharmacy services at cabin hospitals at the coronavirus epicenter in china acknowledgements authors would like to thank dr. shusen sun, pharmd, from western new england university college of pharmacy and health sciences, for the review and critique of the manuscript.funding changsha science and technology project (no. 202003). none declared. key: cord-289322-5ciaonf0 authors: chen, x.; zheng, f.; qing, y.; ding, s.; yang, d.; lei, c.; yin, z.; zhou, x.; jiang, d.; zuo, q.; he, j.; lv, j.; chen, p.; chen, y.; peng, h.; li, h.; xie, y.; liu, j.; zhou, z.; luo, h. title: epidemiological and clinical features of 291 cases with coronavirus disease 2019 in areas adjacent to hubei, china: a double-center observational study date: 2020-03-06 journal: nan doi: 10.1101/2020.03.03.20030353 sha: doc_id: 289322 cord_uid: 5ciaonf0 abstract background: the clinical outcomes of covid-19 patients in hubei and other areas are different. we aim to investigate the epidemiological and clinical characteristics of patient with covid-19 in hunan which is adjacent to hubei. methods: in this double-center, observational study, we recruited all consecutive patients with laboratory confirmed covid-19 from january 23 to february 14, 2020 in two designated hospitals in hunan province, china. epidemiological and clinical data from patients' electronic medical records were collected and compared between mild, moderate and severe/critical group in detail. clinical outcomes were followed up to february 20, 2020. findings: 291 patients with covid-19 were categorized into mild group (10.0%), moderate group (72.8%) and severe/critical group (17.2%). the median age of all patients was 46 years (49.8% were male). 86.6% patients had an indirect exposure history. the proportion of patients that had been to wuhan in severe/critical group (48.0% vs 17.2%, p=0.006) and moderate group (43.4% vs 17.2%, p=0.007) were higher than mild group. fever (68.7%), cough (60.5%), and fatigue (31.6%) were common symptoms especially for severe and critical patients. typical lung imaging finding were bilateral and unilateral ground glass opacity or consolidation. leukopenia, lymphopenia and eosinopenia occurred in 36.1%, 22.7% and 50.2% patients respectively. increased fibrinogen was detected in 45 of 58 (77.6%) patients with available results. 29 of 44 (65.9%) or 22 of 40 (55.0%) patients were positive in mycoplasma pneumonia or chlamydia pneumonia antibody test respectively. compared with mild or moderate group, severe/critical group had a relative higher level of neutrophil, neutrophil-to-lymphocyte ratio, h-crp, esr, ck, ck-mb, ldh, d-dimer, and a lower level of lymphocyte, eosinophils, platelet, hdl and sodium (all p<0.01). most patients received antiviral therapy and chinese medicine therapy. as of february 20, 2020, 159 (54.6%) patients were discharged and 2 (0.7%) patients died during hospitalization. the median length of hospital stay in discharged patients was 12 days (iqr: 10-15). interpretation: the epidemiological and clinical characteristics of covid-19 patients in hunan is different from patients in wuhan. the proportion of patients that had been to wuhan in severe/critical group and moderate group were higher than mild group. laboratory and imaging examination can assist in the diagnosis and classification of covid-19 patients. in december 2019, coronavirus disease 2019 (covid-19) broke out in wuhan, china, and quickly spread to other chinese provinces and 38 countries around the world up to february 26, 2020. owing to its involvement in multiple areas, who declared a public health emergency of international concern on january 30, 2020. up to february 26, 2020, there were 78,630 laboratory-confirmed and clinical-confirmed cases in china and over 3,000 cases outside china while about 2/3 of cases in china was located in wuhan. 1 zhang et al reported the largest epidemiological investigation of 72314 cases and showed the crude case fatality rate in hubei province (2.9%) was 7.3 times higher than other provinces (0.4%) in china, 2 which indicated that there are differences in clinical outcome between the patients in hubei and other provinces. the features and outcomes of patients with covid19 in wuhan have been described in detail in several studies. currently, there has been limited studies about patients with covid-19 in zhejiang and beijing, which is far from hubei. 3, 4 however, the clinical characteristics and progression of disease outside hubei, especially in areas near hubei which have a relative higher risk of importing patients than remote areas, were still unknown. hunan is adjacent to hubei province, and the well-developed transportation system between hunan and hubei provided a high possibility for disease transmission in the early stage of covid-19 outbreak when measures like city lockdown and traffic restriction were not taken. therefore, studies in areas near hubei can provide more information about the clinical characteristics of covild-19 and experience of diagnosis and treatment which can be referenced by areas outside wuhan and countries worldwide under the current epidemic of covid-19. in this study, we aimed to investigate the epidemic history and clinical characteristics of patients with covid-19 in hunan, china. from january 23 to february 14, 2020 , all consecutive patients with confirmed covid-19, admitted to the first hospital of changsha and loudi central hospital in hunan, china were recruited. the first hospital of changsha and loudi central hospital are two of the major tertiary hospitals and are responsible for the treatments for patients with covid-19 assigned by the chinese government. diagnostic criteria and clinical classification of all confirmed covid-19 cases were based on guidelines of national health commission. 5 data collection and analysis of cases and close contacts were determined by the national health commission of the people's republic of china (prc) to be part of a continuing public health outbreak investigation and were thus considered exempt from 93% in resting state; (3) arterial oxygen partial pressure/fraction of inspired oxygen ≤300 mmhg; 4. critical type: any one condition of the followings: (1) respiratory failure need mechanical ventilation; (2) shock; (3) other organs failure need intensive care unit (icu) monitoring and treatment. continuous variables were described as medians and interquartile ranges (iqr). categorical variables were summarized as counts and percentages. we categorized those four clinical types to three groups as mild group, moderate group and severe/critical group for further statistical analysis. differences observed among all the three groups were analyzed by chi-squared test or fisher exact test for categorical data, one-way anova or non-parametric kruskal-wallis test for quantitative data, as appropriate. two-tailed p < 0.05 was thought as having significantly difference between three groups. for further pairwise comparisons, the significance level was adjusted using the bonferroni method. all data were analyzed by spss (version 20.0; spss inc., chicago, il, usa). kaplan-meier curve was constructed by the survival and survminer package in r, version 3.6.0 (http://www.r-project.org/). 291 patients with laboratory-confirmed sars-cov-2 infection were included in this study. epidemiological and baseline characteristics of patients in detail were shown in table 1 . for all the 291 patients, the median age was 46.0 years (iqr, 34.0 -59.0 years; range, 1.0 -84.0 years). half patients (156, 53,6%) aged between 15 -49 years, and 11 (3.8%) patients were aged below 15 years. 145 all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is p=0.007) were higher than that of mild group. similar results were found in the history of any kinds of exposure to source of transmission. for coexisting conditions at admission, the proportion of patients with hypertension in the severe/critical group were higher than mild group (30.8% vs 10.3%, p=0.008) and moderate group (30.8% vs 8.0%, p=0.000). the result was also similar for chronic respiratory disease. a higher proportion of patients in severe/critical group had symptoms like fever, dyspnea and fatigue, while other symptoms like nausea or vomiting were more common in mild group. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint all patients received imaging examination including chest radiography or computed tomography (ct) on admission. typical manifestations in ct and chest x-ray plain film on admission were bilateral and unilateral ground glass opacity or consolidation ( figure 1 ). among all patients, 115 patients performed ct within one week after admission, which showed the medium score of lung involvement in both the whole lung field and each separate lung field (upper, middle, lower) in severe/critical group was higher than moderate group (all p < 0.01). laboratory examinations data were given in table 2 . on admission, 36.1% or 22.7% patients showed leukopenia (white blood cell count < 4.00*10 9 /l) or lymphopenia (lymphocyte count < 0.8*10 9 /l) respectively. neutrophils in 54 (18.6%) patients were below the normal range. thrombocytopenia (platelet count <150*10 9 /l) were observed in 31.3% patients. interestingly, 50.2% patients had eosinophils count lower than 0.02*10 9 /l, and the situation was obviously worse in severe/critical group whose medium eosinophils count was 0.00*10 9 /l. compared with mild or moderate group, severe/critical group had a higher level of neutrophil and neutrophil-to-lymphocyte ratio, and a lower level of lymphocytes, eosinophils and platelets (all p<0.01). biochemistry tests showed 83.5% patients had an increased level of d-dimer and the level was higher in severe/critical group than in mild group (0.39 vs 0.20, p=0.000) and moderate group (0.39 vs 0.24, p=0.002). the coagulation function test showed an increase of fibrinogen in 45 of 58 (77.6%) patients with available results. for liver function test, severe/critical group had a higher proportion of elevated aspartate aminotransferase (ast) than mild group (32.0% vs 17.2%, p<0.001). no obvious abnormality of renal function was found in patients without any history of kidney disease. 10.3% patients had hyponatremia and the proportion were higher in severe/critical group than in mild group (22.0% vs 6.9%, p=0.005). moreover, erythrocyte sedimentation rate (esr) and high-sensitivity c-all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is 285 (97.9%) of 291 patients received antiviral therapy (table 3) patients were discharged from hospital when the symptoms relieved, chest imaging improved, fever abated for at least three days, and two samples taken from respiratory tract 1 day apart were negative for sars-cov-2 rna. until february 20, 2020, 159(54.6%) of all patients had been discharged. the length of hospitalization ranged from 5 to 25 days in discharged patients. we used a kaplan-meier plot to analyze the length of hospitalization for all 291 patients (figure 2 ), which shows a median length of 16 days (iqr 14-17). 2 of 291 (0.7%) patients died during hospitalization, both of whom had an exposure history of having been to wuhan within 14 days prior to onset of illness. in this double-center observational study, epidemiology and clinical characteristics of 291 covid-19 all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint patients in hunan province were collected and analyzed. hunan is adjacent to hubei province, and its provincial capital changsha is 294 kilometers away from wuhan, while another city loudi is about 392 kilometers away from wuhan. given the migrant data in previous years and the lockdown of wuhan on janurary 23, 2020, changsha is a city with a high estimated number of imported cases. 8 our study attempted to provide some experience of diagnosis and treatment for the health workers in other areas. to further show the characteristics in patients with different disease severity, we categorized the 291 by several epidemic prediction models seems to be higher than sars. [10] [11] [12] after the fast increase in the number of patients in wuhan during the middle of january, covid-19 spread to the other provinces rapidly such as neighbor province hunan because of the nearby location, developed traffic and large migrant population. 11 in our study, none of 291 patients had a history of direct exposure to huanan seafood market, but most patients (86.6%) had an indirect exposure history within 14 days before symptoms onset, including being to wuhan (41.6%), having contact with people came from wuhan (14.1%) and having contact with local diagnosed patients (38.5%). our study also showed the proportion of patients who had been to wuhan in severe/critical group (48.0%) and moderate group (43.4%) were higher than mild group (17.2%). besides, both the two death cases in our study had a travel history in wuhan while they both used to be in good health. these showed the infectivity and all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint transmission intensity of the virus, especially in the first or second generation of transmission, and may indicate that the virulence of the virus will decrease after limited generations of transmission. 10, 12 therefore doctors in areas outside wuhan should be more cautious in clinical decision making when the patient have a recent history of exposure in wuhan, including wuhan residents and those who recently traveled to wuhan before disease onset. the proportion of family clusters infection in our study was 39.2% which was lower than other studies. 3 besides, none of our patient was medical staff while 1080 medical staff were infected in wuhan until february 11, 2020. 2 for demographic and clinical characteristics, 53.6% patients aged between 15-49 years, followed by the 50-64 years age group (27.5%). in severe/critical group, 32.0% and 40.0% patients aged from 50 to 64 and over 64 respectively, consistent with report of guan et al. 13 female and male patients both accounted for half in all three groups. the median time from disease onset to first admission in our study was 5.0 days. similar to the recent publications, [13] [14] [15] [16] our data also showed that fever, cough and fatigue were the most common symptoms. the severe/critical group patients were more likely to have two or more symptoms at admission. while most symptoms were more frequently seen in severe/critical group, nausea or vomiting were more common in mild group, which may indicate different body responses to sars-cov-2 infection in patients with different health state and immune system defensive characteristics. 58.0% patients in severe/critical group had at least one underlying disease. in concert with the study of guan et al, 13 bases on these findings, we suggest clinicians pay more attention to and closely observe patients with multiple symptoms and underlying diseases to prevent disease deterioration. for laboratory inspection, blood routine test showed 36.1% and 22.7% of patients had leukopenia and lymphopenia respectively. interestingly, eosinopenia was detected in more than 50% patients, all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint especially in the severe/critical group (74%), which was not emphasized in previous studies. 17 this indicate that eosinophils could assist in the diagnosis and severity assessment of covid-19. inconsistent with the other research 10 , elevated d-dimer was observed in majority of patients (83.5%) in our study, and its level was significantly higher in severe/critical group. consistent with the research of guan, 13 myocardial damage and elevated liver enzyme were not common and mainly happened in severe/critical group. besides, obvious disorder of renal function and electrolyte were relatively rare in our patients. 77.6% patients with available coagulation function test result had elevated fibrinogen on admission, and the proportion in severe/critical group was even higher, which have not been observed in other studies. in the early stages of sars patients, researchers also found an increase in fibrinogen. 18 previous studies had shown that sars-cov 3a protein can up regulate the expression of fibrinogen in lung epithelial cells. 19 we speculate in the lung inflammation caused by sars-cov-2 or the secondary systemic inflammation, the activated body stress system may lead to the increase of fibrinogen. another interesting phenomenon was that considerable proportion of patients had positive results in mycoplasma pneumonia or chlamydia pneumonia antibody tests, which indicate mycoplasma pneumonia or chlamydia pneumonia co-infection, which was higher than other research. previous report indicated that mycoplasma fermentans enhanced the cytotoxicity against vero e6 cells infected with sars-cov. 20 this indicate covid-19 patients co-infected with the two types of pathogens may lead to more severe state, thus clinicians need pay attention to the screening of these two pathogens in these patients. compared with the patient confirmed as covid-19 in wuhan 14-16 , our study showed that patients in hunan had relatively higher discharge rate and lower mortality. in our study, 82.8% patients were prone to a mild or moderate type and 54.6% patients were discharged at the end of follow-up. the all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint length of stay in hospital ranged from 5 to 25 days in discharged patients. 2 of 291 (0.7%) patients died during hospitalization. one death case was a 64 years old man in moderate group without any underlying disease. he had a fever for 3 days before admission and was treated by antiviral therapy including lopinavir and ritonavir tablets. the other death case was a 58 years old man in severe/critical group also without any underlying disease, but had symptoms of fever, cough, dyspnea and fatigue for 7 days before admission. laboratory tests detected a decreased level of wbc (2.26*10 9 /l), lymphocyte although there has been a lack of evidence-based specific antiviral drugs, almost all patients in this study received antiviral therapy (96.6%), lopinavir and ritonavir tablets (75.9%), recombinant human interferon α2b (45.4%) were the most commonly used treatment. besides, chloroquine phosphate was reported to have apparent efficacy and acceptable safety against covid-19 in a multicenter clinical trials 21 and had just been included in the latest edition of the guidelines for china. according to this guideline, two patients in the study were given chloroquine for antiviral therapy. however, the safety and efficacy of antiviral therapies used in covid-19 patients need further studied. our study provided more information about epidemiology and clinical profiles of covid-19 in adjacent area around hubei province. it is hoped that our study may provide the basis for the epidemiology related measures of patients in covid-19 import area as well as for clinicians to make medical decisions. there are several limitations in our study. firstly, due to the limitations of the retrospective study, laboratory examinations were performed according tothe clinical care needs of the patient, thus some patients' laboratory exam results were incomlpeted. secondly, given the short observation period, all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint nearly half of our patients were still receiving treatment in hospital at the end of our follow-up and we could not decide the mortality and prognosis of the whole case series. moreover, it is difficult to distinguish the specific efficacy of one single drug as various treatment were applied simultaneously, and the guideline about diagnosis and treatment of covid-19 were updated frequently. therefore, the treatment experience in our study should be carefully thought when treating patients in different places and circumstances, and further researches are needed to verify the the safety and efficacy. in this double-center observational study of 291 hospitalized patients with confirmed covid-19 in hunan, a province adjacent to hubei, 86.6% patients had indirect exposure history. the proportion of patients who had been to wuhan in severe/critical group and moderate group were higher than mild group. clinical characteristics of patients in this study were different from patients in wuhan. the datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. the authors declare that they have no competing interests. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint data collection and analysis of cases and close contacts were determined by the national health commission of the people's republic of china (prc) to be part of a continuing public health outbreak investigation and were thus considered exempt from institutional review board approval. oral consent was obtained from all patients. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.03.20030353 doi: medrxiv preprint the median length of hospitalization for all patients was 16 days (iqr 14-17). all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is values are numbers (percentages) or medium (iqr) unless stated otherwise. percentages do not total up to 100% owing to missing data. national health commission of thepeople's republic of china home page: coronavirus disease 2019 (covid-19) novel coronavirus pneumonia emergency response epidemiology t. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in china characteristics of covid-19 infection in beijing interpretation of guidelines for the diagnosis and treatment of novel coronavirus (2019-ncov) infection by the national health commission (trial version 5) a novel coronavirus from patients with pneumonia in china severe acute respiratory syndrome: temporal lung changes at thin-section ct in 30 patients nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia epidemiological and clinical features of the 2019 novel coronavirus outbreak in china novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions clinical characteristics of coronavirus disease 2019 in china clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical characteristics of 138 hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of 140 patients infected with sars-cov-2 in wuhan changes in coagulation and fibrinolysis of post-sars osteonecrosis in a chinese population the severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells enhancement of cytotoxicity against vero e6 cells persistently infected with sars-cov by mycoplasma fermentans breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid-19 associated pneumonia in clinical studies we thank all the patients for participating in the present study. values are numbers (percentages) or medium (iqr) unless stated otherwise. percentages do not total 100% owing to missing data. key: cord-282058-it0ojdk3 authors: yu, yuanqiang; chen, pingyang title: coronavirus disease 2019 (covid-19) in neonates and children from china: a review date: 2020-05-15 journal: front pediatr doi: 10.3389/fped.2020.00287 sha: doc_id: 282058 cord_uid: it0ojdk3 at the end of 2019, a novel coronavirus began to spread in wuhan, hubei province, china. the confirmed cases increased nationwide rapidly, in part due to the increased population mobility during the chinese lunar new year festival. the world health organization (who) subsequently named the novel coronavirus pneumonia coronavirus disease 2019 (covid-19) and named the virus severe acute respiratory syndrome coronavirus-2 (sars-cov-2). soon, transmission from person to person was confirmed and the virus spread to many other countries. to date, many cases have been reported in the pediatric age group, most of which were from china. the management and treatment strategies have also been improved, which we believe would be helpful to pediatric series in other countries as well. however, the characteristics of neonatal and childhood infection still have not been evaluated in detail. this review summarizes the current understanding of sars-cov-2 infection in neonates and children from january 24 to may 1, as an experience from china. from 2002 to 2003, the outbreak of severe acute respiratory syndrome (sars) in guangzhou, china, caused a global epidemic, which brought widespread concern about a coronavirus epidemic (1) . later, another zoonotic coronavirus pathogen, known as the middle east respiratory syndrome coronavirus (mers-cov), spread in the middle east from 2012, and the disease was named middle east respiratory syndrome (mers) (2) . a new type of coronavirus was recently reported in wuhan, hubei province, china, which also causes severe respiratory disease. the outbreak of the disease began in china, and has brought a heavy burden on the whole world (3) . considering that newborns and children are susceptible to infectious diseases, the prevalence of the disease among them is the subject of much attention. the strategy in dealing with the cases in neonates and children, as well as a healthy pediatric age group, form elaborate plans in fighting against the novel coronavirus disease. such experience from the chinese government and hospitals may also benefit the rest of the world. here, we review the advances of current research from january 24 to may 1 in the epidemiology, clinical manifestations, management, and treatment of this disease in newborns and children. cases and recommendations in the pediatric age group from china, published either in english or chinese, are included. references for this review were identified through searches of pubmed for articles published from january 1, 2003, to may 1, 2020, by use of the terms "coronavirus, " "neonate, " "children, " "covid19, " and "sars-cov-2." relevant articles published between 2003 and 2020 were identified through searches in the authors' personal files. we further searched the recent online articles from the covid-19 academic research communication platform of chinese medical journal network, where the latest relevant chinese articles are published. some news and policies from who are also involved for the latest information of covid-19. articles published in english and chinese were included. articles resulting from these searches and relevant references cited in those articles were reviewed. in late december 2019, wuhan, hubei province, china reported for the first time a large cluster of patients with unexplained pneumonia associated with the wholesale huanan seafood market (4) . subsequently, the chinese center for disease control and prevention (china cdc) sent a rapid response team to identify the source of the pneumonia virus cluster, and then isolated and sequenced a new coronavirus, named 2019 novel coronavirus (2019-ncov) (5) . the world health organization (who) subsequently named the novel coronavirus pneumonia coronavirus disease 2019 (covid-19) and named the virus severe acute respiratory syndrome coronavirus-2 (sars-cov-2). since the virus was transmitted to additional family members by a family (including a 10-year-old asymptomatic child) returning to shenzhen from wuhan, widespread transmission had quickly emerged from person to person (6) . as the chinese lunar new year festival approached, population mobility had increased and the virus had spread rapidly throughout the country (7) . although the incubation period values are very similar to sars or mers, the transmission of covid-19 may be more rapid, because of the possibility of transmission during the incubation period (8, 9) . specifically, some patients may be completely asymptomatic carriers who have passed symptombased screening, but rt-pcr was positive for sars-cov-2 (10, 11) . who then identified the incident as a public health emergency of international concern (pheic) on january 30, and on march 11 assessed that covid-19 could be characterized as a pandemic (12, 13) . among the previously diagnosed family from shenzhen, the 10year-old asymptomatic boy was the first child confirmed infected with the virus (6) later, on january 19, 2020, a 7-year-old boy with a fever and cough was reported in shanghai after visiting his grandfather in wuhan (14) . the symptoms of covid-19 appear to be less severe in infants and children than in adult patients, similar to the sars-cov infection (15) (16) (17) . the first case series report in children showed that the interval between symptom onset and exposure to index symptomatic case ranged from two to 10 days (mean 6.5 days), which suggests a longer incubation period for sars-cov-2 infection in children (18) . furthermore, the mean number of secondary symptomatic cases in a household exposure setting was 2.43, similar to the basic reproductive number in earlier research on adults (18, 19) . most cases in children were likely to expose themselves to family members or other children with covid-19, and linked directly or indirectly to hubei province, indicating that extra protection of children in families is urgently needed, especially those linked to wuhan (16, 20) . a 13-month-old child was reported as the first severe case on february 8 (21) . furthermore, a 17 day-old newborn was reported as the first neonatal infection on february 5, testing positive with sars-cov-2 in pharyngeal swabs and anal swabs (22) . in another case, pharyngeal swab testing was positive 36 h after birth (23) . china cdc reported that, as of february 8, 2020, of 2,135 pediatric patients <18-years old, 728 (34.1%) were laboratory-confirmed with covid-19 and 1,407 were (65.9%) suspected (16) . nearly 1% of the total population of patients reported were children under 10-years old (24) . two deaths were reported in children. one was a 14-year-old boy and the other was a 10-month-old child (16, 25) . seven neonates were reported with a positive nucleic acid test, and three with elevated igm antibodies to sars-cov-2 and negative nucleic acid tests (22, 23, (26) (27) (28) (29) (30) . therein, no death but one severe case was involved (26) . therefore, we call for preventive and protective measures for pregnant women, newborns, and children against the spread of the disease as soon as possible. the rapid and close collaboration between epidemiologists, virologists, biologists, clinicians, and drug researchers during the covid-19 outbreak is commendable. early in the disease outbreak, different models estimated the basic reproduction number r0 of sars-cov-2, calling for public health interventions and preparation plans (31-34). the chinese government had taken emergency measures, such as organizing medical teams to support wuhan, controlling population movements, establishing more hospitals for the treatment of covid-19, and developing specific vaccines (35) . a nationwide school closure had also been ordered, and children were confined in their homes with online courses offered (36) . based on the epidemiological data, different countries have adopted different measures to limit the spread of the novel coronavirus as well, such as issuing travel warnings, interrupting flights, prohibiting nationals from going to severely affected countries, and adopting 14 day quarantine rules for nationals from affected areas (37, 38) . coronaviruses (covs) are pathogens that can infect humans, domestic animals, and much wildlife, and can invade multiple organ systems such as the respiratory, gastrointestinal, liver, and central nervous systems. this subfamily includes four genera: alpha-coronavirus, beta-coronavirus, gamma-coronavirus, and delta-coronavirus (39) . sars-cov-2 is the seventh cov known to infect humans and cause respiratory diseases. it belongs to the clade 2 of the subgenus sarbecovirus, orthocoronavirinae subfamily of beta-coronavirus, and is different from sars-cov and mers-cov (5, 40) . the novel coronavirus was first isolated from human airway epithelial cells and observed under a transmission electron microscope (5) . electron micrographs showed the distinctive spikes(s) (about 9-12 nm) and corona of the virus particles. in ultrathin sections of the human airway epithelium, virus particles were filled in membrane-bound vesicles in the cytoplasm or distributed in the extracellular matrix (5) . researchers had found that the genome had 89% nucleotide homology with bat sarslike covzxc21, and even 96.2% sequence identity with batcov ratg13 (41, 42) . another study also suggests that pangolins may be possible hosts of sars-cov-2 (43) . in addition, the sars-cov-2 genomic sequence is far from sars-cov (about 79%) and mers-cov (about 50%) (40, 41) . the amino acids in different proteins have also been replaced accordingly, which further explains the structural and functional differences between sars-cov-2 and sars-cov (44) . however, sars-cov-2 has a similar receptor-binding domain structure to sars-cov, which is located in the s1 conserved domain and critical for determining host tropism and transmission capabilities (40) . they may use the same cell-targeted receptor angiotensin-converting enzyme 2 (ace2), and cryo-em showed that sars-cov-2 s had 10-to 20-fold higher affinity to bind with ace2 than sars-cov s (41, 45, 46) . further research and understanding of the structure of sars-cov-2 would better facilitate the development of vaccines as well. it has to be mentioned that the specimens from the respiratory and gastrointestinal tracts were detected as sars-cov-2, which indicates the potential multiple ways of sars-cov-2 transmission, including fecal-oral transmission, and the possibility of targeting different organs (47) . cases in adults with active virus replication in the upper respiratory tract display a shed pattern that resembles patients with influenza (48, 49) . furthermore, from biopsy samples taken from the lung, liver, and heart tissues of infected and dead adult patient, similar pathological features to sars and mers coronavirus infections have been found (50, 51) . the lungs showed evidence of acute respiratory distress syndrome (ards), while the liver showed moderate microvascular steatosis and mild lobular and portal activity. the heart tissue was infiltrated with mononuclear inflammatory cells, without substantial damage (50) . a recent study also found highly expressed ace2 in proximal and distal enterocytes (52) . in human small intestinal organoids (hsios), enterocytes were readily infected by sars-cov-2 (53) . these all reflect the complexity of this novel virus, and we still need more data on transmission dynamics and pathology in neonates and children to further explain the virologic characteristics. during the rapid spread of covid-19 in china and other countries, sars-cov-2 infection in pregnant women seems inevitable. however, there are only several reports of infection in pregnant women and of neonates born to infected mothers in china. of the 34 pregnant women who were confirmed with the sars-cov-2 infection in multiple hospitals in wuhan, including one pregnant woman with a negative nucleic acid test result, 30 had a fever and 16 had a cough (54) (55) (56) (57) . other symptoms included diarrhea in eight patients, myalgia in seven, fatigue in six, sore throat in five, shortness of breath in five, chest pain in three, headache in three, and rashes in two (54) (55) (56) (57) . among them, 30 were in their third trimester and the other four were in the second trimester. fetal distress was monitored in eight of the pregnant women. one case had vaginal bleeding during the third trimester, and six had premature rupture of membranes (prom). in addition, one patient had gestational hypertension and another had preeclampsia (55) . other comorbidities included hypothyroidism and polycystic ovary syndrome (57) . all patients had an epidemiological history and had been exposed to covid-19. most patients showed typical features of chest ct images, such as multiple plaque-like ground glass shadows in the lungs, plaque consolidation, and blurred borders (54, 55) . finally, 26 of the pregnant women delivered their babies by cesarean section, and three of them delivered vaginally. one case with a gestational age of 28 weeks had a benign outcome and did not give birth, with conserved treatment to prolong gestation (56) . furthermore, there was one miscarriage at 26 gestational weeks within the onset of bipolar disorder, and the woman required the termination of her pregnancy. it was unknown whether the outbreak of covid-19 influenced her onset of bipolar disorder. noticeably, four of these 34 patients developed severe pneumonia, in which one developed worse and was transferred into icu (55, 56) . the clinical characteristics of covid-19 in pregnant women appear to be similar to those reported in non-pregnant adult patients with covid-19, which could be further confirmed with recent cases outside wuhan (55, (58) (59) (60) (61) . according to the recent report of 118 pregnant women with covid-19 in wuhan, the risk of severe disease compared favorably with the risk in the general population of patients in mainland china (62) . no maternal death has been reported. comparably, the clinical outcome of pregnant women during sars in hong kong was worse than that of infected women who were not pregnant (63) (64) (65) . pregnant women infected with mers-cov might also develop serious diseases, and even the maternal outcome was fatal (66) . considering the relationship between sars-cov-2 and sars-cov or mers-cov, more cases need to be observed, and covid-19 in perinatal pregnant women needs treatment with more caution. of the 30 pregnant women in the third trimester mentioned above, 29 of them gave birth to 30 babies, including one set of twins (54) (55) (56) (57) . of these, 12 were premature infants (gestational age ranging from 31 weeks to 36 weeks plus 3 days), among them three were low-birth-weight infants, and two were smallfor-gestational-age (sga) infants (54) (55) (56) . the 1-and 5-min apgar scores of all live births were 8-10, except for one lga infant who had a 1-min apgar score of 7-and a 5-min apgar score of 8. pharyngeal swab specimens were collected from 22 of the 30 neonates, and only one was positive at 36 h after birth (54) (55) (56) (57) . six of the newborns developed shortness of breath, in which five were premature and intrauterine fetal distress was found in mothers of four neonates, but no severe neonatal asphyxia was observed. other symptoms included vomiting, moaning, edema and skin damage, fever, milk rejection, and gastrointestinal bleeding (54) . the newborn with positive sars-cov-2 had no fever and cough, with only mild shortness of breath (23, 57) . so far, three patients developed disseminated intravascular coagulation (dic) in two case series, possibly because of immature immune function of the neonates and suspected sepsis (26, 54) . one of them eventually died, one improved with antibiotic treatment, and the other also improved after receiving intravenous immunoglobulins (ivig) transfusion (26, 54) . it suggests that gamma-globulin may be effective in severe cases. however, the dose of ivig was not mentioned in the case and needed further exploration (54) . radiographic findings were non-specific. within the 33 neonates born to affected mothers reported recently, chest radiographic images in the three with positive sars-cov-2 showed pneumonia (26) . recently, another case of neonatal death within 2 hours of birth was reported because of severe neonatal asphyxia. the mother developed severe pneumonia and septic shock after admission (60) . therefore, the severity of neonatal symptoms is closely related to the maternal condition (54) . moreover, maternal chronic illness or complications and effective treatment of the newborns may also affect their outcome (58) . however, there is no evidence that the emergence of covid-19 in the third trimester of pregnancy may result in severe adverse outcomes in neonates, which is caused by vertical transmission in the womb (55) . amniotic fluid, umbilical cord blood, neonatal throat swabs, and even breast milk samples were collected and tested, but no sars-cov-2 was found (55) . pathological analysis has also showed no evidence of viral infection or chorioamnionitis in placental tissue (67) . in addition, one study used public single-cell rna sequencing databases to analyze mrna expression profiles and found that the expression of ace2 in different cell types in the early maternal-fetal interface was very low, which may provide an explanation of low risk of vertical transmission in covid-19 and sars (68) . however, at least five neonates born to covid-19 pregnant women tested positive for sars-cov-2 (23, 26, 27) . three infants born to mothers with covid-19 had elevated igm antibodies to sars-cov-2 (29, 30) . they were delivered in negative-pressure isolation rooms, and the mothers wore masks in delivery. these results remind us that more evidence is still needed to evaluate whether vertical transmission could be a possible way of coronavirus transmission (58, 63) . in addition, a neonate was diagnosed as having covid-19 17 days after birth and he had a history of close contact with two confirmed cases (parents of the newborn) (22, 58) . the patient's early clinical symptoms were mild, such as transient fever and diarrhea, without any severe complications. x-ray imaging of the lungs showed inflammatory changes. repeated positive nucleic acid test results of pharyngeal and anal swabs indicated that the virus could appear in the respiratory and digestive tracts of newborns (22) . this case also indicates that there is a possibility that family members or the community may be a source of neonatal infection. another case recently reported was a 19 day-old baby boy, who also showed gastrointestinal symptoms (28) . although the symptoms could be mild, protection of the newborns still needs to be strengthened. they may show different symptoms from adults, therefore, either the parents or the doctors should be more aware of any abnormal conditions when breastfeeding. additionally, no cases of sars-cov-2 infection have been reported in women in the first trimester of pregnancy. given that the fetus of a mother infected with sars-cov in the first trimester of pregnancy would develop intrauterine growth restriction (iugr), more attention should be paid on the prevention of covid-19 in the first trimester of pregnancy (63) . the proportion of infants and children diagnosed with covid-19 is currently small, which may be related to the lack of pathogen detection among them. it may be because they have a lower risk of exposure, or that they either have mild symptoms or are asymptomatic, which is not easily identified, rather than them being less susceptible than adults (16, 25, 69) . the early stages of the covid-19 epidemic mainly involve adults over the age of 15, indicating confirmed childhood cases are more likely transmitted from family members or the community (19) . in addition, the ability of children to transmit the virus may be limited, and no clear report has been found that children can be the source of infection in adults (70) . the most common symptoms of covid-19 in children were a fever and cough. other symptoms included fatigue, myalgia, nausea, vomiting, and diarrhea, which seems to be milder than adults with covid-19 (table 1) (20, 25, 81, 82) . within 2,135 pediatric patients <18-years old who reported with covid-19, groups of all ages were susceptible (16) . the median age of all patients was 7-years, and no statistically significant difference was shown in gender (16) . among both confirmed and suspected cases, 94 (4.4%), 1088 (51.0%), and 826 (38.7%) were diagnosed as asymptomatic, mild, or moderate, respectively (16) . another report in 171 children with sars-cov-2 infection showed the median age was 6.7-years (25) . fever was present in 41.5% of the children at any time of the illness (25) . specifically, symptoms could be mild in infants (28 days to 1-year), with only fever or mild upper respiratory symptoms (15, 71) . however, the proportion of severe and critical cases amongst pediatric groups was highest in infants <1-year old, which reveals that young children, particularly infants, were vulnerable to sars-cov-2 infection (16) . according to the case of a 55 day-old female infant, multiple organ damage affecting the lungs, liver, and heart may be present (72) . both the nasopharyngeal swab and stool specimen tested positive for sars-cov-2. the symptoms were initially mild but progressed rapidly later. therefore, frequent and careful monitoring, as well as timely and appropriate treatment, are important in infant cases (72) . similarly, children with sars-cov-2 infection may also have severe symptoms. the first severe case of childhood infection was reported on january 27, 2020, in wuhan (21). he was a 13-month-old child, with frequent vomiting and diarrhea at first, which rapidly progressed to other acute symptoms including shortness of breath and oliguria 6 days later, which turned to ards, septic shock, and acute renal failure at last. he had no comorbidities. nucleic acid tests were not positive until it was performed for the third time. given that his immune system may be overreacted, and it was necessary to maintain acid-base balance and improve organ function in the critically ill patient, continuous renal replacement therapy (crrt) was used and finally improved his symptoms. in severe or critically ill pediatric patients, the most common symptom is shortness of breath, and invasive mechanical ventilation may be indicated for effective respiratory support (73) . children with cancer could also be exposed to sars-cov-2 infection. an 8-year-old boy with acute lymphoblastic leukemia was confirmed with covid-19 recently (73) . the symptoms included pancytopenia and fever. the conditions turned critical regardless of assisted ventilation. therefore, development of standardized guidance for prevention in children with cancer and collaboration among the pediatric oncology community are urgently required (83) . in addition, another situation also needs to be paid attention to. this was a case of a child diagnosed with covid-19 with acute appendicitis (75) . he was initially prepared for abdominal surgery for "acute appendicitis, " but he developed a fever before the operation. his mother told the doctor that he had dinner with his grandmother before, who was earlier confirmed to be sars-cov-2 positive. therefore, it has to be considered that children and infants may not cooperate with the examination, and the description may be unclear. respiratory symptoms and physical signs are not obvious among them as well. when the emergence of surgical related symptoms happens, such as acute abdominal pain as the first manifestation, the possibility of sars-cov-2 infection needs to be discussed, and more concern is also needed on the reasonable arrangements for surgical operations during the epidemic. in addition to atypical clinical symptoms, early radiographic findings of children with pulmonary infections were also milder than those of adults, and most were nodular ground-glass changes or unilateral patchy lesions (18, 25, 76, 84) . the ct characteristics were atypical, with a more localized ground glass opacity (ggo) extent, lower ggo attenuation, and relatively rare interlobular septal thickening (85) . furthermore, the ct imaging of severe cases of covid-19 may be similar to the findings of adults, such as pulmonary parenchymal groundglass lesions and consolidative pulmonary opacities in the lung (21, 86, 87) . on the other hand, laboratory tests of the 13-month-old severe case mentioned above showed similar characteristics to adult cases. in the acute phase of the disease, c-reactive protein was significantly increased, cd3 + t cells and natural killer cells were significantly reduced, and c3 and c4 levels were also significantly reduced (21) . the child's t cell activation was inhibited, but the body's immune system can be over-activated, indicating the complex role of the immune system in the progression of covid-19. other abnormal laboratory findings in common and severe cases are elevated creatine kinase mb, decreased lymphocytes, and elevated procalcitonin and alanine aminotransferase, which indicates possible damage of multiple organs (20, 88) . noticeably, the older children may have significantly decreased lymphocytes, elevated procalcitonin, and decreased creatine kinase compared with the younger patients, such as children under 5-years old (20) . the reliability of real-time reverse transcription pcr (rt-pcr) for the detection of sars-cov-2 has been demonstrated, particularly in collected patient saliva or pharyngeal swabs (89, 90) . recommendations from china for the diagnosis of covid-19 also suggest the use of real-time fluorescent rt-pcr to detect sars-cov-2 nucleic acid (80, (91) (92) (93) . it is important especially in children with atypical symptoms (6) . another method suggested is metagenomic next-generation sequencing (mngs) of rna extracted from bronchoalveolar lavage fluid (balf) or other specimens (80, 94) . however, it has to be mentioned that the first two pharyngeal swab nucleic acid tests of the severe 13-month-old child abovementioned were negative, and they were not positive until the third nucleic acid test on the 13th day of onset (21) . the delay in diagnosis and treatment of children may be fatal, since there have been two deaths in children (16, 25) . therefore, other samples should be actively explored and evaluated for the diagnostic value of sars-cov-2 infection in children as in recommendations, such as the upper or lower respiratory tract, blood, stool, and urine, in order to increase the positive rate of nucleic acid detection (80, 92, 93, 95) . given that neonates seem to manifest gastrointestinal symptoms more commonly, persistent anal swab tests might be more useful (22, 28, 52) . however, there are still some atypical cases with epidemiological history, respiratory or gastrointestinal symptoms, and positive chest ct manifestations that may have negative rt-pcr results for sars-cov-2 in adults (96) (97) (98) . in the diagnosis of patients with suspected covid-19, the positive rate of chest ct imaging may be even higher than that of rt-pcr analysis. the patients may first show a positive chest ct, and the improvement of the chest ct can be reflected earlier in recovery, indicating its better sensitivity in diagnosis of covid-19 (99) . given that chest radiographic images could also reflect abnormalities in most cases of neonates and children, the combination of imaging and nucleic acid tests may be a better method for comprehensive evaluation of pediatric patients with covid-19 (25, 26) . additionally, chest x-rays and cts should be performed with more caution in pediatric patients for protection to this vulnerable population from the risk of radiation (85) . moreover, application of pulmonary ultrasounds in neonates may show pulmonary abnormalities of covid-19 with better sensitivity and safety than chest x-rays and cts, which provides more chances in monitoring and evaluation of the disease (100). in addition, specific antibody tests are available for retrospective diagnostic and epidemiological studies, which have already been used as one of the methods for diagnosis of covid-19 according to the latest version of new coronavirus pneumonia prevention and control protocol from national health commission of the people's republic of china (china nhc) (80) . igm antibodies to sars-cov-2 in neonates may also have indication in vertical transmission (29, 30) . recently, a new platform called cas13-assisted viral expression and read restriction (carver) was developed for rapid diagnosis of ssrna viruses. it mainly uses cas13 to detect and destroy viral rna (101). the crispr system seems to illustrate the unique and comprehensive prospect of virus infection diagnosis and treatment in future (101, 102) . finally, the additive effect of seasonal influenza on the covid-19 epidemic may interfere with doctors' clinical decisions, so more tests should be considered to distinguish covid-19 from other acute respiratory infections with similar symptoms in order to strengthen management of covid-19 (77) . in the prevention and management of covid-19, pregnant women, neonates, and children should be considered as the main high-risk population (58) . china nhc has provided prevention and control protocols for covid-19 and updated these during the epidemic. the latest 7th version provided on march 3 covered all populations in china (80) . furthermore, specific recommendations for neonates and children were also provided as national consensus guidelines (91) (92) (93) . the guidelines define the suspected and confirmed cases in different populations, as well as the criteria for discharge (80, 92, 93) . figure 1 is extracted from these guidelines as a concise protocol for management in pregnant women, neonates, and children. according to the management plan in pregnant women and neonates, newborns of mothers suspected or diagnosed with sars-cov-2 infection in delivery should be well-rescued and cared for via the cooperation of the department of obstetrics and neonatology (92) . all neonates with suspected or laboratory-confirmed covid-19 should be admitted to neonatal intensive care units (nicus) (91, 92) . high-risk neonates should be placed in a designated room for medical observation for at least 14 days (91) . if a pregnant woman or newborn is diagnosed or suspected of infection, breastfeeding should be avoided (91) . recently, a global guideline for pregnant women with suspected sars-cov-2 infection has also been provided (103) . moreover, recent research found that there may be potential risks of sars-cov-2 transmission in hospital settings, hence pediatricians and neonatologists should be more careful in treating the patients in nicus and pediatric intensive care units (picus) (104, 105) . home confinement and online courses may have a psychological impact on children and adolescents, emphasizing the importance of the awareness and guidelines provided for students from the government (36, 106) . finally, it must be noted that rt-pcr-positive results may still be found in pediatric patients recovered from covid-19 (47, 71) . in infants and young children, negative pharyngeal swab results may have already been detected, but viral nucleic acid can still be detected in fecal specimens (78) . a contingency plan for nicus recently suggested sars-cov-2 negative results of respiratory specimens or anal swabs should be obtained at least 48 h before discharge (91) . further isolation and long-term follow-up of discharged children with positive results of anal swabs should be considered for their potential transmission in public health (107) . the treatment of neonates and children is similar to that of adults, but it also has its own characteristics. to date, there are no specific drugs that can cure covid-19, and vaccines are still being studied. the purpose of treatment is to improve the patient's symptoms and provide better support. the most effective treatment is oxygen therapy, which is important in treating symptomatic newborns and critically ill children. it is closely related to the children's final outcome, and early treatment can reduce complications, such as ards or respiratory failure (108) . in adult covid-19 cases, severe ards is always associated with high mortality (109) . therefore, timely ventilation might be vital in preventing ards or respiratory failure in pediatric covid-19 cases. secondly, the effect of antiviral treatment in covid-19 is still uncertain. the first reported case in the united states benefited from an investigational antiviral drug called remdesivir, which has also proved to have a clinical benefit in the rhesus macaque model of mers-cov infection (110, 111) . lopinavir-ritonavir treatment reported no benefit in adult severe cases (112) . in 36 pediatric cases, mild cases received interferon alfa by aerosolization twice a day, while most moderate cases were given interferon alfa with lopinavir/ritonavir syrup twice a day (20) . however, no specific improvement of such antiviral treatment has been analyzed in pediatric cases, and it would be helpful to provide more clinical trials in the future. in addition, the use of corticosteroids remains controversial. who's current interim guidelines recommended against the use of corticosteroids unless indicated for another reason (113) . different studies have shown that it could be either beneficial or unfavorable for patients with coronavirus infection (such as sars and mers) (114, 115) . recently, expert consensus in china has advised against the use of corticosteroids in children under 18-years-old (116) . moreover, traditional chinese medicine may have a therapeutic effect on covid-19, but it is not fully recommended for children as well, because childhood toxicity is uncertain (117, 118) . intravenous immunoglobulin (ivig) is used to rescue newborns and critically ill children and may improve the disease (21, 54) . finally, recent studies on the structure of sars-cov-2 spike glycoprotein and cell entry have provided possible solutions for vaccine design and the application of protease inhibitors (119, 120) . the blocking effect of crossneutralizing antibodies may also indicate the feasibility of developing convalescent plasma therapy from healthy donors as a clinical trial in china, which has already been used in severe and critically ill pediatric and adult cases (77, (119) (120) (121) (122) . neonates with epidemiology history such as being born to sars-cov-2 infected mothers within 14 days before and 28 days after delivery, or direct exposure to family members, caregivers, medical staff, or visitors with covid-19 should be suspected with infection, whether with or without symptoms. suspected cases with both negative nucleic acid tests at least 24 h interval and negative igm and igg to sars-cov-2 within 7 days will be suspended quarantine. the management plan in perinatal pregnant women, neonates, and children from the community is from the latest new coronavirus pneumonia prevention and control protocol from china nhc (80) . the management plan in neonates born to the mothers is from the national guideline of perinatal and neonatal management plan of sars-cov-2 infection (92). in elderly patients with covid-19 (>65-years), especially those with comorbidities, clinical outcomes are usually poor (123) . however, to date, only two neonates born to mother with covid-19 and two children with covid-19 have been reported to have died in china, and most newborns and children have eventually recovered. some patients were still isolated in hospital for further observation (81) . further analysis is needed to better understand the prognosis of covid-19 in neonates and children. neonates born to mothers with covid-19 in the first and second trimester need close monitoring and further assessment. in addition, follow-up studies have shown that some children with sars had deficiencies in lung function assessment and decreased exercise capacity (124) . therefore, we call for long-term follow-up and comprehensive assessment of infected newborns and children after discharge to determine the prognosis of covid-19. since 2003, the chinese government has gained many lessons from the sars outbreak. in the covid-19 epidemic, besides china, the global response has been more timely, including coordination among different countries, sharing of disease information and cases, government and media reports, and public response (24, 125) . the chinese government has taken effective measures to control the epidemic. the experts also made recommendations for high-risk groups including pregnant women, newborns, and children. in addition, compared to adults, children have milder conditions, a faster recovery, and a better prognosis (126) . a series of improvements to date have been applied to prevent the prevalence of covid-19 in the global community. however, given that the symptoms of covid-19 in neonates and children are atypical, and transmission within family members is quite common, more effort should be made to protect this high-risk population. although there is still no direct evidence of vertical transmission, the rescue of newborns of infected pregnant women in delivery should not be delayed. furthermore, development of vaccines and effective treatments like novel antiviral drugs is also urgent and necessary. current outbreak will be restricted only if the whole world stands together and cooperates constantly. yy and pc contributed to the conception of the review. yy 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severe acute respiratory syndrome (sars) in neonates and children sars to novel coronavirusold lessons and new lessons clinical and transmission dynamics characteristics of 406 children with coronavirus disease 2019 in china: a review the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright â© 2020 yu and chen. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord-285153-schpgyo0 authors: lin, chen; chen, zixian; xie, bin; sun, zhujian; ding, yuxiao; li, xiaogang; niu, meng; guo, shunlin; lei, junqiang title: covid-19 pneumonia patient without clear epidemiological history outside wuhan: an analysis of the radiographic and clinical features date: 2020-04-24 journal: clin imaging doi: 10.1016/j.clinimag.2020.04.023 sha: doc_id: 285153 cord_uid: schpgyo0 the purpose of this case report is to describe the ct and clinical features of a covid-19 pneumonia patient without clear epidemiological history outside wuhan, china. in december 2019, unexplained pneumonia was found in wuhan, china, and the disease spread rapidly around the country. the virus responsible for this disease [1] has been identified as a novel coronavirus, named by the international committee on taxonomy of viruses (ictv) on february 11, 2020, as the severe acute respiratory syndrome coronavirus 2 (sars-cov-2). as of march 9, 2020, there were 80,906 laboratory-confirmed cases in china, more than 10,000 of which are from outside of hubei. almost all confirmed cases had a clear epidemiological history. the purpose of this case report is to describe the radiographic and clinical features of a covid-19 pneumonia patient without clear epidemiological history outside wuhan, china. a 66-year-old woman was transferred to our hospital in lanzhou, china (1,005 miles from wuhan), for high resolution computed tomography (hrct). the image showed ground glass opacities (ggos) in both lungs. the patient's novel coronavirus nucleic acid test returned positive on january 30, 2020. the j o u r n a l p r e -p r o o f hydrochloride and sodium chloride injection) and gastric mucosa protectants (omeprazol). after 7 days of treatment (february 6, 2020), the patient's hrct showed that her bilateral pulmonary lesions had improved and a little fibrous stripe was evident ( figures 1e and 1f ). her novel coronavirus nucleic acid tests demonstrated 2 consecutive negative results (february 7, 2020 and february 9, 2020). medications were stopped and the patient was discharged on february 10, 2020. she was subsequently isolated at home for 14 days. hrct images obtained after discharge (february 18, 2020) showed that lesion absorption was more obvious (figures 1g and 1h ). the aim of this case report was to describe the radiographic and clinical the patient described in this case report had no clear epidemiological history and has likely been exposed to the virus without her knowledge, hence she can be referred to as " second-generation patients". the patient had similar radiographic and clinical findings to previously reported cases in the literature, but there were some differences. current research demonstrated that the most common hrct features of covid-19 pneumonia are patchy/punctate ground glass opacities (85.7%), patchy j o u r n a l p r e -p r o o f consolidation (19.0%) that are mainly distributed in a sub-pleural area, and the presence of fibrous stripes after the patient's condition improves [2] . the hrct images of this patient demonstrated almost all of these features. a recent retrospective study found that radiographic findings from chest ct were most severe on day 10 of initial symptom onset and began to improve on day 14 of initial symptom onset [3] . the findings from this patient's chest ct were typical of those with covid-19. for this patient, recovery was earlier than usual. in contrast, most patients with covid-19 present with fever (98%), cough (76%), and myalgia or fatigue (44%). fever is the most common feature [4] . the patient described in this case report had no fever onset, which has not been reported previously in patients with respiratory symptoms and ct abnormalities. in conclusion, this case report aimed to communicate and educate radiologists and clinicians in the recognition of this new disease. clinicians need to be vigilant; even patients with respiratory symptoms, without a history of exposure or fever, should be examined radiographically using hrct. moreover, timely nucleic acid testing should be performed when radiographic findings present similarly to those of patients with covid-19. the 2019-new coronavirus epidemic: evidence for virus evolution clinical features of patients infected with key: cord-286854-0s7oq0uv authors: jin, xi; xu, kangli; jiang, penglei; lian, jiangshan; hao, shaorui; yao, hangping; jia, hongyu; zhang, yimin; zheng, lin; zheng, nuoheng; chen, dong; yao, jinmei; hu, jianhua; gao, jianguo; wen, liang; shen, jian; ren, yue; yu, guodong; wang, xiaoyan; lu, yingfeng; yu, xiaopeng; yu, liang; xiang, dairong; wu, nanping; lu, xiangyun; cheng, linfang; liu, fumin; wu, haibo; jin, changzhong; yang, xiaofeng; qian, pengxu; qiu, yunqing; sheng, jifang; liang, tingbo; li, lanjuan; yang, yida title: virus strain from a mild covid-19 patient in hangzhou represents a new trend in sars-cov-2 evolution potentially related to furin cleavage site date: 2020-07-03 journal: emerging microbes & infections doi: 10.1080/22221751.2020.1781551 sha: doc_id: 286854 cord_uid: 0s7oq0uv the mutations in the sars-cov-2 virus genome during covid-19 dissemination are unclear. in 788 covid-19 patients from zhejiang province, we observed decreased rate of severe/critical cases compared with patients in wuhan. for mechanisms exploration, we isolated one strain of sars-cov-2 (zj01) from a mild covid-19 patient. thirty-five specific gene mutations were identified. phylogenetic and relative synonymous codon usage analysis suggested that zj01 may be a potential evolutionary branch of sars-cov-2. we classified 54 global virus strains based on the base (c or t) at positions 8824 and 28247 while zj01 has t at both sites. the prediction of the furin cleavage site (fcs) and sequence alignment indicated that the fcs may be an important site of coronavirus evolution. zj01 mutations identified near the fcs (f1-2) caused changes in the structure and electrostatic distribution of the s surface protein, further affecting the binding capacity of furin. single-cell sequencing and ace2-furin co-expression results confirmed that the furin expression was especially higher in glands, liver, kidneys, and colon. the evolutionary pattern of sars-cov-2 towards fcs formation may result in its clinical symptom becoming closer to hku-1 and oc43 caused mild flu-like symptoms, further showing its potential in differentiating into mild covid-19 subtypes. the outbreak of a novel coronavirus (sars-cov-2) and the associated disease (covid-19) began in wuhan, china, near the end of 2019. the disease quickly affected the whole country. covid-19 continues to pose a severe threat to public health and economic prosperity in china [1, 2] . through a quick response and drastic measures that included quarantining wuhan city beginning on 23 january 2020, the spread of sars-cov-2 in china was effectively controlled. however, its ensuing sporadic global appearance [3, 4] and rapid dissemination in japan, south korea, iran, and italy resulted in the pandemic spread of sars-cov-2 [5] [6] [7] . therefore, it is important to determine the clinical and virologic characteristics of sars-cov-2 during its dissemination. an important and common feature of viruses, including sars-cov-2, is that their increased transmissibility is usually accompanied by decreased virulence, which is reflected in the disease trajectory. covid-19 was more severe in wuhan soon after its appearance, with severe/critical and fatality rates of approximately 32% and 11%, respectively [8, 9] . subsequent data as the disease spread revealed a milder form of covid-19 in zhejiang province [10] and nationwide [11] . on the other hand, the transmissibility increased from a basic reproductive number (r0) of 2.2 [12] and 2.68 [6] in wuhan to 3.77 [13] at the national level. furthermore, the observation of a similar viral load in symptomatic and asymptomatic covid-19 patients revealed the capacity of sars-cov-2 for occult transmission [14] . changes in the epidemiological and clinical features of covid-19 relate to the virologic changes of sars-cov-2, in which the spike (s) surface envelope protein plays an important role [15] . generally, its surface unit (s1) is responsible for host entry by binding to the cell receptor, while its transmembrane unit (s2) drives the fusion of viral and cellular membranes [16] . therefore, it is valuable to focus on the sequence mutation and conformation change in s protein for sars-cov-2 evolution in an established model with the aim of explaining the related changes in covid19. in this study, we identified a severe/critical rate of 9.9% in 788 confirmed covid-19 patients in zhejiang province, and a median of 11 days of positive nuclear acid in 104 patients from our hospital, indicating the tendency of covid-19 progression towards a milder but more infective disease. based on these clinical findings, we performed in-depth bioinformatics analysis by comparing the virologic features of 52 previously reported strains of sars-cov-2, including bat cov, sars-cov and sars-cov-2 in wuhan and zj01. the latter was an isolate we described from a patient with mild covid-19 in zhejiang province. the evidence of continuous evolution of potential furin cleavage sites (fcss) on the s protein of sars-cov-2 suggests that furin may play an important role in viral evolution. the establishment of a novel sars-cov-2 categorization system may facilitate our understanding of virus evolution and its influence on the severity and progression of covid-19. this retrospective study investigating the epidemiological, clinical and virologic features of covid-19 was performed at designated hospitals in zhejiang province between 17 january and 7 february 2020. we subsequently calculated the time period of positive covid-19 nucleic acid in our hospital. all patients were diagnosed with covid-19 according to the world health organization interim guidance [17] and the preliminary data were promptly reported to the authority of zhejiang province. the study was approved by the clinical research ethics committee of the first affiliated hospital, college of medicine, zhejiang university (approval no. iit20200005c). written informed consent was waived by the ethics committee of the participating hospitals, as the study involving an emerging infectious disease and was part of a continuing nationally authorized public health outbreak investigation. the subtypes of covid-19 were categorized as mild, severe and critical, as recently described [11] . the period of positive nucleic acid is defined as the date of confirmed nucleic acid positivity minus the date of confirmed nucleic acid negativity. sars-cov-2 was confirmed from samples of throat swabs and sputum in our hospital and the center for disease control and prevention (cdc) facility in zhejiang province using real-time rt-pcr targeting typical nucleic acids using a previously acknowledged protocol (bio-germ, shanghai, china) [8] . all patients underwent chest radiography or computed tomography (ct) scan on admission. other respiratory viruses including influenza a (h1n1, h3n2, and h7n9), influenza b, respiratory syncytial virus, sars-cov, and middle east respiratory syndrome (mers)-cov were excluded. epidemiological, anthropometric, clinical, and laboratory data were collected on admission, with specific attention paid to the period between symptom onset and outpatient visit/pcr confirmation/hospital admission. one strain of sars-cov-2 was successfully isolated from a single sputum sample of a patient with a mild covid-19 case at the time of admission in our hospital. the sample was sent to the beijing genomics institute (bgi) company for whole genome sequencing using a previously reported method [18] . briefly, 200 μl of the virion suspension was frozen and thawed three times. a 140 μl aliquot of the final supernatant was used for rna extraction using the qiaamp viral rna mini kit (52904; qiagen, hilden, germany) according to the manufacturer's recommendations. the qualified double-stranded dna library was sequenced with pe150 using the novaseq 6000 platform (illumina, san diego, ca, usa). currently, available coronavirus sequences (n = 85) were obtained from the ncbi viral genome database (https://www.ncbi.nlm.nih.gov/, n = 65), genome warehouse (https://bigd.big.ac.cn/gwh/, n = 12), cngbdb (https://db.cngb.org/, n = 3), and nmdc (http://nmdc.cn/#/coronavirus, n = 6). the sequence of zj01 (batacov/zheji ang/zj01/2019) was previously reported by us. the 52 sars-cov-2 sequences were collected from china (n = 30), japan (n = 5), nepal (n = 1), south korea (n = 1), australia (n =1), finland (n = 1), and the united states (n = 13) between 26 december 2019, and 5 february 2020. the furin protein sequence was downloaded from the ncbi database. multiple sequence alignment of all coronavirus genomes was performed using mega v7.0.26. phylogenetic analysis was performed on a total of 80 coronavirus strains, covering six species (human, bat, mink, camel, rat, and pig). sars-cov-2 was acquired from 17 cities in seven countries from 23 december 2019 to 5 february 2020, which overlapped with the time period from virus outbreak to dissemination. the evolutionary history was constructed based on the coronavirus s protein by the neighbour-joining method. the bootstrap consensus tree inferred from 2000 replicates was used to represent the evolutionary history of the taxa analysed. branches corresponding to partitions reproduced in <30% bootstrap replicates were collapsed. the evolutionary distances were computed using the kimura 2-parameter method and expressed as the number of base substitutions per site. evolutionary analyses were conducted in mega7 v7.0.26. relative synonymous codon usage (rscu) analysis was performed to compare the differences between 49 strains of sars-cov-2 and homo. a heat map was drawn using mev 4.9.0 software. all available coding sequences (minimum >28 kbp) were calculated with codon w1.4.2.16, followed by inter-relationship calculation based on the euclidean distance method. simplot v.3.5.1.15 was used to analyse the potential genetic recombination. visualization of the mutation site between ratg13 and zj01 was performed using multalin software (http://multalin.toulouse.inra.fr/ multalin/multalin.html). multiple sequence alignment was applied using the muscle (codons) function of meag v7.0.26. genetic mutation sites were analysed using dnaman v9.0.1.116. the functional domain distribution of sars-cov-2 and s proteins was plotted using ibs v1.0.3. fcs prediction was carried out in prop 1.0 server (http://www.cbs.dtu.dk/services/ prop/) [19] and is presented as furin score (range 0-1). a score closer to 1 indicates a higher possibility of the existence of an fcs. target protein was downloaded from ncbi (https:// www.ncbi.nlm.nih.gov/ protein/1791269092) and the corresponding homology models were predicted by swwiss-model (https://swwassmodel.expasy.org/). protein sequence alignment and apbs analysis were performed using pymol v2.3.3 on an intel i7 9700f processor. apbs was calculated and evaluated using pymol v2.3.3, as previously reported [20] . the raw counts or processed data were downloaded from the tissue stability cell atlas (https://www. tissuestabilitycellatlas.org/) and gene expression omnibus (https://www.ncbi.nlm.nih.gov/). lung, colon and liver data were obtained from the tissue stability cell atlas [21] , gse116222 [22] , and hca [23] , including samples of lung (n = 5), colonic epithelium (n = 3) and hepatic tissues (n = 5) from healthy volunteers and organ donors. lung and liver data were processed before downloading and were directly used for data analysis and visualization. for liver data, cells with <100 expressed genes and 1500 unique molecular identifier counts and >50% mitochondrial genome transcripts were removed. genes expressed in fewer than three cells were also removed. normalization and principal component analysis (pca) were performed using the r package seurat [24] , with different dataset-based data processing methods. for the liver, the first 40 principal components resulting in the pca were used to perform cell clustering and nonlinear dimensionality reduction (uniform manifold approximation and projection, umap). for the colon, the r package harmony [25] was used to remove batch effects with default settings. we used the first 40 components to perform cell clustering and nonlinear dimensionality reduction, similar to liver data. depending on the expression level of cell markers provided in the original article corresponding to the single-cell rna (scrna)-seq datasets, we further estimated which cell types the cell clusters belonged to. annotated clusters were then visualized using umap plots with the "dimplot" function in seurat. normalized gene expression levels were presented in the umap and violin plots using the r package ggplot2 [26] . as shown in table 1 , 51.65% of the 788 enrolled patients were males. the rate of smoking was low (6.85%). the three predominant co-existing conditions were hypertension (15.99%), diabetes (7.23%) and chronic liver disease (3.93%). the median period from illness onset to outpatient visit, pcr confirmation and hospital admission were 2, 4 and 3 days, respectively. the most common symptoms were fever (80.71%) and cough (64.21%). ct/x-ray evidence of disease was greatest for bilateral pneumonia (37.56%). the rates of mild, severe and critical types of covid-19 were 90.1%, 7.74% and 2.16%, respectively. the zj01 patient was male and 30 years of age, with no histories of smoking or any co-existing condition. he visited outpatient clinics one day after symptom onset and was admitted to the hospital with covid-19 on the same day following the pcr result. he had not been to wuhan, and none of his family members have been virus positive at the time of writing. consistent with other covid-19 patients, his symptoms included fever, cough and sputum production, with bilateral pneumonia evident in the ct scan. the patient had mild type covid-19, with normal results for routine blood parameters and inflammation markers (c-reactive protein and procalcitonin). the patients displayed elevated levels of alanine transaminase and serum creatinine, indicating potential liver and kidney injury. an unusual finding was the 24-day period of continuing positive nucleic acid, which was longer than most patients reported from wuhan [27] . phylogenetic analysis suggested that sars, ratg13, and sars-cov-2 exhibited remarkable evolutionary divergence, with potential evolutionary branches within sars-cov-2 ( figure 1(a) ). for instance, minor evolutionary divergence existed between wiv02 (2019-12-31)/wh19008 (2019-12-30), and mt0270641 (2020-1-29)/zj01(2020-1-23), which were collected in the early and widely disseminated stages of the epidemic, indicating the potential for the formation of evolutionary branches during dissemination. rscu analysis revealed various differences among the eight strains (mn938384, cna0007334, wiv06, zj01, nmdc60013002-05, cna0007332, mn988668, and wiv07) and other members of the sars-cov-2 family ( figure 1 (b)), where mn938384, cna0007334, wiv06, and zj01 were the closest to human rscu. among the eight strains collected in wuhan, guangdong, and hangzhou, six were collected at the early stage of covid-19 (26 december 2019 to 2 january 2020). the collection time of mn938384 was not later than 14 january 2020 (virus submission time), while zj01 was collected on 23 january 2020. the entire sequence of zj01 is presented in the appendix. sequence alignment analysis indicated 38 mutation sites for zj01 compared with other sars-cov-2 family members ( figure 2(a) ). of these, 35 mutations were unique to zj01, including seven deletions, four insertions, and 24 substitutions. for the remaining three mutation sites, mutation site 20 was caused by a sequencing error, while mutations 14 and 38 are widely distributed in the sars-cov-2 family. among the unique zj01 mutations, 10 (mutations 22-31) were located on the s protein. these included three same sense mutations, two deletion mutations, and five missense mutations, which led to amino acid changes of ser596, gln613, glu702, ala771, ala1015, pro1053, and thr1066. a similarity analysis indicated that the main difference among various coronaviruses located in the receptor-binding domain region of s1. intriguingly, the differences between zj01 and other members of sars-cov-2 mainly resided in s2 ( figure 2 (figure 3(b) ). although it is still unclear whether 8824t/28247c appeared in the intermediate host stage or at human infection stage, we speculate that sars-cov-2 maintained mutation during human transmission and formed the specific strain zj01 (8824t/28247t). we proposed a novel categorization system for sars-cov-2 and defined type c as 8824c, type t for 8824t, and type tt for zj01 as a special case. according to this system, we further categorized 54 strains of sars-cov-2-related viruses (figure 3(c) ). we found a prevalence of the t type of 83.3% in china (n = 30) and 95.7% in wuhan (n = 23); 60% of the c type in japan (n = 5) and 100% in tokyo (n = 3); 53.8% of the c type in the united states (n = 13), 83.3% of the t type in california (n = 6), and 100% of the c type in washington d.c. (n = 3). intriguingly, for two cases from the us state of illinois, one was the t type and the other was designated the y type because of the presence of y at both nucleotide positions 8824 and 28247, indicating the possibility of co-infection with both t and c types. worldwide, only one case of the tt type has been found, in hangzhou. whether this is an occasional single mutated strain or a novel potential subtype of sars-cov-2 warrants more indepth virologic analysis. there were three potential fcss on the s protein. f1, f2 and f3 were separately located in s1/s2, s2 and the n-terminal domain (ntd) of s1 (figure 4(a) ). further comparative alignment analysis of gz02 (sars viral strain), wuhan-hu-1 (the earliest sequenced sars-cov-2), ratg13, hku9-1 (the potential ancestor of sars and sars-cov-2), hku-1 and oc43 showed that the variation of fcs sequence had certain regularity in coronavirus evolution ( figure 4(b) ). in detail, there was no fcs in hku9-1, but one potential fcs in the f2 locus of gz02 (furin score 0.366) showed effective furin binding capacity [28] . for ratg13, the f2 locus was slightly changed (furin score 0.333) and a novel fcs was formed in the f1 locus (furin score 0.279). although the changes in these two sites were inherited in sars-cov-2, marked differences in the f1 site between ratg13 and sars-cov-2 were evident. strikingly, compared with ratg13, we found an additional prra sequence at the f1 site of sars-cov-2 forming a strong and reliable fcs (furin score 0.62). although the source of insertion was unknown, the prra sequence was common to avian influenza virus [29] . we deduced that it might have been inherited from hku1 and oc43, which had effective fcs at the f1 site (furin score 0.878 and 0.744) and the respective amino acid sequence of ssrrkrr and tkrrsrr, with high similarity of nsprrar in sars-cov-2. hku1 and co43 could cause human upper respiratory tract infections, but the symptoms were milder than those caused by sars and sars-cov-2. epidemiological investigations indicated that oc43 and hku-1 may be widely present in patients with flu-like symptoms in autumn and winter [30, 31] . coronaviruses may cause co-infection with other respiratory viruses. therefore, oc43 and hku-1 are much likely to genetically interact with original sars-cov-2. this genetic recombination may have caused the original sars-cov-2 to acquire an fcs at the f1 site and eventually become highly infectious and pathogenic (figure 4(c) ). we also found a similar fcs on the s protein of mers-cov. whether this also originated from the genetic recombination of oc43 and hku-1 is unknown. the source of prra on the s protein of sars-cov-2 is yet to be confirmed by scientific experiments. the present epidemiological and bioinformatic findings only support speculations. zj01 had a glu702 to lys702 substitution at amino acid 18 behind the f1 site, and deletion (ala771 to -) at amino acid 37 ahead of the f2 site. these mutations may influence the tertiary and quaternary structures of the s protein and finally change the furin binding capacity. the f1-3 sites were conserved in sars-cov-2 and sars (figure 4(d) ), indicating the importance of mutations in these sites. protein structure analyses imply that mutation in the f1and f2-related areas of zj01 may influence binding with furin protein homology modelling revealed the position of the f1-3 sites in the s protein of sars-cov-2 ( figure 5(a) ). f1-3 were located on the surface of s protein and protruded outward, and thus, had great potential as substrate-binding sites. f1 was located in the transition area of s1 and s2 (s1/s2) with an obvious outward protrusion. f2 was located on the mid-lower position of s2, whereas f3 was located on top of s1-ntd. further homology modelling of the s proteins of gz02, ratg13, wuhan-hu-1, and zj01 revealed significant differences in protein conformation of the f1 locus. from sars and ratg13 to sars-cov-2, the f1 site showed a tendency towards outward protrusion ( figure 5(b) ). although wuhan-hu-1 and zj01 shared the same amino acid sequence at the f1 site, the mutation (glu702 to lys702) near the f1 site of zj01 might have changed its protein conformation and resulted in further outward extension by 11.6 å. furthermore, ratg13, wuhan-hu-1, and zj01 displayed a high degree of consistency in the f2 site. the f2 site of gz02 was deeply buried in the inner region of the s protein, which was the biggest difference from sars-cov-2, whose f2 site was on the surface of the s protein. finally, ratg13, wuhan-hu-1, and zj01 displayed high similarity at the f3 site that was missing in gz02. apbs analysis revealed that furin was a protease with a negative charge. its substrate-binding site (191-192, 253-258 and 292-295) was covered with a large number of negative charges ( figure 6 ). the f1 sites from sars-cov-2 related viruses (zj01, wuhan-hu-1 and ratg13) were predominantly positively charged, while sars comprised negative and positive charges. compared with wuhan-hu-1, the f1 site of zj01 was more positively charged in its protruding head and more negatively charge in its basal part. the f2 site of gz02 was covered with a negative charge, whereas the f2 sites of wuhan-hu-1 and ratg13 were covered with a low level of positive charge. the f2 site of zj01 was more positively charged than in the other strains, probably due to the nearby gene deletion (ala 771 to -). gz02 had many negative charges at the f3 site, while few negative charges were identified in sars-cov-2 related virus. we speculated that, despite the gene similarity between zj01 and wuhan-hu-1, the mutation near the fcs changed the protein structure conformation and surface electrostatic potential of zj01, which further influenced its binding capacity with furin. the protein and rna expression levels of ace2 and furin in human major tissues were explored in the human protein atlas (https://www.proteinatlas.org/). ace2 was predominantly expressed in tissues of the small intestine, duodenum, colon, kidneys, and testis, while expression was relatively low in the lung tissue (figure 7(a) ). furin was expressed in most human tissues and organs, and expression of rna was highest in the salivary glands, placenta, liver, pancreas, and bone marrow (figure 7(b) ). the expression of the furin protein was very low in the lungs compared with other tissues. to further explore the correlation between ace2 and furin expression, we reanalysed single-cell rna sequencing (scrna-seq) data in the lung, liver, and colon (figure 7(c) ). since ace2 and transmembrane protease, serine 2 (tmprss2) co-expression have been reported recently [32] , we also examined tmprss2 expression levels in these tissues. in the scrna-seq datasets, ace2, furin and tmprss2 showed higher expression levels in the liver and colon than in the lung (figure 7(e) ). consistent with a previous report [33] , ace2 was mainly expressed in alveolar type 2 cells in the lungs (figure 7(d and e) ). ace2 was highly expressed in liver cholangiocytes, liver hepatocytes, colon colonocytes and colon crypt top (ct) colonocytes compared with other liver or colon cell types. this expression pattern was the same as tmprss2, but the expression of tmprss2 was higher in each cell type. in contrast, furin was expressed in all cell types of the three tissues, with little co-expression with ace2. cd147 (basigin), a newly identified sars-cov-2 receptor, can bind to spike proteins and mediates viral invasion [34] . recently, elevated plasmin was reported in covid-19 with comorbidities such as hypertension, diabetes, et al while plasmin or other proteases may be able to cleave fcs [35] . therefore, we analysed and compared the expression of these genes in the lungs, liver, and colon. we found that cd147, the plasma precursor plasminogen, trypsin, and cathepsin displayed similar expression patterns as ace2 and tmprss2 ( supplementary fig. 2) . however, the expression levels of plasminogen in the lungs and colon were very low under physiological conditions. these results suggest that furin and other proteases may play important roles in increasing the ability of virus to enter host cells by cleaving the fcs of s protein. covid-19 rapidly spread throughout china and has causing enormous damage. during the nationwide dissemination, its epidemiological and clinical features changed. accumulating evidence indicates the appearance of several unique characteristics distinct from cases in wuhan [8, 9, 36] , including a higher rate of mild disease, lower rate of severe/critical type and mortality, and longer period of nucleic acid positivity [10, 11, 27, 37] . moreover, the increased transmission route of sars-cov-2 has been gradually unmasked, from previous recognition of respiratory transmission to faeces [38] and even tears and conjunctival secretions [39] . however, recently published virus sequencing results [18] demonstrated that the sars-cov-2 family members share similar gene sequences, with only a few essential changes. how could the contradicting phenomenon regarding the change of clinical features f1 is located at s1/s2, f2 at s2 and f3 at the ntd of s1. (b) differences in the tertiary structure of the protein at the f1-3 sites of gz02, ratg13, wuhan-hu-1 and zj01. the difference between zj01 and wuhan-hu-1 may be caused by the mutation of zj01 near the fcs. and the conservation of viral genome homology be explained? to provide clarity, we selected a covid-19 patient who experienced a mild disease and isolated the causative virus (zj01) for comparative analysis. we found 37 gene mutations, of which 35 were unique to zj01. further bioinformatics analysis highlighted the difference between zj01 and other strains of sars-cov-2, as well as the important roles of furin. thus, we conclude that sars-cov-2 may be evolving in a milder direction with increased fcss. analysis of 788 covid-19 patients in zhejiang province revealed mild and severe types of sars-cov-2. although we do not currently have evidence to prove whether patients with mild covid-19 are directly affected by virus mutation or other factors, we found a significant difference between zj01 and other members of sars-cov-2. zj01 had a relatively high number of 37 mutations, and its rscu was closer to humans than most members of sars-cov-2. more importantly, zj01 was the only tt type of the 54 strains in our c/ t categorization system. although the sequence of zj01 was still close to wuhan-hu-1 (the earliest identified sars-cov-2) and its mutations were not sufficient to reach the threshold of forming an independent subtype, our evidence indicates that zj01 may represent a specific evolutionary direction of sars-cov-2. in this study, we developed the c/t categorization system for sars-cov-2, which revealed the occurrence of possibly inheritable mutations at the very early stage of its evolution and the potential for continuing c/t subtype formation. the tt type zj01 was unique in our system. although a similar categorization system has been recently proposed [40] , the authors did not report a tt type in their 120 strains of sars-cov-2. in addition, the c/t pattern could also be used to trace the route of virus infection and evolution. for instance, we found eight t type strains with 29198t, including ratg13, mp789, 2019-ncov_hku-sz-005b_2020, and 2019-ncov_hku-sz-002a_2020 from shenzhen (china), 2019-ncov/ usa-az1/2020 from phoenix, arizona in the usa, 2019-ncov/japan/ty/wk-501/2020, 2019-ncov/ japan/ty/wk-012/2020 and 2019-ncov/japan/ty/ wk-521/2020 from tokyo, japan. the other 43 strains of sars-cov-2 harboured 29198c. since ratg13 and mp789 both had 8824c/28247t/29198t, we can speculate that these eight strains of 29198t appeared earlier than strains of 29198c. using this method, we reckoned that the earliest strain of sars-cov-2 infected one patient admitted to shenzhen hospital on 10 january 2020. the type was 8824c/28247t/ 29198t/ 2682c/3812c/9606c/11125g/15667t/ 29808g. the earliest strain in the usa was the aforementioned strain from phoenix on 26 january 2020 (type was 8824c/28247t/29198t/2682c/3812c/ 9606t/11125g/15667c/29808g). patients with these two earliest strains had an exposure history in wuhan. therefore, we speculated that the origin of sars-cov-9 remains wuhan, but that the source of the earliest predecessor virus remains vague due to lack of sufficient samples ( supplementary fig. 1 ). furin is a well-recognized and important serine protease, which has a minimum enzyme restriction site of arg(r)-x-x-arg (r). furin is essential in influenza infection. the binding capacity change of furin in avian influenza may influence its pathogenicity [41] . although furin is not the most common protease in coronaviruses, previous studies have indicated its pivotal roles in sars and mers [28, 42] . ratg13 is the closest strain to sars-cov-2 with 96% sequence similarity [43] . however, sars-cov-2 has a highly conserved prra insertion at amino acid 690 amino acid of the s protein, with high conservation [44] . this insertion may become a critical point for the animal-to-human change of the host of ratg13. sequence alignment revealed that this inserted sequence may arise from the translocation between human coronavirus hku1 and oc43 (figure 4 ). sars-cov-2 harbours three fcs (f1-3). f1 hydrolyses s protein to s1 and s2 and promotes virus-cell fusion. f2 hydrolyses s2 and participates in virus pathogenicity after cell entry. f3 functions through ntd and promotes adhesion between the virus and cell surface. however, whether the f3 site really exists and, if it does, what its' function is needs further investigation. furthermore, the target cell binding site of hku1 and oc43 was on the s a segment of the s protein, while its corresponding site in sars-cov-2 was ntd. therefore, except for the potential interaction at the f1 site, there also exists the possibility of interaction in the ntd segment between sars-cov-2 and hku1/oc43. viruses frequently undergo mutation and adjust their rscu under evolutionary selection pressure to adapt to the host, thereby acquiring better replication and dissemination capacity [45] . the fcs might be an outstanding marker for coronavirus evolution. although these three fcss are very conservative during the evolution of the sars-cov-2 family, the evolution of fcs seems to proceed in a different way. we found that although the fcss of zj01 and wuhan-hu-1 were identical, the mutations of zj01 near the f1 and f2 sites changed their three-dimensional protein structure and apbs significantly (figures 5 and 6 ). this change is due to the substitution or deletion of amino acids 25-27 on the peptide chain ( figure 2 ). although the fcs itself has not changed, the changes in the spatial structure and electrostatic potential of fcs are likely to cause a significant change in the ability of furin to digest. therefore, the difference between the sars-cov-2 family and other coronavirus families is mainly reflected in the fcs structure. the differences within the sars-cov-2 family are likely to be reflected in fcs function. the collective data indicate that furin plays a pivotal role in the pathogenicity of sars-cov-2. the evolutionary trend of increasing fcs in sars-cov-2 observed in this study is more prone to influenza-like clinical manifestations, such as human hku1 and oc43 [46] . single-cell sequencing analysis revealed a higher expression level and wider organ distribution of furin than ace2, especially in the salivary glands, lachrymal glands, colon, liver, and kidneys. therefore, sars-cov-2 might evolve to utilize this specific feature by increasing fcs to become more infectious at multiorgan levels. our hypothesis is consistent with changes in the clinical characteristics of covid-19 from published data and our observations, including detection of virus in faeces [38] and conjunctival secretions [39] , decreased severity/fatality, increased liver/kidney damage and symptoms of the gastrointestinal tract, increased transmissibility, and prolonged period of nucleic acid positivity. since ace2 expression was quite low in the whole body, including the lungs, we speculate that on one hand, the inflammatory reaction rather than the viral load may trigger the severe respiratory damage; on the other hand, the utilization of furin may help the virus disseminate from the lungs to other organs, leading to decreased severity but increased liver/ kidney dysfunction. these speculations must be investigated further. the transmissibility and tropism of sars-cov-2 must also be carefully considered. in summary, zj01 isolated from a patient in zhejiang province with mild covid-19 patient represents a potential branch in virus evolution. sars-cov-2 may adopt a similar mechanism that depends on furin for invasion as do hju1 and oc43. such a potential change in evolutionary direction may promote the appearance of a mild subtype of covid-19. front-line medical staff of zhejiang province for their bravery and efforts in sars-cov-2 prevention and control. no potential conflict of interest was 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reality with unitymol-apbs scrna-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation colonic epithelial cell diversity in health and inflammatory bowel disease single cell rna sequencing of human liver reveals distinct intrahepatic macrophage populations comprehensive integration of single-cell data fast, sensitive and accurate integration of single-cell data with harmony ggplot2: elegant graphics for data analysis clinical characteristics of coronavirus disease 2019 in china different host cell proteases activate the sars-coronavirus spike-protein for cell-cell and virus-cell fusion protective role for the n-terminal domain of alpha-dystroglycan in influenza a virus proliferation human coronavirus in hospitalized children with respiratory tract infections: a 9-year population-based study from norway epidemiology and clinical features of human coronaviruses in the pediatric population the insert sequence in sars-cov-2 enhances spike protein cleavage by tmprss single cell rna sequencing of 13 human tissues identify cell types and receptors of human coronaviruses sars-cov-2 invades host cells via a novel route: cd147-spike protein elevated plasmin(ogen) as a common risk factor for covid-19 susceptibility clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china presumed asymptomatic carrier transmission of covid-19 viral load of sars-cov-2 in clinical samples evaluation of coronavirus in tears and conjunctival secretions of patients with sars-cov-2 infection on the origin and continuing evolution of sars-cov-2 a novel activation mechanism of avian influenza virus h9n2 by furin host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein a pneumonia outbreak associated with a new coronavirus of probable bat origin a furin cleavage site was discovered in the s protein of the wuhan 2019 novel coronavirus genetic analysis and evolutionary changes of the torque teno sus virus human coronavirus infections in israel: epidemiology, clinical symptoms and summer seasonality of hcov-hku1. viruses we thank the health commission of zhejiang province, china for coordinating data collection, thanks to all the please see the sequence of zj01 in the appendix of this paper. hangping yao http://orcid.org/0000-0001-6742-7074 liang wen http://orcid.org/0000-0002-4600-6999 yida yang http://orcid.org/0000-0001-6261-0953 key: cord-279415-s823mver authors: guo, xiaodong; wang, jiedong; hu, dong; wu, lisha; gu, li; wang, yang; zhao, jingjing; zeng, lian; zhang, jianduan; wu, yongchao title: survey of covid-19 disease among orthopaedic surgeons in wuhan, people’s republic of china date: 2020-04-23 journal: j bone joint surg am doi: 10.2106/jbjs.20.00417 sha: doc_id: 279415 cord_uid: s823mver coronavirus disease 2019 (covid-19) broke out in wuhan, the people’s republic of china, in december 2019 and now is a pandemic all around the world. some orthopaedic surgeons in wuhan were infected with covid-19. methods: we conducted a survey to identify the orthopaedic surgeons who were infected with covid-19 in wuhan. a self-administered questionnaire was distributed to collect information such as social demographic variables, clinical manifestations, exposure history, awareness of the outbreak, infection control training provided by hospitals, and individual protection practices. to further explore the possible risk factors at the individual level, a 1:2 matched case-control study was conducted. results: a total of 26 orthopaedic surgeons from 8 hospitals in wuhan were identified as having covid-19. the incidence in each hospital varied from 1.5% to 20.7%. the onset of symptoms was from january 13 to february 5, 2020, and peaked on january 23, 8 days prior to the peak of the public epidemic. the suspected sites of exposure were general wards (79.2%), public places at the hospital (20.8%), operating rooms (12.5%), the intensive care unit (4.2%), and the outpatient clinic (4.2%). there was transmission from these doctors to others in 25% of cases, including to family members (20.8%), to colleagues (4.2%), to patients (4.2%), and to friends (4.2%). participation in real-time training on prevention measures was found to have a protective effect against covid-19 (odds ratio [or], 0.12). not wearing an n95 respirator was found to be a risk factor (or, 5.20 [95% confidence interval (ci), 1.09 to 25.00]). wearing respirators or masks all of the time was found to be protective (or, 0.15). severe fatigue was found to be a risk factor (or, 4 [95% ci, 1 to 16]) for infection with covid-19. conclusions: orthopaedic surgeons are at risk during the covid-19 pandemic. common places of work could be contaminated. orthopaedic surgeons have to be more vigilant and take more precautions to avoid infection with covid-19. level of evidence: diagnostic level iv. see instructions for authors for a complete description of levels of evidence. in contrast to severe acute respiratory syndrome (sars), covid-19 is more transmissible, especially in the incubation or prodromal period [2] [3] [4] , which could place populations at a higher risk of exposure, especially for health-care workers. as of february 11, 2020, 1,716 health professionals were recorded as having confirmed covid-19 in the people's republic of china 5 , with a majority (1,080 [63%]) from wuhan, the epicenter of this pandemic. at present, there is a great need to assess the covid-19 infection status of health-care workers in wuhan and to gain experience for future battles. a report 6 from wuhan suggested that hospital-associated transmission might serve as the mechanism of covid-19 infection for health-care workers. among 138 patients, 40 (29.0%) were health-care workers who were presumed to have been infected in hospitals at the early stage of the outbreak. these infected health-care workers largely worked in general wards (31 [77.5%]), which are not generally regarded as the front lines of the pandemic as are fever clinics and designated isolation wards. so far, the situation of covid-19 infections in health-care workers not working on the front lines of the pandemic in wuhan has remained obscure. to characterize this situation, we aimed to study orthopaedic surgeons, a particular group of the health-care workers not working on the front lines, as an indication to the overall infection situation of health-care workers. we investigated the situation of infection of orthopaedic surgeons and trainees working in general wards, outpatient clinics, intensive care units, or operating rooms in wuhan hospitals, and we further explored the possible risk factors at the individual level using a matched case-control study. we identified orthopaedic surgeons and trainees (hereinafter referred to as orthopaedic surgeons) who were infected with covid-19 from december 31, 2019, to february 24, 2020, in the urban area of wuhan. cases of covid-19 were defined according to the guidance of the world health organization (who) 7 , based on the history of exposure to covid-19, symptoms, pathogen test, chest computed tomographic (ct) scan, and hematological examination. the exclusion criteria ruled out orthopaedic surgeons who assisted in fever clinics and designated covid-19 wards in hospitals. to explore the possible risk factors at the individual level, we conducted a 1:2 ratio matched case-control study. the controls were selected from uninfected orthopaedic surgeons who worked in the same department as the case at each hospital. the age difference between case and control was limited to within 3 years. we investigated 24 hospitals in the urban area of wuhan. a total of 26 orthopaedic surgeons with covid-19 were identified from 8 hospitals. two of the 26 orthopaedic surgeons were excluded from further study because 1 orthopaedic surgeon had assisted in the fever clinics and designated covid-19 wards, and the other orthopaedic surgeon was hospitalized in an isolation ward with severe covid-19 and could not finish the questionnaire. of 24 cases, 21 were confirmed cases with positive reverse transcription polymerase chain reaction (rt-pcr) tests or antibody tests, and 3 were clinically diagnosed cases with a history of exposure to covid-19, fever and respiratory symptoms, a chest ct scan with ground-glass opacity and consolidation, leucopenia and/or lymphopenia, and negative influenza virus tests. the latter 3 cases were negative on rt-pcr tests and had not taken any antibody tests at the last follow-up. in total, 24 infected and 48 matched healthy orthopaedic surgeons were included for further analysis. there was no significant difference of demographic variables (age, sex, job title, and work years) between infected and matched orthopaedic surgeons. questionnaire a self-administered questionnaire was developed and was distributed online for data collection (see appendix). the questionnaire included the information about demographic characteristics, clinical manifestations, awareness to the outbreak at an early stage, covid-19 exposure history, availability of and participation in the infection control training provided by the hospital, and individual protection practices (e.g., good hand-washing hygiene and wearing face masks). the study was approved by the ethics committee of tongji medical college, huazhong university of science and technology. all of the participants signed the digital informed consent form. the database was established using microsoft excel, and all analyses were performed with sas 9.3 software (sas institute). significance was set at p < 0.05. descriptive characteristics are presented as the mean and the standard deviation for normally distributed quantitative variables, and categorical variables are presented as numbers and percentages. the differences of means such as age were compared using the student t test, and the chi-square test or the fisher exact probability test was employed to compare the differences of categorical variables, such as health status and job title, between the case and control groups. univariate conditional logistic regression models were used to assess the associations between the potential exposures and covid-19 morbidity and to estimate the corresponding odds ratios (ors). the number of cases in each hospital varied from 1 to 8 and the incidence of infection ranged from 1.5% to 20.7%; 5 of 8 hospitals had only 1 case. the distance from these hospitals to the huanan seafood market (a live animal and seafood market), the presumptive ground zero of the covid-19 pandemic, varies from to 1.1 km to 11.2 km, and 6 of 8 hospitals are within 6 km of the market (table i) . the mean age (and standard deviation) of 24 infected orthopaedic surgeons was 36.1 ± 6.3 years (range, 25 to 48 years) (table ii) . they all reported having a good health condition before infection, except 1 orthopaedic surgeon (4.2%) who had diabetes mellitus (table iii) . the onset of symptoms among the cases was from january 13 to february 5, 2020, largely between january 15 and january 24, and peaked on january 23 (table iii, fig. 1 ). the top 5 symptoms were fever (83.3%), cough (62.5%), fatigue (70.8%), diarrhea (37.5%), and headache (33.3%). the symptoms of these surgeons were mostly mild. hematological examination showed lymphopenia (58.3%), increased c-reactive protein (25.0%), and leucopenia (12.5%). fifteen surgeons were admitted to the hospital for treatment, and 9 surgeons were self-isolated at home or hotels with medicine for at least 2 weeks. all 24 surgeons recovered after treatment. according to the questionnaire responses, suspected sites of exposure were general wards (79.2%), public places at the hospital (20.8%), operating rooms (12.5%), intensive care units (4.2%), and outpatient clinics (4.2%). there was confirmed transmission from these doctors to others in 25% of cases, including to family members severe fatigue of orthopaedic surgeons during the 2 months before the outbreak of covid-19 was found to be a risk factor for the infection (table iv) (or, 4 [95% confidence interval (ci), 1 to 16]). the case group had a higher proportion (79.2%) who slept <7 hours per night than the control group (60.4%), although significance was not reached (p = 0.1246). we surveyed the awareness of human-to-human transmission of covid-19 by the orthopaedic surgeons at the early stage of the outbreak. before january 20, 2020, the date when the national health commission of the people's republic of china confirmed and officially announced the human-tohuman transmission and the outbreak of covid-19 8 , 33.3% of infected orthopaedic surgeons were aware of human-toepidemic curve showing the date of onset of symptoms and of diagnosis of infected orthopaedic surgeons in wuhan. the onset of symptoms was from january 13 to february 5, 2020, largely between january 15 and january 24, and peaked on january 23. human transmission, whereas the rate of awareness of humanto-human transmission among the control group was 47.9%. however, the difference between the 2 groups was not significant. the univariate analysis conditional logistic regression showed that lack of knowledge of infection prevention and control measures for highly contagious diseases among orthopaedic surgeons could be a risk, as it showed a trend toward significance (p = 0.0650). the participation in real-time training on infection prevention and control measures was found to have a protective effect against covid-19 (or, 0.12; p = 0.0072). not wearing n95 respirators was found to be a risk factor (or, 5.20 [95% ci, 1.09 to 25.00]) for becoming infected with covid-19. before january 20, 2020, 83.3% of infected orthopaedic surgeons did not use n95 respira-tors. compliance with wearing n95 respirators or face masks was significantly different (p = 0.0038) between the case cohort (29.2%) and the control cohort (68.8%). wearing respirators or masks all of the time was found to have a protective effect against becoming infected with covid-19 (or, 0.15; p = 0.0038). there was no significant difference (p = 0.7458) between cases (45.8%) and controls (50.0%) in adherence to recommended hand-hygiene practice. the majority of orthopaedic surgeons in both the case group (87.5%) and the control group (77.1%) faced the situation of insufficiency of personal protective equipment (ppe) during the early stages of the outbreak. we studied measures for infection source control in orthopaedic wards to prevent the transmission of covid-19. we found that, for orthopaedic patients with suspected covid-19, not wearing masks was a risk factor to surgeons (or, 6.05 [95% ci, 1.70 to 21.51]). eight hospitals in wuhan had orthopaedic surgeons infected with covid-19, with an incidence range of 1.5% to 20.7% at the early stage of the outbreak. hospitals without any infection cases among orthopaedic surgeons were not included in this current study. the incidence difference could be associated with the number of early admissions of patients with covid-19, which was associated with the distance from the hospitals to the huanan seafood market. for example, as the nearest hospital to the huanan seafood market, the hospital designated as h4 in our study had the highest infection rate of 20.7% and was among the very first hospitals in wuhan that admitted patients with covid-19. the difference might also relate to the early awareness, alertness, and infection prevention and control measures taken by hospitals, but the answers regarding these hypotheses need more data at the hospital level. according to analyses of the questionnaire, the main suspected site of infection was general wards. this is in line with another report about health-care workers infected with covid-19 6 . in the orthopaedic wards at that time, there were several cases in which patients were admitted for elective or trauma surgical procedures during their incubation period of covid-19. during the early stage of the outbreak in wuhan, because of the serious shortage in virus test kits, testing for the pathogen could be performed only in suspected cases with symptoms that were severe or not self-limited. the real situation regarding how many patients in the orthopaedic wards had the comorbidity of covid-19 was unknown. one surgeon consulted in the intensive care unit, where there was a patient with traumatic injury and fever of an unknown origin, which was later diagnosed as due to covid-19. three surgeons were exposed during operations on patients who were diagnosed as having covid-19 several days after the surgical procedures. thus, it is wise to minimize, postpone, or cancel elective operations during the pandemic. family members of the patients and visitors also could be the source of virus in the wards. public places at hospitals (e.g., elevators) could be contaminated and the virus could be transmitted from there by contact or droplet. there are many asymptomatic patients with covid-19 who are, nevertheless, shedding the virus and are unwittingly exposing other inpatients, outpatients, and health-care providers to the risk of contracting covid-19 9 . patients normally have compromised immunity, so, during the pandemic, inpatients should wear face masks, provided by the hospitals, to protect themselves, fellow patients, and health-care workers. the onset of symptoms was largely from january 15 to january 24, and the largest number of patients (7) started to show symptoms on january 23 (table iii, fig. 1 ). the reported median incubation period of covid-19 is 4 days (interquartile range, 2 to 7 days) 1 , so the possible exposure dates were before january 20, 2020, and the total number of confirmed cases in wuhan was only 258 on january 20, 2020 10 . by comparing the epidemic curve among the public 5 with that of orthopaedic surgeons (fig. 1) , we found that the peak date of onset of orthopaedic surgeons' infection was 8 days earlier than that of the public, indicating that these orthopaedic surgeons more likely were exposed to covid-19 in the hospitals, rather than in the community. transmission of covid-19 from these infected orthopaedic surgeons to others happened in one-fourth of the cases. the transmission of covid-19 to family members created great stress and depression for these surgeons. the high rate (20.8%) of transmission to family members raises the need for doctors to be cautious of household transmission. it is recommended that orthopaedic surgeons who still work in hospital settings during the covid-19 pandemic period manage to avoid close contact with family members at home. during the early stages of the outbreak of covid-19 in wuhan, knowledge of infection prevention and control measures was limited among orthopaedic surgeons in wuhan. this limited knowledge may be due to little or no experience of these orthopaedic surgeons to cope with the highly contagious diseases in their routine practices, insufficient training in higher levels of infection prevention and control measures, and, in some cases, even a lack of awareness of the importance of such measures. the effect of real-time training could not be well defined in the current study because some of the surgeons were exposed before such training became available in the middle to late january. wearing n95 respirators was found to have a protective effect against covid-19. normally, orthopaedic surgeons do not need to use n95 respirators in the hospital, so the behavior of wearing n95 respirators is an indicator of their awareness and vigilance regarding transmission. the vigilance could help doctors to ensure compliance with infection prevention and control procedures, as shown in our results that a higher ratio of orthopaedic surgeons in the control group wore the respirators and/or masks all of the time than orthopaedic surgeons in the case group did. the availability of ppe was insufficient for orthopaedic surgeons, which increased the risk for these doctors. there was a sudden, increased need for ppe, and the orthopaedic surgeons were not prioritized for the supply. a status of severe fatigue was found to contribute to infection with covid-19 (table iv) . severe fatigue from overwork, less sleep, and mental stress are common issues for orthopaedic surgeons. reducing workload could be a strategy for orthopaedic surgeons to defend against becoming infected with covid-19. there were several limitations to this study. one was the lack of data at the hospital level, the reasons for which have not yet been totally determined. the case-control study design was useful to test the possible link between the exposures and the outcome, but not to confirm the causal relationship, and recall bias could have occurred because of its nature. nevertheless, because the recall period in the study was less than about 1 month, we assumed that the recall bias, if any, would have been minor. the number of surgeons infected could have be higher than reported, as we could have missed the infected orthopaedic surgeons in some small hospitals, but we assume that the number will be very small. the orthopaedic surgeons in wuhan were infected by covid-19 in the early stage of the epidemic. understanding the related risk factors is of great importance, especially when many countries are currently facing a situation similar to what wuhan faced in january 2020. a serious challenge in responding to covid-19 is how to better protect health-care workers and prevent nosocomial infection 11 . we make some specific recommendations, based on our study, to prevent orthopaedic surgeons from becoming infected with covid-19 in a territory reporting local transmission: 1. orthopaedic surgeons should stay more vigilant, have a high level of clinical suspicion, and take more precautions to avoid covid-19 infection. 2. medical and orthopaedic associations should be prepared early, address the uncertainty of infection prevention and control procedures, provide real-time training as needed, and also address the shortage of ppe. 3. it is wise to minimize, postpone, or cancel elective operations. have the patients tested for covid-19 before the operation if resources allow. place face masks on patients. 4. for the orthopaedic surgeons who still work in hospital settings, it is wise to adhere to the u.s. centers for disease control and prevention (cdc) recommendations for infection prevention and control and to wear n95 respirators all of the time when necessary during the pandemic. 5. after being exposed in environments contaminated by patients with confirmed or suspected covid-19, orthopaedic surgeons should manage to avoid close contact with family members at home and maintain social distancing in other situations. 6. orthopaedic surgeons should try to avoid long-term overwork and fatigue, which could compromise immunity against covid-19. it has been shown that health-care workers at risk require clear communication, emotional support, and effective leader-ship. we believe that a united global orthopaedic community can contribute to the fight against covid-19. zhong ns; china medical treatment expert group for covid-19. clinical characteristics of coronavirus disease 2019 in china transmission of 2019-ncov infection from an asymptomatic contact in germany who scientific and technical advisory group for infectious hazards. covid-19: what is next for public health? lancet presumed asymptomatic carrier transmission of covid-19 characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the chinese center for disease control and prevention clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china global surveillance for human infection with coronavirus disease (covid-19) interim guidance national health commission of the people's republic of china. announcement by the national health commission substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) national health commission of wuhan. notification of pneumonia associated with new coronavirus at national health commission of wuhan.accessed2020-feb27 priorities for the us health community responding to covid-19 supporting material provided by the authors is posted with the online version of this article as a data supplement at jbjs.org (http://links.lww.com/jbjs/f828). n key: cord-285403-h8ahn8fw authors: zhang, liangsheng; shen, fu-ming; chen, fei; lin, zhenguo title: origin and evolution of the 2019 novel coronavirus date: 2020-02-03 journal: clin infect dis doi: 10.1093/cid/ciaa112 sha: doc_id: 285403 cord_uid: h8ahn8fw nan to the editor-the 2019 novel coronavirus disease (2019-ncov or covid-19) recently reported from wuhan (china), which has cases in thailand, japan, south korea, and the united states, has been confirmed as a new coronavirus [1] . the 2019-ncov has infected several hundred humans and has caused many fatal cases. determining the origin and evolution of 2019-ncov is important for the surveillance, drug discovery, and prevention of the epidemic. with more and more reported pathogenic 2019-ncov isolates, it is necessary to reexamine their origin and diversification patterns. based on our phylogenomic analysis of the recently released genomic data of 2019-ncov, we showed that the 2019-ncov is most closely related to 2 severe acute respiratory syndrome (sars)-like cov sequences that were isolated in bats during 2015 to 2017 [2] , suggesting that the bats' cov and the human 2019-ncov share a recent common ancestor ( figure 1a) . therefore, the 2019-ncov can be considered as a sars-like virus and named sars-cov-2. the 2 bat viruses were collected in zhoushan, zhejiang province, china, from 2015 to 2017 [2] . there is speculation that the 2019-ncov may have originated near zhoushan or elsewhere. the new coronavirus was first isolated from stallholders who worked at the south china seafood market in wuhan. this market also sells wild animals or mammals, which were likely intermediate hosts of 2019-ncov, which originated from bat hosts ( figure 1b ). it has been speculated that the intermediate hosts (wild mammals) may have been sold to the seafood market in wuhan. the 2019-ncovs have long branches (0.09) for the 2 isolated in the phylogenomic tree ( figure 1a) , indicating that the 2019-ncovs likely share bat hosts. similarly, the 2003 sars-covs (human sars-covs) had short branches (0.03) for the bat hosts ( figure 1a) . this indicates that there should be more bat viruses closer to 2019-ncov. according to their phylogenetic relationships, the 27 isolates of 2019-ncov examined in this study can be divided into at least 6 genotypes (i-vi; figure 1c ). the 27 isolates were mainly obtained from 4 different places-thailand and the 3 chinese cities of wuhan, zhejiang, and guangdong-and all of them were present in people who visited or had contact with people from wuhan. the genotypes vi, v, and iv (guangdong and shenzhen) are located at the basal branch in the phylogenetic tree of 2019-ncov, indicating that those patients infected by these genotypes of cov were among the earliest groups to be infected. there were 3 genotypes present in samples from guangdong province, indicating that the 6 strains were infected from different places in wuhan. there were 2 genotypes found in the zhejiang province, suggesting that the 2 strains were infected from different places in wuhan. the 2 strains detected in nonthaburi, thailand, are from the same genotype and perhaps originated from the same place in wuhan. the sequence diversification between the 24 strains of 2019-ncov are small, and it is difficult to separate them in the phylogenomic tree. compared with the rapid reassortment and mutation of avian influenza (h7n9) [3, 4] , the degree of diversification of 2019-ncov is much smaller. but the 27 isolates can be divided into 6 genotypes, indicating that the 2019-ncov has mutated in different patients. the magnitude of this variation is worthy of attention in the future, and it is necessary to be vigilant for any noticeable, rapid mutations. as of today, the intermediate host of 2019-ncov has not been determined ( figure 1b) . considering that intermediate hosts are generally mammals [5] , they are likely the living mammals sold in the south china seafood market. therefore, strengthening the monitoring of wild mammals is an urgent measure needed to prevent similar viruses from infecting humans in the future. more than 1000 confirmed cases have been reported in china. the number of provinces and cities in china, as well as in other countries, with confirmed cases is steadily increasing. it is necessary to further strengthen monitoring to ensure that these virus strains will not cause diseases like the global outbreak of 2003 sars. supplementary materials are available at clinical infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. genomic characterization and infectivity of a novel sars-like coronavirus in chinese bats rapid reassortment of internal genes in avian influenza a(h7n9) virus substitution rates of the internal genes in the novel avian h7n9 influenza virus origin and evolution of pathogenic coronaviruses the authors thank the creators of the originating and submitting laboratories of the nucleotide sequences from betacov2019-2020 of the global initiative on sharing all influenza data's epiflu database (23 january 2020; 18 isolates).potential conflicts of interest. key: cord-278325-ykcd7d59 authors: cheung, carmen ka man; law, man fai; lui, grace chung yan; wong, sunny hei; wong, raymond siu ming title: coronavirus disease 2019 (covid-19): a haematologist's perspective date: 2020-07-28 journal: acta haematol doi: 10.1159/000510178 sha: doc_id: 278325 cord_uid: ykcd7d59 coronavirus disease 2019 (covid-19) is affecting millions of patients worldwide. it is caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), which belongs to the family coronaviridae, with 80% genomic similarities to sars-cov. lymphopenia was commonly seen in infected patients and has a correlation to disease severity. thrombocytopenia, coagulation abnormalities, and disseminated intravascular coagulation were observed in covid-19 patients, especially those with critical illness and non-survivors. this pandemic has caused disruption in communities and hospital services, as well as straining blood product supply, affecting chemotherapy treatment and haematopoietic stem cell transplantation schedule. in this article, we review the haematological manifestations of the disease and its implication on the management of patients with haematological disorders. coronavirus disease 2019 is caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), a positive-strand rna virus belonging to the family coronaviridae with about 80% genomic similarities with sars-cov [1] [2] [3] . the virus is highly contagious, with over 3 million confirmed cases causing more than 190,000 deaths worldwide, reported to the who by the end of april 2020 [4] [5] [6] [7] [8] . viral infection is well known to be associated with abnormal haematological parameters. autopsy of patients who died of covid-19 showed markedly shrunken spleen with reduced lymphocyte, macrophage proliferation, and phagocytosis [9] . lymphocytes were also depleted in lymph nodes, and all haematopoietic cell lineages were reduced in the bone marrow. the battle against covid-19 is likely to be a marathon and the pandemic has a major impact on health care systems in many countries [10] . the virus will continue to pose a risk to people without immunity to it. in this article, we review the haematological manifestations of covid-19 and its implications on the management of patients with haematological disorders. lymphopenia is a common finding in viral infection. in a multicentre study including 1,099 patients from 552 sites in china, lymphopenia was present in 83.2% of patients on admission [11] . many other studies in china reported rates of lymphopenia ranging from 26% to 80% (table 1) [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] . in a large us series that included 5,700 patients, lymphopenia was present in around 60% (3, 387) of patients on initial laboratory tests [31] . lymphopenia was observed on admission in 36.9 and 25% of cov-id-19 patients reported in singapore and korea, respectively [32, 33] . lymphopenia has been consistently found to correlate with the severity of covid-19 infection and might have a predictive value in the clinical setting. zhou et al. [34] evaluated risk factors for mortality in a retrospective cohort study involving 191 patients and showed that baseline lymphocyte count was significantly higher in survivors than non-survivors (1.1 × 10 9 /l versus 0.6 × 10 9 /l, p < 0.0001). in survivors, lymphocyte count was lowest on day 7 after onset of illness and improved during hospitalization, whereas severe lymphopenia was observed until death in non-survivors. in another retrospective analysis of 95 cases, zhang et al. [35] demonstrated that the level of lowest lymphocyte count correlated with disease severity and a composite endpoint including intensive care unit (icu) admission, mechanical ventilation, or death. among patients with lymphocyte counts < 0.4 × 10 9 /l, 81.8% were classified as severe cases and all of them reached the composite endpoint, while in patients with lymphocyte counts > 0.8 × 10 9 /l, only 11.9% were severe cases and 9.5% reached the composite end point. in a retrospective cohort including 201 patients, lymphopenia during the disease course was also reported to be associated with the development of acute respiratory distress syndrome (ards) [36] . a significantly higher number of patients requiring treatment in icu had low lymphocyte counts on presentation [13, 30, 32] . fan et al. [32] also found that on serial monitoring, the median nadir absolute lymphocyte count in the icu group was 0.4 × 10 9 /l compared to 1.2 × 10 9 /l in the non-icu group. wang et al. [13] analysed dynamic changes in the haematological parameters of 33 patients from day 1 to day 19 after onset of disease and showed that non-survivors developed more severe lymphopenia over time. lymphopenia was frequently encountered in patients requiring icu care, ranging from 67% to 85% in various case series [37] [38] [39] . however, there was no significant difference in median lymphocyte counts between survivors and non-survivors in a retrospective observational study involving 52 critically ill patients in wuhan [39] . depletion of t cells and nk cells was seen in patients suffering from covid-19 [32, [40] [41] [42] . lymphopenia on presentation correlated with a high viral load, as reflected by the low cycle threshold value in respiratory samples [43] . liu et al. [44] analysed the correlation between dynamic changes in the nasopharyngeal viral load and the lymphocyte count. it was found that the higher the rna load in the nasopharynx, the lower the cd4+ and cd8+ t lymphocyte count and these changes were closely related to the severity of covid-19. jiang et al. [45] evaluated lymphocyte subsets in 103 patients, which revealed that cd3+, cd4+, and cd8+ t cells and nk cells were significantly decreased in covid-19 patients with a more severe decrease in cd8+ t cells compared with cd4+ t cells. in addition, severe covid-19 patients showed significant decreases in lymphocyte subset counts compared to mild to moderate patients, especially in cd3+, cd4+, and cd8+ t cells [45] . another study analysed lymphocyte subsets of 44 patients at presentation and found that both cd4+ and cd8+ t cells were below normal levels in patients with covid-19 infection, but the decline in cd4+ cells was more pronounced in severe cases [40] . the percentage of naïve helper t cells (cd3+, cd4+, cd45ra+) increased and memory helper t cells (cd3+, cd4+, cd45ro+) decreased in severe cases when compared with non-severe cases [40] . wan et al. [46] analysed lymphocyte subsets in 123 patients on the first day of hospital admission and 1-3 days before discharge. although there was a greater reduction of cd4+ and cd8+ t cells in the severe group, both cd4+ and cd8+ t cells improved before discharge, suggesting that the cellular immunity had been restored. liu et al. [47] reported that the decrease of t cells, especially cd8+ t cells, in the severe patient group reached its lowest within the first week during the course of the disease, and then t cell numbers gradually increased during the second week with recovery to a level comparable to that of the mild patient group in the third week. all the severe patients survived the disease in the study [47] . another study which compared lymphocyte subsets before and after treatment showed that post-treatment decrease of cd8+ t cells and b cells and increase of cd4+/cd8+ ratio were independent predictors of poor treatment efficacy [48] . lower cd4 t lymphocyte counts may predict a longer persistence of sars-cov-2 rna in stool, where viral clearance may be further delayed by corticosteroid [49] . hence, lymphocyte subset may serve as a biomarker for disease evolution, and its monitoring may help to predict disease outcome. sars-cov-2 could trigger necrosis or apoptosis of lymphocytes resulting in lymphopenia. the virus induced nkg2a expression and possibly correlated with functional exhaustion of nk and cd8+ t cells at an early stage, resulting in disease progression [50] . a dysregulated/exuberant innate response also contributed to sars-cov-mediated pathology [51] . cytokine storm with elevation of interleukin (il)-2r, il-6, il-1β, il-8, il-17, granulocyte colony-stimulating factor (g-csf), tumour necrosis factor-α (tnf-α), ip10, mcp1, and mip1α was seen in covid-19 patients and may also lead to lymphopenia [52] . compared to lymphopenia, thrombocytopenia is less commonly seen in patients suffering from covid-19. the reported rates of thrombocytopenia varied from less than 5% to about 53.6% (table 1) [11, 12, 16, 17, 22, 27, 28, 30, 32, 33] . platelet count has been evaluated as a biomarker to predict the severity of covid-19 in multiple studies, but the results were confounded by heterogeneity regarding definitions of thrombocytopenia and endpoints used. two meta-analyses showed that a lower platelet count is associated with an increased risk of severe disease and mortality in patients with covid-19 and may serve as a marker for progression of illness [53, 54] . in the multicentre study by guan et al. [11] , thrombocytopenia (platelet count < 150 × 10 9 /l) on admission was more commonly seen in severe (57.7%) than nonsevere (31.6%) patients [11, 55] . zhou et al. [34] reported that 20% of non-survivors had platelet counts less than 100 × 10 9 /l on admission compared to only 1% in survivors (p < 0.0001). in contrast, no difference in platelet count on admission was observed between patients requiring icu care compared with those that did not in other studies [13, 30] . a study that monitored the sequential changes in platelet count in the first 3 weeks after admission found that there was a gradual drop in platelet counts with a lower nadir among non-survivors compared to survivors (79 vs. 203 [155-257], p < 0.001) [56] . dynamic changes of platelets were also reported to be closely related to mortality [57] . an increment in platelets was associated with decrease in mortality, suggesting the role of monitoring platelets in predicting prognosis during hospitalization [58] . a case series including 30 hospitalized covid-19 patients evaluated the prognostic value of dynamic changes in platelet count and found that a higher platelet-to-lym-phocyte ratio (plr) at peak platelet count was associated with longer hospital stay and the change in plr was more prominent in severe patients, which may be caused by cytokine storm provoking inflammation resulting in the stimulation and release of platelet [59] . yang et al. [60] analysed the predictive role of plr and showed that a higher plr was seen in severe patients (436.5 ± 329.2) compared to non-severe patients (176.7 ± 84.2; p < 0.001). elevated plr showed a trend of association with disease progression (hazard ratio [hr] 1.023, 95% ci 0.921-1.756 by multivariate cox regression), but the statistical significance was lost after adjustment of gender and age, limiting its clinical utility [60] . experience from previous sars patients, caused by sars-cov-1, suggested that coronavirus could cause thrombocytopenia by direct viral infection of bone marrow haematopoietic stem cells via cd13 or cd66a, formation of auto-antibodies and immune complexes, disseminated intravascular coagulopathy (dic), and consumption of platelet in lung epithelium [61, 62] . higher soluble vascular cell adhesion molecule-1 (svcam-1) level was found in sars patients, which enhanced vascular sequestration resulting in thrombocytopenia [63] . several mechanisms by which covid-19 causes thrombocytopenia have been proposed, including (a) reduction in platelet production due to direct infection of bone marrow cells by the virus, destruction of bone marrow progenitor cells by cytokine storm, and indirect effect of lung injury; (b) increased platelet destruction by autoantibodies and immune complex; and (c) platelet aggregation in the lungs, resulting in microthrombi and platelet consumption [64] . cytokine storm of severe disease may lead to secondary haemophagocytic lymphohistiocytosis, which can also result in thrombocytopenia [65] . thrombocytopenia-associated bleeding is uncommon in covid-19. platelet transfusion is recommended in patients with active bleeding and a platelet count less than 50 × 10 9 /l. for patients at high risk but without active bleeding, platelet transfusion may be considered if the platelet count is less than 20-25 × 10 9 /l [66] . anaemia is not a major problem in patients suffering from covid-19 [11, 12, 17, 27, 28, 30, 32, 33] . in a cohort of 572 patients with covid-19, only 1.6% of them required blood transfusion, while the transfusion requirement was higher in those admitted to icu [67] . been reported, including blood loss during continuous renal replacement therapy and gastrointestinal bleeding with or without anticoagulant use [67] . autoimmune haemolytic anaemia was also reported in patients with covid-19 within a timeframe compatible with the development of cytokine storm [68] . sars-cov-2 can enter epithelial cells of the gastrointestinal tract via the angiotensin-converting enzyme 2 (ace2) receptor [69] . endoscopy revealed oesophageal bleeding caused by erosions and ulcers with detection of sars-cov-2 in a patient with severe infection [70] . sars-cov-2 was demonstrated in gastric, duodenal, and rectal epithelial cells by rna detection and intracellular staining of viral nucleocapsid protein [69] . the direct viral invasion into the gastrointestinal tract may result in mucosal damage resulting in bleeding and subsequent need of blood transfusion. ribavirin has been used as treatment for covid-19 [71, 72] . haemolytic anaemia is one of the major side effects of ribavirin, but most patients did not require transfusion according to previous sars experience [73] . a randomized controlled trial on the safety and efficacy of its use in covid-19 patients is ongoing [74] . adequate haemoglobin level is important to ensure sufficient tissue oxygenation. phlebotomy by small-volume blood tubes may help to reduce iatrogenic blood loss [75] . iron replacement should be given to patients with pre-existing iron deficiency anaemia. use of erythropoiesis-stimulating agents in critically ill patients should be cautious if thromboembolic event is a concern [76] . decision on allogeneic red cell transfusion should be individualized. a single-unit policy should be followed whenever possible [77] . diverse coagulation abnormalities in covid-19 infection have been described [12, 13, 16, 17, 30, 36, 78, 79] . a study in chongqing showed that the majority of the patients had normal coagulation indexes, probably explained by the fact that 70% of the included patients had mild disease [17] . dic is characterized by activation of coagulation and generation and deposition of fibrin, leading to microvascular thrombi deposition in various organs and subsequently multiple organ dysfunction, which predicts mortality in septic patients [80] . tang et al. [79] studied coagulation parameters in 183 patients suffering from covid-19 and found that 71.4% of non-survivors devel-oped overt dic compared to only 0.6% among survivors. patients who died had significantly higher d-dimer, fibrin degradation product levels, and longer pt on admission [79] . the study by guan et al. [11] showed that 69.4% patients who reached the primary composite endpoint (icu admission, mechanical ventilation, or death) had elevated d-dimer level (≥0.5 mg/l) on admission compared to 44.2% not reaching the primary endpoint. wu et al. [36] showed that significant prolongation of pt (median 11.70 s) and higher d-dimer level (1.16 μg/ml) at presentation were observed in patients with ards compared to those without (median pt 11.70 vs. 10.60 s, median d-dimer level 1.16 vs. 0.52 μg/ml, p < 0.001 for both comparisons). elevated d-dimer level has been shown to be associated with higher mortality rates in various studies [34, 36, 57, 81] . in a retrospective study including 343 patients in wuhan, patients with d-dimer levels ≥2 μg/ ml on admission had higher mortality compared to those with d-dimer level < 2 μg/ml (hr 51.5, 95% ci 12.9-206.7) [81] . a d-dimer cut-off value of ≥2 μg/ml on admission could predict in-patient mortality with a sensitivity of 92.3% and a specificity of 83.3% [81] . prolongation of pt and markedly elevated d-dimer on admission were associated with poor prognosis and were more commonly seen in patients requiring icu care [13, 30] . in addition to coagulation parameters on presentation, dynamic change in coagulation profile could predict disease severity and progression. tang et al. [79] reported dynamic changes in coagulation parameters from day 1 to day 14 after admission. non-survivors demonstrated significant increase in d-dimer and fibrin degradation product as well as prolongation of pt by day 10-14, while fibrinogen and antithrombin activity were significantly lower when compared with survivors [79] . other studies also showed similar findings of a gradual increase in d-dimer levels among non-survivors [13, 34] . pooled results in a metaanalysis including 9 studies revealed that pt and d-dimer levels were significantly higher in patients with severe covid-19 [82] . dynamic change in fibrinogen concentration has also been shown to correlate with an increased risk of death [57] . covid-19 patients with acute respiratory failure presented with severe hypercoagulability due to hyperfibrinogenaemia resulting in increased fibrin formation and polymerization that may predispose to thrombosis [83] . the systemic inflammatory response triggered by viral infection results in an imbalance in homeostatic procoagulant and anticoagulant. cytokine storm, endothelial dysfunction, von willebrand factor elevation, tolllike receptor activation, and tissue-factor pathway activa-6 doi: 10.1159/000510178 tion may contribute to hypercoagulability [84] . overactivation of nadph oxidase-2 (nox2), resulting in increased reactive oxidant species, is implicated in arterial vasoconstriction, clotting, and platelet activation [85] . tang et al. [86] provided data in a retrospective study on 449 patients and showed that anticoagulant with unfractionated heparin (10,000-15,000 u/day) or low-molecular-weight heparin (lmwh, enoxaparin 40-60 mg/ day) reduced mortality in patients with sepsis-induced coagulopathy score (a scoring system including platelet count, pt, and major organ failure assessment) of ≥4 (from 64.2% to 40.0%, p = 0.029) [86, 87] . a 20% reduction in mortality was also seen in patients with d-dimer level 6-fold the upper limit of normal who received anticoagulant [87] . interestingly, no improvement in mortality was seen in anticoagulation therapy for patients with severe pneumonia caused by pathogens other than sars-cov-2 even with high d-dimer level [88] . a brief report showed that 25% of 81 patients with severe covid-19 requiring icu care developed venous thromboembolism (vte) [89] , which may explain the promising results of anticoagulation. in a cohort of 184 patients admitted to the icu who received at least standard doses of thromboprophylaxis, the cumulative incidence of vte and arterial thrombosis was 31% [90] . coagulopathy, defined as spontaneous prolongation of pt > 3 s or aptt > 5 s, was an independent predictor of thrombotic complications (adjusted hr 4.1, 95% ci 1.9-9.1). in another multicentre prospective cohort of 150 patients with ards admitted to icu, 25 (16.7%) of them developed pulmonary embolisms and 3 (2%) developed deep vein thrombosis despite prophylactic or therapeutic anticoagulation [91] . since diagnostic tests were only performed based on clinical suspicion, the actual incidence of thrombosis could have been underestimated. llitjos et al. [92] conducted a retrospective study on 26 patients admitted to icu with systematic screening of vte using complete duplex ultrasound performed on days 1-3 of icu admission, followed by a second scan on day 7 if the first one was negative. the incidence of vte was 69% in the group of patients who received anticoagulation [92] . autopsy of 12 consecutive covid-19 deaths revealed deep vein thrombosis in 7 patients (58%) in whom vte was not suspected before death. pulmonary embolism was the direct cause of death in 4 patients [93] . histologic analysis of pulmonary vessels in 7 patients who died from covid-19 showed widespread thrombosis with microangiopathy and a much higher prevalence of alveolar capillary microthrombi when compared with those who died from influenza-associated respiratory failure [94] . in addition to vte, arterial thromboses such as acute myocardial infarction have been reported [95] . large vessel stroke can be a presenting feature in young patients [96] . in a retrospective study of 214 hospitalized patients from wuhan, 5.7% of the severe patients suffered from acute cerebrovascular disease [97] . hypercoagulability was also demonstrated in icu patients with respiratory failure by thromboelastography [98] . all these findings suggested a pro-coagulant tendency in covid-19 patients, especially if critically ill. middeldorp et al. [99] administered thromboprophylaxis to all patients admitted for covid-19. patients admitted to the general ward received nadroparin 2,850 iu once daily or 5,700 iu for patients with a body weight of ≥100 kg. from april 3 onwards, the dose of anticoagulation in icu patients was doubled. symptomatic vte was detected in 21 out of 75 (28%) icu patients and 4 out of 123 (3.3%) ward patients (sub-distribution hazard ratios 3.9; 95% ci 1.3-12) [99] . lodigiani et al. [100] studied venous and arterial thromboembolic complications in 388 hospitalized patients. thromboprophylaxis was used in all icu patients and 75% of those on the general ward. eight events occurred in icu patients (16.7%; 95% ci 8.7-29.6%), while 20 events occurred in patients on the general ward (6.4%; 95% ci 4.2-9.6%), corresponding to cumulative rates of 27.6 and 6.6%, respectively. importantly, 7 events in the general ward occurred in patients with cancer, highlighting that additional risk factors might further increase the risks of vte [100] . racial difference on thrombotic risk should also be taken into consideration [101] . the international society on thrombosis and haemostasis (isth) suggested all patients (including non-critically ill) who require hospital admission for covid-19 infection should receive a prophylactic dose of lmwh unless contraindicated (table 2 ) [102] . lmwh was the preferred drug of choice due to a high instability of international normalized ratio for vitamin k antagonists and drug-drug interaction between direct oral anticoagulants and anti-viral agents [103] . the american society of hematology (ash) recommended all hospitalized patients with covid-19 should receive pharmacological thromboprophylaxis. if it is contraindicated or unavailable, mechanical prophylaxis should be implemented [104] . however, the recommendations of pharmacological thromboprophylaxis on non-critically ill patients are still controversial [105, 106] . we recommend physicians stay vigilant to thrombotic complication. decision on thromboprophylaxis should also be based on clinical judgement and other risk factors, such as prolonged immobilization, active malignancy, obesity, previous history of vte, and ethnicity. the efficacy, safety, and optimal dosage of anticoagulation in non-critically ill covid-19 patients need to be confirmed by prospective studies. a more recent consensus statement recommended vte risk assessment for non-critically ill patients, and only to consider pharmacological thromboprophylaxis in patients with a moderate to high risk of vte [107] . a significant reduction of blood donations has been reported after the outbreak [108] . possible reasons include lockdown, stay-at-home order, anxiety for volunteer donors to attend blood donation centres, and additional deferral policy on travel history. the number of eligible donors may further decrease if the outbreak continues to evolve. establishment of a crisis system to reduce usage (e.g., deferring elective surgery), coordination of blood products delivery to areas with a shortage, use of social media to promote blood donation, etc. might help to overcome the crisis of paucity in blood supply [109] . if the supply of blood product is limited, there may be a need to adopt a more restrictive blood transfusion approach. transfusion alternatives such as use of iron supplement in iron deficiency anaemia and erythropoiesisstimulating agents should be encouraged. currently there is no reported case of transmission of the coronavirus from donor to recipient through blood product transfusion or cellular therapies, but given that sars-cov-2 rna was detected in the serum of covid-19 patients [30] , the actual risk of transfusion transmission of sars-cov-2 remains unknown [110] . there is no additional screening test for blood donors recommended by the american association of blood banks (aabb) at the moment [111] . use of riboflavin and ultraviolet light-based photochemical treatment to plasma and platelet products may be effective in reducing the theoretical risk of transfusion-transmitted sars-cov-2 [112] . the covid-19 pandemic poses a big challenge for the medical community, with a great impact on management of patients with haematological conditions. in a cohort study of 128 hospitalized subjects with haematological cancers at two centres in wuhan, they have a similar rate of covid-19 compared with normal health care providers but have more severe disease and a higher case fatality rate [113, 114] . non-hospitalized patients with haematological cancers may also have a higher chance of developing symptomatic covid-19. in a study using a questionnaire to evaluate 530 subjects with chronic myeloid leukaemia in hubei, prevalence of covid-19 in chronic myeloid leukaemia patients was 9-fold higher than the 0.1% reported in normal [114, 115] . chemotherapy and transplant schedules have been affected during the outbreak when hospitals are overwhelmed by confirmed covid-19 cases. the huge demand in isolation facilities compromises the care of patients who have received myelosuppressive therapy complicated with profound neutropenia requiring isolation rooms and prolonged hospitalization. treatment may also be deferred due to lockdown, quarantine order, disrupted medical health care service, shortage of isolation bed and blood product, and phobia towards attending hospital. delay in treatment may have a negative impact on the clinical conditions and outcomes of patients, especially those with more aggressive diseases. their need for timely treatment should not be neglected. in general, less essential service should be postponed [116] in order to reduce the number of patients requiring hospital care so as to minimise risk of nosocomial covid-19 infection, to conserve personal protective equipment for high-risk clinical activities, and to maintain the capacity of the health care system. monitor d-dimers, pt, platelet count, and fibrinogen can help to stratify patients who may need admission and close monitoring prophylactic dose lmwh should be given to all patients (including non-critically ill) who require hospital admission unless contraindicated (active bleeding and platelet count <25 × 10 9 /l) transfuse and aim platelet count above 50 × 10 9 /l; fibrinogen above 2.0 g/l; pt <1.5 lmwh, low-molecular-weight heparin; pt, prothrombin time. cheung/law/lui/wong/wong acta haematol 8 doi: 10.1159/000510178 table 3 . suggested strategies in the management of haematological malignancies under covid-19 pandemic [103, [114] [115] [116] disease management recommendation aml induction and consolidation -all patients should be tested for covid-19 prior to initiation of intensive chemotherapy -delay treatment if possible for patients positive for covid-19 -standard induction therapy should be offered to eligible patients -intermediate-dose cytarabine (1.5 g/m 2 ) or decreasing the number of consolidation cycles can be considered in patients who achieve complete remission salvage therapy -intensive re-inductions should be performed according to the algorithms of the individual centre -for patients without proliferative disease or significant transfusion dependence, therapy may be temporarily postponed hsct -consider cryopreservation of donor cells prior to the start of conditioning apl -standard regime including atra and ato should be given -prophylactic dexamethasone should be considered for patients at high risk of differentiation syndrome all induction and consolidation -all patients should be tested for covid-19 prior to initiation of intensive chemotherapy -delay treatment if possible for patients positive for covid-19; intrathecal chemotherapy may be given if cns symptoms are present -philadelphia chromosome negative -proceed with standard curative induction therapy -dose reduction may be considered for patients at high risk for complications -philadelphia chromosome positive -consider tki with minimal steroid exposure as initial treatment salvage therapy -treatment that can be administered at outpatient setting such as inotuzumab or blinatumomab should be considered for b-all hsct -allogeneic hsct should be considered for patient who achieved cr2 despite the pandemic aggressive lymphoma -standard regime such as r-chop for diffuse large b-cell lymphoma and da-epoch-r for double-hit and primary mediastinal b-cell lymphomas should be offered -dose reduction or limiting treatment cycle can be considered for elderly or early stage disease -consider subcutaneous rituximab to reduce patient's time spent in clinical area -for relapse/refractory disease, admission for asct may be delayed if another cycle of outpatient chemotherapy can be administered indolent lymphoma -treatment deferral with close monitoring is recommended for asymptomatic patients -when treatment is indicated, consider rituximab monotherapy rather than chemoimmunotherapy -treatment options that minimize clinic or chemotherapy unit visits are preferred hl initial therapy -strategies to reduce the risk of bleomycin pneumonitis should be prioritized especially during the pandemic -standard treatment such as abvd, aavd, and radiotherapy should be given general recommendation -patients should be tested for covid-19 before hospital admission, starting a new treatment, cell apheresis, or asct in countries with high spread of sars-cov-2 -treatment re-schedule and de-intensification can be considered for responding patients -patients receiving bisphosphonates should reduce frequency of drug infusion to every 3 months or temporarily withheld transplant eligible -bortezomib, lenalidomide, or daratumumab-based triplet therapy for 6-12 cycles should be offered -for patients with standard risk disease, delay asct by additional induction cycles and/or lenalidomide maintenance -patients with high-risk disease may proceed with asct after exclusion of covid-19 infection transplant ineligible -dexamethasone should be reduced to 20 mg weekly -all-oral drug combinations, e.g., lenalidomide with dexamethasone, are preferred -addition of bortezomib or daratumumab can be considered for patients with high-risk disease relapsed/refractory -watchful waiting may be considered for biochemical relapses -orally administered agents (such as ixazomib, lenalidomide, pomalidomide, and panobinostat) should be considered -modify treatment regime to minimize clinic/hospital visit, such as once weekly instead of twice weekly bortezomib/ carfilzomib and monthly daratumumab infusions are recommended confirmed covid-19 -if anti-myeloma treatment has been started, therapy might be continued for asymptomatic covid-19 infection, although pausing of treatment is also an option; steroids and drugs inducing lymphopenia should be de-intensified -for symptomatic infection, treatment should be interrupted and steroids should be tapered to zero until full recovery from covid-19 aavd, brentuximab vedotin, adriamycin, vinblastine, dacarbazine; abvd, adriamycin, bleomycin, vinblastine, dacarbazine; all, acute lymphoblastic leukaemia; aml, acute myeloid leukaemia; apl, acute promyelocytic leukaemia; asct, autologous stem cell transplantation; atra, all-trans-retinoic acid; ato, arsenic trioxide; bcr, b-cell receptor; cll, chronic lymphocytic leukaemia; cml, chronic myeloid leukaemia; cns, central nervous system; cr, complete remission; da-epoch-r, dose-adjusted etoposide, prednisolone, vincristine, cyclophosphamide, doxorubicin-rituximab; hl, hodgkin lymphoma; hsct, haematopoietic stem cell transplantation; mm, multiple myeloma; nhl, non-hodgkin lymphoma; pd-1, programmed cell death protein 1; r-chop, rituximabcyclophosphamide, doxorubicin, vincristine, prednisolone; tfr, treatment-free remission; tki, tyrosine kinase inhibitor. life-saving chemotherapy for conditions such as acute leukaemia or aggressive lymphoma should not be delayed. watchful waiting approach may be considered for patients with indolent diseases if the risk of severe co-vid-19 infection outweighs treatment benefit, while single-agent monoclonal antibody instead of combination chemoimmunotherapy can be considered in patients who require treatment. oral formulation is preferred to intravenous injection to minimize hospital visit. prioritization and triage of anti-cancer therapy should be based on disease-and patient-specific considerations through communication with specialists and patients [117] . recommendations on induction, consolidation, and salvage therapies on haematological malignancy during the pandemic by the ash, european hematology association (eha), and international myeloma society are summarized in table 3 [104, [118] [119] [120] . primary prophylaxis using g-csf in patients receiving intensive chemotherapy reduces the risk of febrile neutropenia and the risk of hospitalization and thus should be considered [121, 122] . effective non-immunosuppressive treatments, such as intravenous immunoglobulin and thrombopoietin receptor agonists, may be considered in lieu of high-dose steroid for patients with immune thrombocytopenia purpura and severe thrombocytopenia. if patients are stable on low doses of immunosuppressive drugs, no modification of drug regimen is needed. infection prevention measures such as hand hygiene in ambulatory chemotherapy centres or clinics should be implemented. screening procedures, including questionnaire on respiratory symptoms, travel and contact history, and measuring of body temperature, should be performed for patients and hospital visitors [123] . patients may benefit from increased surveillance of sars-cov-2 infection and protective isolation [113] [114] [115] . psychosocial support should be provided where possible, when measures of social distancing might have affected the well-being of patients with haematological malignancies. great obstacles on allogeneic haematopoietic stem cell transplantation have been encountered during the co-vid-19 outbreak. closure of international borders, travel restriction, and shutdown of air travel has affected international donor travel and the shipping of cellular products. cryopreserved stem cell transplantation during the pandemic can be considered if alternative cellular products or donors are not available and does not appear to have a negative impact on the long-term outcome [124, 125] . appropriate measures such as home quarantine and screening of donors for covid-19 prior to donation should be implemented in areas with a high frequency of sars-cov-2 infection [126] . all transplant recipients should also be tested negative for sars-cov-2 irrespective of respiratory symptoms before initiating conditioning chemotherapy [127] . treatment cycles may be increased to achieve a deeper remission before proceeding to allogeneic haematopoietic stem cell transplantation. the european society for blood and marrow transplantation (ebmt) proposed suggestions on haematopoietic stem cell transplantation during the covid-19 pandemic, which is shown in table 4 [127] . in summary, the covid-19 disease has had notable haematological manifestations. lymphopenia, thrombocytopenia, and coagulation abnormalities on presentation and during the disease courses have been associated with poor outcomes, and serial monitoring is recommended. physicians should stay vigilant against vte and for transplant candidate ---for confirmed covid-19 patients with high-risk malignancy, hsct should be deferred for a minimum of 14 days until the patient is asymptomatic and has two negative virus pcr swabs taken at least 24 h apart in patients infected with covid-19 with low-risk malignancy, a 3-month hsct deferral is recommended for patients who had close contact with a person diagnosed with covid-19, any transplant procedures (pbsc mobilization, bm harvest, conditioning) shall not be performed within at least 14 days from the last contact for donor ---donors should have been asymptomatic for at least 14 days before donation and a negative test for covid-19 is recommended in case of diagnosis of covid-19, donor should be excluded from donation. stem cell collection should be deferred for at least 28 days after recovery. if the recipient's need for transplant is urgent and the donor is completely well and there are no suitable alternative donors, an earlier collection may be considered if local public health requirements permit, subject to careful risk assessment in case of close contact with a person 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related and unrelated donors is associated with delayed platelet engraftment but has no impact on survival long-term follow-up of leukaemia patients after related cryopreserved allogeneic bone marrow transplantation coronavirus and haematopoietic stem cell transplantation. worldwide network for blood & marrow transplantation. wbmt coronavirus disease covid-19: european society for blood and marrow transplantation (ebmt) recommendations update the authors have no relevant conflict of interest to disclose. carmen k.m. cheung: acquisition, analysis, and interpretation of data/references; drafting and approving the manuscript. man fai law: acquisition, analysis, and interpretation of data/references; drafting and approving the manuscript. grace c.y. lui: analysis, interpretation of data/references; revising critically and approving the manuscript. sunny hei wong: analysis, interpretation of data/references; revising critically and approving the manuscript. raymond s.m. wong: analysis, interpretation of data/references; drafting, revising critically, and approving the manuscript. key: cord-333262-xvfl7ycj authors: robson, b. title: covid-19 coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 journal: comput biol med doi: 10.1016/j.compbiomed.2020.103749 sha: doc_id: 333262 cord_uid: xvfl7ycj abstract this paper continues a recent study of the spike protein sequence of the covid-19 virus (sars-cov-2). it is also in part an introductory review to relevant computational techniques for tackling viral threats, using covid-19 as an example. q-uel tools for facilitating access to knowledge and bioinformatics tools were again used for efficiency, but the focus in this paper is even more on the virus. subsequence krsfiedllfnkv of the s2′ spike glycoprotein proteolytic cleavage site continues to appear important. here it is shown to be recognizable in the common cold coronaviruses, avian coronaviruses and possibly as traces in the nidoviruses of reptiles and fish. its function or functions thus seem important to the coronaviruses. it might represent sars-cov-2 achilles’ heel, less likely to acquire resistance by mutation, as has happened in some early sars vaccine studies discussed in the previous paper. preliminary conformational analysis of the receptor (ace2) binding site of the spike protein is carried suggesting that while it is somewhat conserved, it appears to be more variable than krsfiedllfnkv. however compounds like emodin that inhibit sars entry, apparently by binding ace2, might also have functions at several different human protein binding studies. the enzyme 11β-hydroxysteroid dehydrogenase type 1 is again argued to be a convenient model pharmacophore perhaps representing an ensemble of targets, and it is noted that it occurs both in lung and alimentary tract. perhaps it benefits the virus to block an inflammatory response by inhibiting the dehydrogenase, but a fairly complex web involves several possible targets. coronaviruses have been known to medicine for some time [1] , but it is of course only very recently that the coronavirus sars-cov-2, the covid-19 virus new and dangerous to humans, was identified. it is believed to be related to an initial cluster of pneumonia cases associated with a seafood and fresh meat market in wuhan, china, [2] . current case rates at the time of writing are close to one million with close to 60,000 deaths. the genomic relationships to other coronaviruses were quickly examined by lu et al. to shed light on the origins, epidemiology, and receptor binding of the virus [2] . on january 17th , 2019, the wuhan isolate genbank entry mn908947.3 replaced mn908947.2, and mn908947.3 probably represents an adequate stable description of the sequence for research into that strain isolate, and was immediately investigated by the present author [3, 4] . originally, it was seen by authorities as a coronavirus outbreak but not as sars (severe acute respiratory syndrome). however, its genomic relationships examined in refs [3, 4] also showed many fairly close correlations with the genomes of sars-cov in the previous human (but not pandemic) outbreaks and in pigs, bats and civets, and the emphasis was on finding subsequences that are well conserved across coronavirus strains and species. the earliest patients suffering from what is now called covid-19 had overall 99·98% genome sequence identity to the above wuhan isolate, so that one may reasonably say that it is the origin of covid-19, and its virus sars-cov-2 [2] . the earlier wuhan isolates also related (with 88% identity) to two bat-derived severe acute respiratory syndrome (sars)-like coronaviruses collected in 2018 in zhoushan, china, but differed more from sars-cov (at about 79%) and mers-cov (at about 50%) [2] . the wuhan and related isolates revealed a coronavirus that resides in the subgenus sarbecovirus of the genus betacoronavirus [2] , and although genetically distinct from its predecessor sars-cov it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. see section 1.3 below for introduction to this protein, which also discusses some further early identified genomic correlations. in addition, the rest of this present paper discusses many other genomic relationships relevant to the design of synthetic vaccines and therapeutic antagonists againstcovid-19. one problem is that covid-19 is a new pathogen posing a global threat and so presents new challenges both in primary prevention, where a vaccine is required, and in secondary prevention, where a therapeutic compound (ideally, "in a pill") is required to treat patients who are infected. it might also present challenges for tertiary prevention, which seeks to remedy a persistent level of infection, or to prevent recurrence even to essentially the same strain, as discussed in section 1.2. a main problem of concern, and a point of the present paper, is the likely appearance of new strains with resistance to vaccines and therapeutic agents. at the time of writing, confirmed cases double globally every 6 days, and undetected cases are expected to be much higher (the current plateauing of reported cases in china offers a glimpse that this this should attenuate soon, but estimates of how and when are varied). with a significant portion of humanity already infected, there is enhanced probability of successful "escape mutations" in the genome of the virus. development of vaccines and perhaps particularly therapeutics that could, but do not, take account of this by targeting less variable protein regions could be a huge waste of resource and a dangerous delay. covid-19 is, of course, by far the most serious, but not the first sars outbreak of concern to humans, and coronaviruses have for decades been of veterinary concern [1] . however, it still remains true that zoonotic coronaviruses have only rather recently seriously impacted humans, as far as is known. they include sars-cov (2002, betacoronavirus, subgenus sarbecovirus), and mers-cov (2012, betacoronavirus, subgenus merbecovirus). although the idea that sars-cov-2 was distinct from sars-cov was originally discouraged, distinction is here a matter of degree. by usual criteria they are fairly closely related, genetically clustering within betacoronavirus subgenus sarbecovirus. until very recently, sars-cov, effectively sars-cov-1, was the primary reference point and model regarding molecular and functional details, and it remains important. shortly after the appearance in genbank of the apparently final version of the wuhan seafood market isolate mn908947.3 [2] , the present author compared a variety of coronavirus genomes [3, 4] . the krsfiedllfnkv protein subsequence was seen as a potential achilles' heel because it is exposed or potentially exposable, being required for proteolytic activation cleavage, and importantly is also a well-conserved feature on the surface of the virus [3, 4] . being well conserved suggests that mutations are much less easily "accepted", meaning that the virus is less likely to survive more than one or two generations. as discussed below, the conservation is in a region of protein on the virus surface concerned with at least one step of lung cell entry, interesting because coronaviruses seem to be able readily adjust to alternative means of entry, possibly hinting at additional roles for the subsequence. whether or not that is the case, the above motif seems a likely primary target for synthetic vaccines and a basis for drug discovery, and was proposed as such [3, 4] . it is a motif that was found to be quite well conserved even in more distantly related coronaviruses [3, 4] , and the present paper also explores how far that seems to extend. it includes the common cold coronaviruses. another potential subsequence of interest popular with researchers is also examined (the ace2 binding domain discussed below), but the above remains popular with the present author because of its relatively high degree of conservation. present authors' opinion, however, it relates to a specter that recently haunted covid-19 vaccine research, and which might still cause some concerns. this is the question of why there is no significant immunity acquired by the body to prevent recurrence of common cold, of which up to roughly 30% of cases are believed to be due to coronaviruses. fortunately, at time of final writing of this paper, news reports indicate that neutralizing antibodies can be found in patients who have had covid-19. however, with the risks of escape mutations of the virus in mind, it remains worthwhile considering whether the subsequence krsfiedllfnkv, again, found to be well conserved [3, 4] across many coronaviruses [3, 4] , is still present in common cold coronavirus. this is in order to force better immune response by targeting using synthetic or cloned vaccines with this epitope. most common cold strains fall into one of two coronavirus serotypes: oc43-like and 229e-like, which are the main examples discussed below. while the common cold is generally considered as mainly an upper respiratory tract infection and a mundane inconvenience, common human coronaviruses betacoronavirus hcov-oc43 and hcov-hku1, as well as alphacoronavirus hcov-229e, also cause severe lower respiratory tract infections in children and the elderly. some discussion is also given to hcov-hku1 in this paper. the above motif krsfiedllfnkv occurs in the spike glycoprotein [4] responsible for initial binding of previous sars coronaviruses to lung cells and their activation of the spike protein by a proteolytic cleavage [5] [6] [7] . the spike glycoprotein (or just "spike protein") is the familiar spike that studs the surface of the coronavirus, giving it the appearance of a crown to electron microscopy, hence "corona" (latin: crown). after the completion of the first version of the previous paper [3] , a bat virus with 97.41% identity of the amino acid sequence of the spike protein discussed extensively in the present paper, was entered into genbank as entry qhr63300.1. as of the time of final writing this on april 2 nd 2020, there is 100% match of this protein with entry yp_009724390.1 that appears to be a same or similar to the above wuhan isolate. the top hundred nonredundant matching entries found using mn908947.3 by blastp at https://blast.ncbi.nlm.nih.gov/blast.cgi (see below) for mn908947.3 spike protein used here vary from the above 100% match down to 75 .80%, such as aau04646.1, which is a civet isolate. in viruses, proteins of a similar protruding nature, e.g. the hemagglutinin of influenza a, are primary targets for vaccine development, and important targets for development of therapeutic drugs that seek to block the virus from infecting host cells. at the time of the current project, only the three dimensional structures of the sars-cov spike proteins of the earlier sars outbreak was known (e.g. ref [8] ), which has only 75%-81% sequence match to sars-cov-2 [3] . note that it is customary to write sars-cov rather than sars-cov-1. rna viruses mutate with high frequency but so far the differences in spike proteins in emergent sars-cov-2 variants are much less. at the time of the study in late february and early march 2020, the amino acid residue sequences of the spike proteins of covid-19 isolates from different states and countries, such as california, brazil, taiwan, and india, remain identical or almost so. for example, with respect to the original wuhan isolate [2] , phenylalanine (f) is replaced by cysteine (c) as residue 797 in a swedish isolate, and alanine (a) is replaced by valine (v) as residue 990 in an indian isolate. as of 21 st march 2020, largest variants in the sars-cov-2 genome as a whole show 99.9% nucleotide sequence match, which for a genome of 29,858 rna bases, suggests approximately 30 base changes, and of the order of 5 in the spike glycoprotein gene of 3821 nucleotides. that then suggests roughly 1 to 3 amino acid differences in the spike protein of current (march 2020) sars-cov-2 variants, consistent with the above more specific observations of isolates from california etc. a single amino acid change can, of course, sometimes have significant effect, e.g. on the aggressive character of a coronavirus, and so be considered as creating a new strain. some new strains are being reported at the time of writing, but to the author's knowledge none of them are spike protein variations, and more specifically none are as yet in the krsfiedllfnkv subsequence. the left hand side of fig. 1 shows the sars-cov (previous sars) s1 spike glycoprotein within the trimer that makes up the spike. the right hand side shows sars-cov-2, the sars of current concern. all human sars coronaviruses (and indeed the spike proteins of many other related coronaviruses) appear similar in overall conformation, and the variations seen in experimental structures are probably more to do with crystallization or other preparation methods, particularly regarding solvent details and ligands. sars-cov, on the left, has been well studied and still serves as the reference model. in order to fuse with and infect cells, the spike protein needs to be in an open state; presumably the closed state makes it less vulnerable to antibodies. on the left, fig. 1 also shows the approximate positions of the cleavage points superimposed on the protein data bank (pdb) entry 5xlr for sars-cov. reading from the n-terminus of s1, the important functional elements of sars coronaviruses deduced from sars-cov studies [5, 6] and applicable to sars-cov-2 are the s1 nterminal domain (s1-ntd), the s1 c-terminal domain (s1-ctd), the s1/s2 site as the first protease cleavage site as a loop between a pleated sheet and a-helix, the fusion peptide (fp) associated with a highly disordered loop between two a-helices which contains the second cleavage site s2', and a heptad repeat (hr). the arginine (r) in the conserved motif krsfiedllfnkv that was of interest in the previous study [2] is the cleavage point in s2'. recall that the krsfiedllfnkv subsequence associated with s2' is potentially important, not least because it must be exposed or exposable (because it permits proteolytic cleavage) and therefore the site cannot be well shielded. the experimental three dimensional structures of coronavirus spike proteins do not for the most part reveal the large amount of glycosylation that protects most of the spike protein surface. possibly the major problem, however, is not so much in the selection of accessible surface regions as a basis for design entry inhibitor and vaccine design [8, 9] but that the coronavirus readily escapes from such agents by mutation, including in the spike protein [10, 11] . this is the further importance of being a highly conserved motif, i.e. a subsequence that does not readily change from strain to strain except for a conservative sidechain replacement in more remote strains. of course, as one carries the study forward to more distantly related viruses, one expects the motif to differ at some stage, and this is investigated later below. in contrast, nonetheless, the pigag motif "associate with the s1/s2 cleavage site disappears in coronaviruses that are not too distantly related [3, 4] . as noted above, a high degree of conservation of krsfiedllfnkv in the face of genetic indicates that it is in some way important to the virus, presumably for the proteolytic activation cleavage, and/or initial binding to lung cells, but there could be other interactions with other proteins, i.e. to reduce an inflammatory response, as discussed later below. agents. modern computer-driven strategies, and the kind of chemical products that they help produce, differ substantially from the earlier and more familiar approaches in which the computer played little if any role. in large part this is due to the invention of automatable peptide synthesis by merrifield in 1963, who used solid phase peptide synthesis based on crosslinked polystyrene beads [12] . traditional vaccines are purely biological, being composed of dead or attenuated strains of pathogen (meaning mainly, viruses and bacteria). in contrast, a synthetic vaccine is a vaccine consisting mainly of synthetic peptides but also sometimes carbohydrates, often linked to a carrier protein to render it immunogenic. such vaccines produced via chemical synthesis are safer because they do not involve cell-derived material or biological processes for production. their purity can be controlled as in the case of classical drugs. the world's first synthetic vaccine was created in 1982 from diphtheria toxin by louis chedid (scientist) from the pasteur institute and michael sela from the weizmann institute. in 1986, manuel elkin patarroyo created spf66, the first version of a synthetic vaccine for malaria. primarily applications so far have been veterinary. many early vaccines used dead samples of foot and mouth disease virus to inoculate animals, but they caused real outbreaks. scientists discovered that a vaccine could be made using only a single key protein from the virus, and later also found that loops from the surface proteins could be cloned or used in cloned or synthetic constructs. novartis vaccine and diagnostics, among other companies, developed a synthetic approach that very rapidly generates vaccine viruses from amino acid sequence data in order to be able to administer vaccinations early in a pandemic outbreak. traditional vaccines have so far remained the popular choice, but during the h1n1 outbreak in 2009, they only became available in large quantities after the peak of human infections. this was a learning experience for vaccine companies. creating vaccines synthetically would be currently more expensive but has the ability to increase the speed of production and to retune and fine tune the solution to combat new variations in pathogens. this is all especially important in the event of a pandemic. synthetic vaccines are also considered to be safer by researchers than vaccines grown from e.g. eggs or from bacterial cultures (in the latter case there may even be other viruses present). cloned proteins can however reflect the same desirable principles; regions of pathogen amino acid sequence acting as epitopes (see below) can be presented as loops at the surface of a cloned protein. the general idea is that synthetic vaccines are freer of contaminants and focus on the essential features of the required immune response. they can also be developed in a more logical step by step approach. for example, sometimes diagnostics are considered as a useful early step on the way to a vaccine, since they are only required to raise antibodies in animals such as sheep for diagnostic kit production, not to be safe in humans and also raise immune system memory and a cellular as well as antibody response. synthetic vaccines also have the advantage that they can be seen as cartridge vaccines, meaning that they contain bits and pieces that can readily be replaced by others to update the vaccine in order to combat new strains of pathogen. a synthetic vaccine thus has several functional components, looking somewhat like a swiss army knife under the electron microscope. the key component reproduces the essential features of a pathogen protein that the immune system sees. it is an epitope that typically means a patch of some 5 to 20 amino acid residues. reproduced as a short peptide, epitopes can be considered as haptens. haptens are substances with a low molecular weight such as peptides, small proteins and drug molecules that are generally not immunogenic and require the aid of a carrier protein to stimulate a response from the immune system in the form of antibody production. there are two main types of epitope, b and t, discussed in theory section 2. a synthetic vaccine consists of t-epitopes as haptens (for cell response and immune system memory), molecular adjuvant (e.g. muramyl dipeptide), and possibly excitatory or anti-inhibitory peptides. b-epitopes are good for raising antibodies in e.g. sheep to use in diagnostics/biosensors, all attached to, or cloned into, a carrier protein. the latter must be safe but at the same time sufficiently different from any human protein to avoid autoimmune disease. used extensively as a carrier protein in the production of antibodies for research, biotechnology and therapeutic applications, keyhole limpet hemocyanin (klh) is the most widely employed carrier protein, and least for studies using laboratory animals. for humans the food and drug authorities may have other preferences for carrier protein, but klh illustrates the desired features. its large size and numerous epitopes generate a substantial immune response, and abundance of lysine residues for coupling haptens allows a high hapten:carrier protein ratio, increasing the likelihood of generating hapten-specific antibodies. because klh is derived from the limpet, a gastropod, it is phylogenetically distant from mammalian proteins, thus reducing false positives in immunologically-based research techniques in mammalian model organisms, and clinically avoiding autoimmune effects. so far, the food and drug authorities do not seem to have favored synthetic vaccines for human use, but this may be more to do with the peptides themselves than the carrier proteins available. the earlier methods of peptide synthesis did not achieve high levels of purity. however, this has changed and quite elaborate peptides as well as proteins can be made, facilitated by making peptide synthesizers run fast to avoid the slower side reactions, and by methods that join shorter synthetic peptides into longer chains [43] [44] [45] [46] . one of the original motivations for the present study was to capture experience and design strategies from vaccine, diagnostic and antagonist design [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] . methods by the author and colleagues ranged from the expert system approach to automated bioinformatics and protein modeling [26] [27] [28] and automated drug design (e.g. refs [29] [30] [31] [32] ). see also ref [33] . more recently there has been an automated approach based on the proposed q-uel language [34] [35] [36] [37] . the more fine-grained principles for the design of synthetic peptide vaccines, and antagonist peptides made of d-amino acids, are discussed in some detail in the previous paper [3] . a variety of bioinformatics techniques are available to help in development of these solutions (e.g. ref [38] [39] [40] [41] [42] ), as well as computational (e.g. refs [33] ) and synthetic techniques (e.g. ref [43] ). the q-uel language [33] [34] [35] [36] [37] used in the preceding work [3] is also a means of gathering relevant information from the world wide web efficiently when encountering a new problem such as an epidemic caused by a new virus, or at least a problem new to the researcher [3, 4, 38] . it also enables more automated interaction with websites for publically available bioinformatics tools. the motivation for this was all the stronger because the popular highly integrated approach to bioinformatics' called the biology workbench at the university of san diego supercomputer center has been no longer available for some time [39] . however, the standard bioinformatics tools (e.g. refs [40] [41] [42] ) used in the present study can of course be used readily by researchers reasonably experienced in bioinformatics. although peptidomimetics (containing amino acids that would not occur in normal ribosome-based biosynthesis) have been considered by authors as a basis for haptens in synthetic vaccines, they are in the author's opinion probably best considered as potential therapeutic antagonists. in the present study, the specific aims include design of molecules to impede binding and activation of the spike glycoprotein at the surface of lung cells [5] [6] [7] . synthetic peptides copied from subsequences in the spike protein could be used directly for such clinical purposes, but then an important design step would be to render them resistant to biodegradation by human proteases. this is typically by inclusion of d-amino acid residues [44] [45] [46] [47] . previously, in the author's personal opinion, peptides and peptidiomimetics have been currently best considered as first steps in the research and development of small organic "in a pill molecules" of the traditional kind favored the by the pharmaceutical industry. their role there nonetheless is a powerful one, linking amino acid sequences seen in nature, conveniently already "designed" by millions of years of evolution, to (typically) smaller novel organic molecules designed to have van-der-waal's and electrostatic features in the binding site. however, the author's reticence has been largely based on cost, including cost in changing traditional production strategy, and in the reservations of food and drug authorities, but fairly recently all that appears to be changing. thpdb (http://crdd.osdd.net/raghava/thpdb/) includes an example of a manually curated repository of peptides and related molecules approved by the us food and drug administration (fda). over some 70 peptide drugs are approved in the us and other major markets, and those in pipelines and in or approaching clinical trials may now be exceeding 200 entries. as natural compounds, peptide drugs are typically less toxic than more traditional chemical candidates. although d-amino acids are not natural features of ribosomal production of peptides and proteins, human metabolism can handle them. they occur in gut microbes and ingested material and in human proteins they form spontaneously in a kind of aging process from some amino acids in situ in protein sequences (e.g. l to d-aspartate). diverse d-amino acids such as d-serine, d-aspartate, d-alanine, and d-cysteine are found as free amino acids and small peptides as well as in some proteins, and quite commonly in mammals. they are often found having playing important roles in the nervous system. for example, n-methyl-daspartate (nmda) receptors are associated with learning and memory and d-serine, daspartate, and d-alanine bind to those receptors. hydrogen sulfide generated from dcysteine reduces disulfide bonds in receptors and potentiates their activity. peptides made of d-amino acids resist not only normal proteolytic degradation but also resist an immune response (unless attached to a carry protein) [44, 46] . they persist some 4-6 days in the body, which is an ideal time period for pharmaceutical action, and are ultimately degraded to safe products (probably mainly in the peroxisomes and by enzymes in the kidneys) [44, 46] . the negative aspect is that they do have higher entropy to overcome than many drugs of more traditional form, but in practice this appears to be more a barrier to computer simulation of binding than to the real molecule, as extensively discussed below. studying the binding of synthetic peptides or small organic molecules to human proteins benefits from computer simulations of the solute-solvent system, and it was early found that these should ideally include water molecules in a detailed way because there are hydrogen bonding options between water molecules and amino acid residues which are not particularly intuitive [48, 49] . in most cases, the spatial locations of hydrogen atoms are deduced rather than seen in experimental protein and peptide three dimensional structures. this is likely to impact considerations of docking ligands to protein targets. in the present author's opinion, this provides a beneficial possibility for retroinverso designs [3] made by reversing the sequence and using d-amino acids that has the unfortunate or complicating effect of interchanging the c=o and n-h groups in the backbone of the synthetic peptide [3] . the beneficial possibility is that, for example, a repulsive c=o…o=c electrostatic interaction between a synthetic peptide and the spike protein could be ameliorated in the manner c=o…h…o=c where the h is a water, serine or threonine hydrogen atom, or by c=o…h-o-h…o=c, albeit that in practice the water molecule likely lies more to the side of the o..o interaction vector. somewhat similar considerations apply to any n-h…h-n interactions that can ameliorated by the lone pair orbitals of an oxygen atom. both could also involve tautomerization and/or rearrangement of internal hydrogen bonding networks (e.g. in the manner …o-h…o-h…. to …h-o..h-o…). today, to take care of such matters, researchers consider docking of ligand to protein and high grade molecular dynamics simulations of the overall solute-solvent system by molecular dynamics, at least as the final refinement step [50] , but even the awareness that the above compensations and others can take place can make it worthwhile to synthesize and test a proposal. somewhat similarly, design of peptide synthetic vaccines and diagnostics can make direct use of peptides duplicating sequence motifs in the pathogen protein found by bioinformatics and relatively simple computational tools. after that, researchers often go straight to synthesis and experimental immunological testing of the constructs rather than using complex simulations [51] [52] [53] . epitope predictions for sars-cov-2 (simply meaning the choice of amino acid residue subsequences to synthesize for synthetic vaccines, but also for peptidomimetic antagonists) have been made by several authors (e.g. ref [54] ). they have typically made use of extensive historical experimental data about the amino acid residue sequences of epitopes such as the epitope database and analysis resource (iedb) and the virus pathogen resource (vipr) (e.g. ref [54] ). the immune system by its nature can make its own adjustments to recognize pathogens and vaccines, but designing some kind of therapeutic antagonist against virus binding to the lung cells requires rather more consideration about what human protein the spike protein is binding. bioinformatics as the study of biosequences is a powerful tool, but it is well known that having the detailed three dimensional structure of the human protein target for a potential new pharmaceutical agent, or to which a virus attaches, is a great benefit to rational computer-aided design. studies specifically investigating human protein binding and activation of previously known sars viruses have for some years been carried out by several groups (e.g. [54] [55] [56] [57] ). it seems reasonably well agreed that angiotensin converting enzyme type 2 (ace2) is responsible for binding the sars associated with the 2002 outbreak, combined with a proteolytic cleavage to activate the spike protein, for which type ii transmembrane serine protease (tmprss2) is the current popular candidate [3] . several three dimensional structures are known for ace2 complexed with sars spike protein e.g. protein data bank (pdb) entry (6acg) and of variants of the latter (e.g. tmprss2 protein data bank entry 2oq5). however, the full story involving human cell surface proteins (with which sars-cov-2 interacts in order to infect and replicate) is possibly not quite as firmly established at the time of this present study as some summaries would suggest. the origin of the general problem for a more detailed conformational chemistry approach is that diversity of genome and means of infecting cells are readily generated in nature in the case of different virus hosts, virus strains, and species jumps, and it is long established that the binding shows variation in the receptors used that correspond to viral groups. there have been alternative proposed candidates for initial binding receptors, e.g. carcinoembryonic antigen-related cell adhesion molecule 1 (ceacam1), and various dipeptidyl peptidases. highly virulent coronaviruses that form syncytia between cells can even spread in a receptor-independent fashion. even when an initial binding receptor such as ace2 is identified for a coronavirus, initial uncertainty or enduring complexity for the rest of the entry process may be the norm. many other human proteases present in the lung seem capable of cleaving various sites on the spike protein and which could cause its activation. for example, a variety of proteases such as trypsin, tryptase clara, mini-plasmin, human airway trypsin-like protease (hat), and tmprss2 (transmembrane protease, serine 2) are known to cleave the glycoprotein hemagglutinin (ha) of influenza a viruses as prerequisite for the fusion between viral and host cell membranes and viral cell entry. human airway trypsin like protease (hat), tmprss3, tmprss4, tmprss6 have also all been considered by sars researchers at various stages. other human proteins that might have similar involvement to the above in the sars-cov-2 case, and that are also affected by the same antagonists against the sars-cov-2 targets in the preceding paragraph, have also attracted the attention of researchers. the trypsin-like serine protease hepsin which has a fairly broad action and which is significantly inhibited by a diverse set of ligands, a particular example of one such binding is represented by protein data bank entry 5ce1. even intracellular proteases could be released on cell damage resulting from the first wave of lung infection or from other disease or tissue trauma. some variants and strains may use other, as yet unknown, proteins, or sugars, to assist entry. it is also plausible the spike protein might be activated by other proteases on exit from the epithelial lung cells, so allowing it efficiently to infect other cells. the spike glycoprotein of sars-cov-2 also has the so-called furin cleavage sequence (prrars or prrars), which is an extension to the so-called pigag motif of ref [3] . consistent with the present author's preferred choice of krsfiedllfnkv motif, coronaviruses with high sequence homology (such as that isolated from a bat in yunnan in 2013), lack the furin cleavage sequence. nonetheless, because furin proteases are abundant in the respiratory tract, sars-cov-2 spike glycoprotein might be cleaved on exit from cells. even if the means of binding, activation and entry is well established for a viral strain, recall that a single rna base difference resulting in a single amino acid residue difference could alter all that, and there also appear to be several other possibilities that the virus can exploit in parallel. indeed, somewhat similarly, potential inhibitors of sars entry and/or activation proposed by researchers (e.g. refs [55] [56] [57] [58] [59] [60] [61] ) may work by several routes in parallel, and significantly at least three mechanisms were reported in one relevant study [61] . once a target protein and its relevant binding site are clearly understood, methods are available for screening available ligands (binding molecules) to bind to those sites as potential antagonists, or even for "growing" or evolving antagonist molecules in those sites, whether smaller organic molecules [29] [30] [31] or peptides [32] . pharmaceutical chemists have long used evidence and hunches to deduce a pharmacophore, i.e. an abstract description of recurrent molecular features that are necessary for molecular recognition of the ligand by the protein [3] . a pharmacophore ultimately implies at least a schematic model of the interfacial surface between ligand and protein, but in practice, a pharmacophore tends to be either considered from the perception of the ligand (one compares similar inhibitors etc.) or from the perception of the binding site (one compares positions of key residues in the binding site). the choice depends on the quality of each kind of data, but could involve both. historically, drug design was frequently based only on indirect deduction of binding site features using the chemical features of the ligands which successfully inhibit (or in a few instances excite) a response. this is essentially the use of quantitative structure activity relationships (qsar). in effect the perception of the binding site was indirect and typically based on the chemist's expertise and hunches, and so often extremely "fuzzy". subsequent elucidation of many protein structures with clear pictures of their binding sites led to a crisper physical perspective, exemplified by a study [50] that included many ligand molecules in the present investigation, and so faced some similar issues. in the approach which may now be considered traditional, docking calculations are fast, using grid maps that consist of a three dimensional lattice of regularly spaced points, centered on some region of interest of the protein target under study. as discussed above, ace2 and tmprss2 are very likely correct targets, but again they are not necessarily the only targets even for cell entry of current sars-cov-2, and the mechanisms used by each new coronavirus strain can differ, as the result of even a single amino acid residue change. in such circumstances, the conservation of the krsfiedllfnkv motif might be considered suspicious. the activation cleavage is at the arginine (r) and workers tend to conclude that this site is more essential for action than s1/s2, and mutation of the arginine (r) specifically inhibits trypsindependent fusion in both cell-cell fusion and laboratory assays. but also, with the arginine retained, many other proteases can active the spike protein as above, and others can do so in laboratory conditions. because of the conservation, one might therefore hold the seemingly reasonable hypothesis that this site is not also susceptible to cleavage and activation by other extracellular proteolytic enzymes, but also doing something else. whether or not this is so, all this complexity makes detailed interaction models of spike protein binding and activation difficult, and while the "best bet" for ranking the choices of target protein may currently seem obvious, making a reasonable, currently conventional, choice which is actually an incorrect assumption can delay productive research into therapeutic agents. in the case of the hunt for prevention and cure of virus diseases, and particularly covid-19, there seems to be increased justification for a "fuzzier" set-theoretic picture of a pharmacophore as an ensemble of different binding sites, or of ligands in a ligand-oriented perspective, as follows. many of these, and perhaps all, suggest that even if one is using an incorrect picture of the mechanisms of entry and replication, even using the "wrong" or less important protein target, one might achieve some success. in brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). to the above may be of course added the fact that even if an experimental researcher is convinced of the value a specific protein as appropriate target, the picture for the computational chemist is a fuzzy one. the system itself, real and simulated, is to be seen as a statistical mechanical ensemble of multiple states, sampled over the population of molecules and across their conformational behavior in time. not least, protein binding sites are often partially disordered before binding, and in any case there may be several binding modes. picking the right one can be difficult because there is a fine balance between solvent and conformational entropy, and entropy is notoriously hard to compute [12] . given this argued uncertainty as to the nature of the target protein and its binding site, a broader initial net as an ensemble pharmacophore can help. docking approaches are continually being improved by researchers, and recently include ways of combining features that could ultimately relate to different protein binding sites. while many authors of these studies include the word "ensemble" in their discussion of pharmacophores, they appeared to be significantly different to the particular means of combining multiple pharmacophores that was explored here. however, the present author has had his attention drawn to some that are rather similar and the approach of kumar [33] appears to particularly akin, especially in regard to distributions of expected values and use of weighting. kumar's description [33] thus suffices, and briefly stated, it explores the ability of an ensemble of selected protein-ligand complexes to populate pharmacophore space in the ligand binding site, assesses the importance of pharmacophore features using poisson statistical and information-theoretic entropy calculations, and generates the pharmacophore models with high probabilities. a scoring function then combines all the resultant high-scoring pharmacophore models. there is one significant operational difference between kumar's approach and that used here. recall that in the more traditional docking approach, it is the ligand as candidate drug that is typically seen as the variable and constantly changing and in many studies "evolving" the ligand chemistry with the pharmacophore is the basis of drug design [29] [30] [31] [32] . ref [50] , related to the present study, has aspects of that applied in a different way. kumar's approach can, however, combine the perspective of both pharmacophore and ligand as conceptual variables. despite that, the present author's approach, as used in the present overall project, considers one candidate ligand at a time. this seems less efficient from the point of view of designing candidates, and not even as smart as the older single, non-probabilistic pharmacophore approaches [29] [30] [31] [32] . nonetheless, a single, simpler one-ligand-at-a-time strategy is both adequate and appropriate in the present case. this is because there is already a data collection of candidate antagonists to build on [50] , as discussed in section 1.7. approaches of the ensemble pharmacophore kind are currently highly recommended for investigation of sars-cov-2 and for the spike protein in particular, again because of some uncertainties and the likely multiple functions of some spike protein features. however, it has not as yet had significant impact in the present study. the approach actually taken remains consistent in the sense that inclusion of one particular source for a pharmacophore, an enzyme considered by the author, was evidently going to dominate the ensemble because of certain similarities in the antagonists of sars virus entry and inhibitors of the enzyme [3] , given the knowledge available at this time. that choice is not, however, obvious, as follows. pharmacophore. what may be more controversial is the case when there is a representative choice and it is a protein that is not obviously relevant to the target protein, or simply not "on the radar" of coronavirus researchers. what makes it a candidate is not necessarily that it is relevant to viral infection and not necessarily that it has an evolutionary relationship to proteins that are considered relevant, although this is a question addressed briefly in this paper. rather, it may simply be based on the pragmatic notion that there may be ligands, potential binding molecules as antagonists, which are common to both more popular choices human target proteins and a less obvious candidate. the small organic molecule emodin has been found to inhibit sars coronavirus entry [59, 60] , as also so have other compounds some of which have emodin-like features [3, 61] . similar molecules, and importantly emodin itself, are also inhibitors of 11β-hydroxysteroid dehydrogenase type 1, an example of a steroid binding enzyme [62] . it is normally anchored within the endoplasmic reticulum through an nterminal transmembrane domain. its involvement as a protein target is here based on a chemical justification. a biological justification might be that this enzyme is involved in the inflammation response which a coronavirus might also benefit by inhibiting. if so, the goal is not, of course, to help the virus by inhibiting at the same target which it would also gain by inhibiting, but rather to inhibit protein targets more crucial to it, i.e. for cell entry and possibly replication which are even more crucial to the virus. some inhibition of 11β-hydroxysteroid dehydrogenase type 1 might even be a desirable thing because excessive or prolonged inflammation (including in response to pathogens) is well known to be potentially damaging to the host. an excessive inappropriate immune response may also include the basis of allergic reactions and even of autoimmune diseases. a pragmatic reason for this choice of protein as pharmacophore is that was also one of those protein-ligand interaction systems that have been well studied by the present author and collaborators [50] . such studies pursued the idea of using a more rigid molecular framework, including the steroid framework and fragments of it, as a more rigid scaffold for active drug groups [50] . importantly, that study and subsequent work has already established data base of compounds that bind to 11β-hydroxysteroid dehydrogenase type 1, and it includes many molecules including some discussed in this paper that again have some of the features of emodin. it also includes many weak binders that could also be much stronger binders at what turns out to be a more obviously relevant protein target. these issues can be addressed quickly in the laboratory and certainly seem worthy of investigation before addressing the more popular targets. there was a further implication in the previous paper [3] , though not a requirement for its main arguments, that the peptides designed on the basis of the krsfiedllfnkv motif bind the same krsfiedllfnkv site as do emodin-like molecules. that seems currently to be an even less reliable assumption than the assumption that the above steroid dehydrogenase enzyme is relevant to coronavirus biology, and it is not of course an assumption that even matters if either a peptidomimetic and/or small organic molecule is found effective. however, again keeping in mind that there are a limited number of accessible, conserved sites in the spike protein, and that these may be involved in multiple mechanisms as discussed above, common targets for action of both peptides and smaller organics like emodin seems plausible. partially the problem is extensive glycosylation. it is well known that glycosylation plays an important role in receptor-ligand recognition but also have structural influence in receptor-ligand recognition because of its bulky shape caused by branched side chains. for that and other reasons it may be that the krsfiedllfnkv site is, with just a little variation, almost the only site on the spike protein that is persistently recognizable in coronavirus strains, and so presumably carrying out an important function and accessible, as also discussed in this paper. angiotensin converting enzyme 2 (ace2) binding is however also considered in this paper. a number of ideas and principles, borrowed in established and recent design of synthetic vaccines and petidomimetics, were used (see ref [3] for discussion and e.g. refs [63] [64] [65] [66] [67] [68] [69] ), as well as some of the ideas that lie behind the popular zinc data base [70] . as discussed in refs [3, 4] , the present investigation started as a use case for the hyperbolic dirac net (hdn) and particularly the associated q-uel language for automated inference [34] [35] [36] [37] . the theory has been discussed elsewhere, e.g. in refs [34] [35] [36] [37] , which relate more to the practical and general uses of q-uel. these considerations are less important here because present studies can be reproduced by standard bioinformatics and molecular modeling means. nonetheless, it is doubtful that the research for refs [3, 4] could have been done and written up so rapidly without the aid of q-uel to interact with websites of the world wide web, gather knowledge, and facilitate use of the publically available bioinformatics tools [3] . the challenge is ultimately one of molecular recognition but in practice many key principles for hapten design relate to distinguishing types of naturally occurring epitope. by the term "epitope" in this paper is meant "continuous epitope", though several smaller epitopes may be joined to represent a discontinuous epitope in which conformation and relative position in space can sometimes be important. while a synthetic construct implies the use of synthetic chemistry typically combined with a judicious carrier protein to which the peptide is linked chemically, constructs can also be obtained by cloning, using protein engineering principles [12] . the terms b-epitope and t-epitope relate to the traditional picture of a bone marrow b or thymus t response. b cell epitopes occur at the surface of the protein against which an immune system response is required. they are recognized by b cell receptors or antibodies in their native structure, and are concerned with the bone marrow response and antibody production. t epitopes may be buried inside protein structures and released by proteolysis, and are traditionally considered as concerned with a cellular response and immune system memory, i.e. active immunity. continuous b cell epitope prediction is very similar to t cell epitope prediction. the focus is on b-epitopes here, though a bepitope can also be (or overlap with) a t-epitope especially if it has a significant content of hydrophobic residues. prediction of these has traditionally been based has mainly been based on the amino acid properties such as hydrophilicity, charge, exposed surface area and secondary structure. there are many predictive algorithms available, but the present author prefers a more "expert system" kind of approach that incudes experimental data, though the above biophysical considerations certainly still play a strong role (see below). infection. the previous paper [3] focused primarily on design of synthetic peptides as infection antagonists. however, partly for the reason of greater conformational flexibility discussed below, smaller less flexible organic molecules (i.e. with fewer rotatable bonds) are the traditional province of the synthetic chemist rather than use of an automated peptide synthesizer, are preferred for pharmaceutical application. consideration of peptides is more often considered as merely a useful intermediate step in more traditional pharmaceutical compound design. biodegradability per se of peptides is not the main concern, since including d-amino acids in the design prevents proteolysis. in preliminary docking and simulation studies, the peptides do bind to 11βhydroxysteroid dehydrogenase type 1, but less strongly and with several binding modes [3] . this weaker binding is not in itself a contraindication of the idea that these peptides bind at the same site as the more rigid non-peptide molecules, because it is an expected consequence of the much greater flexibility of peptides compared with molecules with, for example, multiple aromatic ring scaffolds. conventional wisdom (e.g. ref [12] ) frequently uses the rule-of-thumb that the total change in intramolecular (bond rotational) entropy of a peptide ligand is roughly t∆s total = 1.5 kcal⋅mol −1 per residue at 300 k, corresponding approximately to a 12-fold reduction in conformational freedom per residue on binding. because van der wall's and hydrogen bonding tend to be very roughly equivalent for peptides in water and in well bound forms, the water entropy effects known as hydrophobic effects (along with electrostatic forces) play an important role in determining the balance of energies and final outcome. krsfiedllfnkv would thus cost about +19.5 kcal/mole entropic contribution to bind rigidly, primarily compensated by hydrophobic contacts at up to about -1.7 kcal/mole in going from an aqueous to a non-polar environment, i.e. -22.1 kcal/mole for a 13 residue peptide or analogue of krsfiedllfnkv. that example would not favor binding, but the proper calculation is in the details which of should show balance that favors good binding if that is found to be the case experimentally. despite the above comments, the flexibility of peptides does provide more opportunities to fit a specific binding site, i.e. they can show some accommodation and they are more tolerant to imperfections in the design process. however, this is also an argument for their importance as an intermediate step in the design of more conventional pharmaceutical agents. the main methods are essentially standard bioinformatics approaches as used in refs [3, 4] . some methods, e.g. rules for epitope prediction, are best discussed in context in results section 4. the q-uel methods specifically for bioinformatics are discussed in [38] , and those for computational chemistry and docking of compounds are those using krunch as described in ref [3] and the appendix to ref [50] . they are somewhat unorthodox by focusing on heuristics to handle the multiple energy minimum problem, but the end effect is probably similar to that of long runs using high grade molecular dynamics calculations, given opportunities for calibration [50] . epitope predictions lie in more traditional "one dimensional" bioinformatics, and in this paper and the previous paper depended on predictions using a gor4 secondary structure prediction of α-helix (h), extended chain or β-sheet (e), and coil or loop (c). the reason for this and the particular use of gor4 is discussed in ref [3] , but briefly, it is in part because sections predicted by runs of c tend to be immunogenic even if they are incorrect as structure predictions [3] . however, charged residues in α-helices and βsheets are believed to be occasionally b-epitopes, and short sections extended chain can effectively imply loops. the core and initial rules for b-epitope prediction used in the present study consider (i) surface exposure when a three dimension structure is known, but allowing for conformational adjustment to expose residue when in a likely disordered or flexible loop, scores +2, (ii) known exposure based on other kind experiment, which also recognizes the possibility that a partially buried site by the above criteria can be brought to the surface on binding, notably for proteolytic cleavage [3] , (iii) runs of amino acid from the set [stnqy] score +1, from the set [dekhr] they score +2, and from the set [livfcm] they score -1, (iv) runs of secondary structure prediction as coil or loop c, though runs of three or less e and the first and last three of helix h can be considered as c for this purpose, score +1, and (v) the motif nx(s/t)x of asparagine (n) serine (s) or threonine (t), where x means "not a proline" (p) scores +2. however, this will not permit a corresponding peptidomimetic or vaccine without considering glycopeptide synthesis technology. see discussion below, which would justify a negative score, depending on the technology available. in addition, these may be combined with predictions based on significant homology with proven epitopes in data bases, which has already been done by several groups for sars-cov-19 (e.g. ref [54] ). for sources of data concerning covid-19 virus spike proteins, genbank and the protein data bank were the main sources. there was some use of in-house collections of data, e.g. of typical b-epitopes and t-epitopes, although publically available collections would probably serve the same function. there was also use also of a data base of non-peptide ligand molecules of potential interest already generated during and since the work described in ref [50] that was used where appropriate. many of these molecules (including emodin) are also found on the public zinc data base [70] as indicated in results section 4 below, but several, including derivatives of carbenoxelone, are not, and these derivatives are of interest as potential coronavirus antagonists. to look up an entry on the zinc data base by the codes used in this and other papers, one can go to http://zinc15.docking.org/ substances/ and enter zinc00011032. in an automated approach such as that favored by q-uel, a variable (such as a perl variable $mol) to zinc00011032 and is set an the q-uel application goes to http://zinc15.docking.org/substances/search/?q=$mol. any references to experimental binding results concern data from cited papers, and see for example ref [69] for typical methods used for natural herbal compounds. as discussed in ref [3] , q-uel helped gather these in the form of q-uel knowledge representation tags, so they become part of the growing knowledge representation store. in regard to peptides and proteins, table 1 used in ref [3] shows the standard iupac one-letter codes used for amino acid residues in sequences throughout this paper. table 1 . one letter amino acid codes used in the text. conservative replacements are those common substitutions from a peptide design perspective, but for example phenylalanine (f), isoleucine (i), and alanine (a) are seen as natural substitutions that appear in discussion of spike protein sequence motifs later below. these amino acid residues have hydrophobic sidechains but they are not conservative replacements but rather substantially different size. a reasonable explanation is of course that sidechain size conservation matters less when the sidechains are at exposed at the surface of the protein. similar notions underlie the idea that what can readily replace what is not always an equal probability in each direction. in that respect, table 1 tends to reflect the changes that are used in the present project for design, when starting from epitopes. the previous paper [3] should not give the impression that the specific motifs discussed (and particularly krsfiedllfnkv) are the only sections likely of the sars-cov-2 spike protein to be of interest in the above respect. the preference for one choice was based on (a) conservation across many strains, suggesting that the site has an important function and is likely at the spike surface, and (b) avoiding the shielding of the spike protein by extensive glycosylation. the dramatic effect of relaxing these restrictions is a major point of this section, in which a large number of candidates are found. over-prediction is not necessarily a bad thing, because once a laboratory has a peptide synthesizer and other tools for constructing and testing designs, it is relatively easy and cheap to test and reject ideas, and more problematic to miss opportunities. the intention here is also to cover most possibilities, to enable index numbers to be assigned to them according to their order in the sequence (putative epitope 1 etc). consequently, in future one may then readily refer to the index number, or speak of a new proposal or experimental epitope extending, overlapping, or even lying between two of these epitopes. they are primarily to be seen as b-epitope predictions, though they are favored if some t-epitopic character is also expected. an initial step is based on adding up weights as described in methods section 3.2. in practice, there was also some judicious use of expertise and an epitope data base in an attempt to refine assignments. recall that the trimeric sars coronavirus (sars-cov) spike glycoprotein consists of three s1-s2 heterodimers. some of these will be shielded by that configuration during most of the life cycle of the virus, but not necessarily in every s protein monomer, and also shielded by glycosylation. the higher scoring predicted epitopes in the sequence below are underlined and in bold, and are primarily to be considered as b-epitopes but with some extension to include t-epitope character where possible. also included in these predictions are those using the immune epitope database and analysis resource (iedb) and the virus pathogen resource (vipr) which have already been made [54] (see later below). these are shown in underlined, bold, and in italics in the following, and since some are contiguous sections that look like a single long representation in the following, they are also stated separately below. it is apparent that while focus was on just krsfiedllfnkv, if strain variation and glycosylation are ignored then much of the spike protein sequence contains epitope candidates. 10 20 many of the epitopes predicted in the present study overlap with prediction made using the immune epitope database and analysis resource (iedb) and the virus pathogen resource (vipr) [54] , and these comprised the following. recall that one of the reasons for the original single preferred candidate krsfiedllfnkv was that many of predicted epitopes contain evidence of glycosylation, reflecting the last of the "rules" (v) in methods section 3.1 above. that rule has, however, a special status, and the present author has tended to consider them undesirable for synthetic vaccine or diagnostic development. it indicates likely glycosylation of the protein. the bulky oligosaccharides so attached can be immunogenic, but they are rather difficult to work with synthetically, traditionally expected to make bulk production expensive, and may be variable in structure which cannot typically be seen in detail in experimental three dimensional protein structures (typically as obtained by x-ray crystallography or high grade electron microscopy). antibodies that are raised against the glycosylated surface patch of the protein or corresponding synthetic glycopeptides may be specific for their carbohydrate units. these can be recognized irrespective of the peptides, or in the context of the adjacent amino acid residues. conformation and exposure of b-peptide epitopes of glycoproteins may be modulated by glycosylation because of intramolecular carbohydrate-protein interactions. the beneficial versus undesirable effects of glycosylation in synthetic vaccines is also a complex matter. glycosylation may be essential for reactivity with the antibody, but conversely it may in effect inactivate the capabilities of a section of amino acid sequence to function as a b-epitope, which seems to be a very good reason for giving the glycosylation motif a strong negative rather than positive score. unfortunately this will depend on the structure of the antigenic site and antibody fine specificity, and the recognition mechanisms involved are not fully clear. there is a (usually) positive aspect, however, in the current view that similar effects of glycosylation apply to t-celldependent cellular immune and igg antibody responses, and that glycosylated peptides can elicit glycopeptide-specific t cell clones after being bound and presented by mhc class i or ii molecules. it is of course only a positive aspect if the intended effect is obtained by the synthetic construct. the overall spike glycoprotein protein sequence shown above changes across the coronaviruses, but the krsfiedllfnkv subsequence is most notable amongst the exceptions. it extends to the common cold coronaviruses with minor variation, and may imply a better targeted approach to stimulate immunity. for common colds caused by the rhinovirus, recent research suggests misdirection of antibody responses against a non-protective epitope as a mechanism how the virus escapes immunity and so permits recurrent infections [71] . a clearer understanding of conserved subsequences in coronaviruses may also help tune the action of toll-like receptors to initiate the appropriate response. these are a class of proteins that play a key role in the innate immune system. they are single-pass membrane-spanning receptors usually expressed on sentinel cells (e.g. macrophages and dendritic cells) that recognize structurally conserved molecular features of pathogens [72] . despite concerns about two or more strains of covid-19 virus appearing, these are not big changes for present purposes. it is sufficient to consider the sequence of the original wuhan isolate as reference in comparisons for present purposes, i.e. for comparing the spike protein sequences of other coronaviruses. recall that as discussed in introduction section 1.3, at the time of the study in late february and early march 2020, the sequences of the spike proteins of covid-19 isolates from different states and countries, such as california, brazil, taiwan, and india, remain identical or almost so. for example, with respect to the original wuhan isolate [2] , phenylalanine (f) is replaced by cysteine (c) as residue 797 in a swedish isolate, and alanine (a) is replaced by valine (v) as residue 990 in an indian isolate. neither of these relate to the sequence motif krsfiedllfnkv of particular interest here. in the initial studies [3, 4] , the genome of the common cold coronavirus, and particularly the sequence of the spike protein, was considered sufficiently far from that of the covid-19 virus so as to be less relevant to that problem. while looking at differing sequences is essential for detection of conserved motifs, very different and less relevant pathogens are unlikely to preserve them, except perhaps as pattern matches involving quite complex substitution rules. however, the appearance of the covid-19 krsfiedllfnkv motif does appear in common cold coronaviruses and with typically at most two relatively conservative substitutions. that is in the sense of preserving hydrophobic sidechain as discussed above in methods section 3. the conservative aspartate (d) and asparagine (n) replacement is also fairly common in the motif in the sequences examined. an example shown below is a clustal omega alignment of the covid-19 virus spike protein original wuhan seafood market isolate (genbank entry mn908947.3) with spike proteins representatives members of the two major common cold coronaviruses strains 229e and oc43 (genbank entries np_073551.1 and aiv41987.1). despite radical sequence differences for the spike protein sequences overall (only 12.8% identity, well within the range for a random match), the underlined sequence motif krsfiedllfnkv of covid-19 virus is essentially retained as that sequence, except that alanine (a) replaces phenylalanine (f) in the common cold coronavirus (which is moderately conservative at the surface of a protein) and a conservative leucine for valine substation in one case. in the sequence (not shown) of hcov-hku1 which is often associated with more serious cases of cold-like diseases the above motif is still noticeable as rsffedllfdkv in which the isoleucine (i) is replaced by phenylalanine (f). the "a for f" modified motif rsaiedllfdkv is also found in the coronaviruses of dogs, cats, rodents, pigs, rabbits, camels, ferret badgers, raccoon dogs, amongst others. all of these might be eaten by humans in certain countries and notably they are, for the most part, species that live in close proximity to humans. the "pigag" motif does not show up in the above alignment, as is also the case in many other distantly related coronaviruses [3, 4] . however there is a subsequence pigtnyrscestt in the hcov-hku1 spike protein that appears to relate to pigagicasyqtq in the covid-19 virus (recall that hcov-hku1 is a common cold virus, albeit usually associated with more severe, lower respiratory tract cases). in contrast, not only does the krsfiedllfnkv motif stand out as potentially important to the covid-9 virus by virtue of such comparisons, but also a match with that motif is almost the only continuous stretch of amino acid residues in most alignments like that above. the subsequence kwpwyiwl is an exception that is of interest and a characteristic feature of many sars coronaviruses. it is not, however, considered further in the present paper, except to note that it does not appear to be associated with a covid-19 virus spike protein proteolytic cleavage site. these sites are most prominently trypsin: s1/s2 htvsllrstsqksivaytmsl, s2' lpdplkptkrsfiedllfnkv; cathepsin: s1/s2 htvsllrstsqksivaytmsl; elastase: s2' lpdplkptkrsfiedllfnkv, plasmin: s1/s2 htvsllrstsqksivaytmsl, s2' lpdplkptkrsfiedllfnkv, tmprss1: s1/s2 htvsllrstsqksivaytmsl; tmprss2: multiple sites; tmprss11a: s1/s2 htvsllrstsqksivaytmsl, s2' lpdplkptkrsfiedllfnkv. as one looks out to more distant relatives, there are a number of variations in the krsfiedllfnkv motif which, despite large variations in spike protein sequence as a whole, are still recognizable in the spike proteins of coronaviruses of diverse various host species, as shown for some examples in table 2 . the most noticeable variation is the occasional substitution of the cleavage point arginine (r) by a g. rather than disrupt the possibility of cleavage, however, it is seemingly displacing that role to a arginine (r) or lysine (k) that lies to the n-terminal (left) side of the motif. it is interesting that this commonly retains firmly the iedllf core of the motif. the notion that the krsfiedllfnkv motif overall plays an important role, and presumably a common or similar function across at least a very large number of known coronaviruses, still seems a reasonable one. most important of course is that it is at least the case for the sars-cov-19 virus and its near relatives. at this time, no match with a coronavirus in genebank has been detected by the author by blast-p using queries with no phenylalanine (f), e.g. rsaiedllldkv, rsaiedllidkv, rsaiedlladkv, rsaiedllmdkv, rsaiedllwdkv, and rsaiedllydkv as queries, but the search has not been exhaustive because it would not be too contradictory to any of the current hypotheses if some were found. in the group with the inserted glycine (g) replacement of initial argine (r) by the similar positively charged lysine (k) is common. however, as long as the motif is significantly recognizable, no histidine (h) as opposed to initial arginine (r) has been found. the motif cannot extend to other strains indefinitely as recognizable because at some point the evolutionary tree will bring up virus and hosts subject to quite different selective pressures, and the motif is not the definition of coronaviruses. however, it still persists as recognizable in birds such as duck (e.g genbank kx266757, kc119407 white-eye bird cov hku (nc016991), magpie-robin (shama) cov hku18 (nc016993)) strains, a selction which spans a large range of coronavirus genome sizes. see the alignments below compared with the wuhan seafood market isolate genbank mn908947.3, showing the motif underlined and in bold. :.: .: : : eeyihklnatlvdldwlnrvetyikwpwwvwllitlaivafvvilvtiflctgccggcfg 1188 : . ** ::::*: *. : *:****::** : .: : : : *.**. some indication of the limit of the survival of the motif rsfiedllfnkv as the researcher departs from sars-cov-19 might be given by the nidoviruses other than coronaviruses. somewhat coronavirus-like nidoviruses are common as e.g. reptile viruses. the order nidovirales contains enveloped, positive-strand rna viruses with the largest known rna genomes. nidoviruses have been identified in snakes. they appear to be most closely related to coronavirus subfamily torovirinae, and might be best represented as a genus in this subfamily. sequences suggestive of rsfiedllfnkv, e.g. knfidlllagf do occur in genomes such as the ball python genome, but these really lie beyond the limit of serious detection. for example, clustal omega gives 18% exact match between the wuhan isolate and spike protein nidovirus 1 of the reptile shingleback, but the motif is barely recognizable. including fish nidovirus of the pacific salmon (genbank qeg08239.1) is notable here because it supports the above alignment because it is preserved, but gtlywldy of the salmon nidovirus is far from krsfiedl and the nearest preceding plausible cleavage point is an arginine (r) 10 residues in the n-terminal direction (to the left). however, a similar occurs in some mammalian coronaviruses and so that residue may still play a similar role as an activation cleavage. looking for similar motifs in human proteins has a somewhat different motive. it makes sense in that, if there is significant match with subsequences, they might represent features of proteins to which both the spike protein and other human proteins may bind, irrespective of any other justification for commonality. even if coincidental, as epitopes similar to those in a proposed synthetic vaccine they are always of possible interest in assessing the risk of cross-reaction and inducing autoimmunity in synthetic vaccine designs, and on certain occasion with peptidomimetics that induce an immune response, perhaps by a binding strongly to a human protein that the designer did not intend. as discussed in ref [3] , there is a motif match at 56% identity with 77% coverage is with tumor protein d55 isoform 2 [homo sapiens], id: np_001001874.2, and similarly with tumor protein d52-like 3 [homo sapiens] id: aah33792.1. next match is in regard to neprilsyn entries at only 56% match and 55% coverage. none of these are sufficient close of concern regarding induction of an autoimmune response. some fairly close matches of krsfiedllfnkv and of the "a for f" modified motif rsaiedllfdkv have come to light that might plausibly have a biological significance if supported by biological relevance, but are more likely to be random matches. selecting only for human proteins, hits vary from 100% cover with 50% identity to 62% cover with 92% identity. these hits cannot be considered significant for peptides of this length in isolation from other evidence. however, a few seem worth recording for future reference in regard a potential biological function for the virus. as already noted [3] , rrsfidelafgrg a section of a human semaphorin (genbank np_001243276.1) produced in response to lung disorders. running rsaiedllfdkv itself in blastp generates 100 coronavirus hits. rnareellfd is found in human mhc class ii antigen, genbank axn55588.1. rnareellfd is found in human immunoglobulin heavy chain junction region genbank mcg49633.1. dllfekv is found in human tubulin, gamma complex associated protein 6, isoform cra_d genbank eaw73510.1. e3 is of interest with 75% identity 87% matches for sfleellfin khksfleellf in ubiquitin. the cellular e3 ubiquitin ligase ring-finger and chy zinc-finger domain-containing 1 (rchy1) have been identified as interacting partners of the viral sars-unique domain (sud) and papain-like protease (pl pro ), with the involvement of cellular p53 as antagonist of coronaviral replication. down-regulation of p53 is a major player in antiviral innate immunity [72] . again, however, these matches remain tenuous. genbank has of the order of 0.2 billion nucleic acid sequences but a 13 residue peptide can have 81,920,000 billion sequences. while the krsfiedllfnkv motif remains favored by the author as a target at this time, identifying the amino acid residues in ace2 and the spike protein is important. it may for example involve conserved residues that are not together in a continuous sequence. while a conserved run of amino acid residues is sufficient to be on the list of candidates for an important site, important sites are not necessarily conserved runs of amino acid residues. here is shown that there is some conservation, but significant variation compared with rsfiedllfnkv. subsequences rsfiedllfnkv and pigagicasy…r discussed in ref [3] as motifs associated with activation cleavage sites do not lie in the receptor (ace2) binding domain of the sars-cov-2 spike glycoprotein. the relationships between the whole spike protein and the receptor binding domains in pdb entries 6m17 and pdb 6vw1 are shown in the alignment below. note that the above receptor binding domain precedes the above motifs in the sequence. a three dimensional perspective is required for an appreciation of the important sequence features. in fig. 2 , the pdb 6vw1 binding domain is on the right, bound to ace2 on the left. fig. 2 of course, not all the receptor binding domain is interacting intimately with ace2. the sections of the receptor binding domain that do interact with ace2 are also shown (underlined). to facilitate deeper analysis, the loops on the spike protein receptor binding domain were initially classified as loops a,b,c,d,e, and f in order of visual perspective, then joined into three subsequences 1, 2, 3 that contain these loops. the part of the spike glycoprotein sequence that represents the receptor (ace2) binding domain can be shown by considering the proteins used in the two structural determinations 6m17 and 6vw1 in the protein data bank, shown below in an alignment made using clustal omega alignment. note that the above receptor binding domain precedes the above motifs in the sequence. the amino acids residues in bold and underlined font are the subsequences of ace2 that interact with the above spike protein ace2 binding domain loops, which are indicated above each subsequence. these include some longer range electrostatic interactions and potential solvent effects. those also in italics dkfnheaedlfy, dkfnheaedlfy and kgdfr have particularly strong interactions. as a reference perspective, the full sequence for ace2 as angiotensin-converting enzyme 2 isoform x1 [homo sapiens] genbank entry xp_011543851.1, is as follows. the part in the three dimensional structure above is in bold underlined font. note that at least in these particular experimental structures there is an involvement of "glycosylation-like" molecules. for example, in 6vw1 there are well localized n-acetyl-d-glucosamine, β-d-mannose, and 1,2-ethanediol molecules that make significant interactions in a glue-like manner, and essentially "glue around the edges". however there no obvious indication of involvement of glycosylation in the main interior interaction face of the complex. the intimate interactions are proteinprotein, i.e. between amino acid residues. primarily, but not solely, ace2 and spike glycoprotein association involves interaction between the bent α-helix residues 19-54 (stiee…nyntn) of ace2 and an extended chain configuration, effectively a stretched loop, that runs from residue 485-500 (gfncy….ygqpt) of the spike glycoprotein and involves or ends in loops 3a, 3b, and 3f. in the case of ace2 interacting with the ace2 binding domain of the spike glycoprotein, one could in principle imagine blocking the ace2 as receptor with a mimic of the spike protein surface, or blocking the receptor binding site of the spike glycoprotein protein with a mimic of the ace2 receptor surface. in other kinds of infection the former is usually considered more plausible, but the latter would not interfere with normal function of ace2 and it is of course essentially the way in which immune system, and notably antibodies, work. possibly the main argument against this second choice it is that it is essentially equivalent to using antibodies raised against the spike protein, i.e. in effect, passive immunization. at the time of final writing, various news articles are drawing attention to potential use of the upper sequence or parts of it, which is that of the α-helix of ace2 (for example https://scitechdaily.com/mit-chemists-have-developed-a-peptide-that-could-block-covid-19/). in the above "alignment", the helix contains 35 residues and the extended chain below contains 16. they have similar length as is as expected for such structures. an αhelix has a rise of 1.5 å per residue along its axis and there are in typical protein helices with turn variations that imply up to 2.0 å. the β-strand or a similar extended chain in the spike glycoprotein that interacts with it has a rise of circa 3.5 å per residue. this general geometry naturally puts the two sequences above in roughly the one-to-one spatial correspondence shown. note that this is not intended to be a sequence match representation; these chains have to interact. in that respect, there is a lack of charged residues (acidic and basic sidechains) in the extended chain of the spike glycoprotein in structure 6vw1, although an aspartic acid (d) replaces the serine (s) in some strains, arginine (r) replaces asparagine (n) in others, and so on (e.g. see blastp alignments later below). a detailed backbone view is confusingly cluttered, but one may identify residues that interact at the boundary between ace2 and spike protein. all sidechains in the above spike protein subsequence gfncyfplqsygfqpt either make close contact or are likely to have some influence at the interface. it is perhaps useful to have the initial mental picture that, very roughly speaking, the planes of the peptide groups are tangential to the above α-helix surface, rather than constituting an extended chain that makes an edge-on approach. as even fig. 2 suffice to makes clear, however, the extended chain, like any so-called extended chain in proteins in practice, is essentially a visible helix of larger pitch, resembling a very stretched-out α-helix, and is itself slightly supercoiled to wrap around the ace2 α-helix. in this case, this tends to follow the elbow or bend in the α-helix, staying roughly parallel to the local axis of the α-helix, so as to make intimate contact overall. if gfncyfplqsygfqpt is to be use as an epitope analogue, the cysteine (c) may be tested as a convenient linker to a carrier protein, otherwise replaced by serine (s) as a close analogue. as far as peptide antagonists are concerned, the difficulty with using the above sequences stiee…. and gfncy…. is that they are readily degraded by host proteases. this would not occur if the peptide is made entirely of d-amino-acid restudies. a retro-inverso peptide [3, 46] is made up of d-amino acids in a reversed sequence to the subsequence which is seeks to mimic, and in the extended conformation assumes a side chain topology similar to that of the original native peptide, but with backbone n-h and carbonyl c=o groups interchanged. these are peptidomimetics of the subsequences sequences stiee…. in ace2 and gfncy….. in the spike glycoprotein respectively. the cysteine (c) in ….cnfg in the second molecule may be a convenient linker for an epitope for a vaccine but should be replaced by serine (s) in an antagonist. recall that the problem of having the backbone amide n-h and carbonyl c=o groups interchanged is that if, in the original section of backbone being mimicked, any n-h and c=o groups form a hydrogen bond with recipient and donor groups in the protein, those hydrogen bonds are now disrupted in the intended competitive antagonsist, e.g. they would be unstable n-h…h-n or c=o…o=c interactions. it would thus seem a significant advantage in using the ace2 mimic, because that is essentially an α-helix which uses up its backbone amide and carbonyl groups. however, retro-inverso α-helices are not typically found in the areas that have shown some degree of success [47] , such as antigenic mimicry. it would nonetheless seem to be of value to test both of the retro-inverso peptides in laboratory studies. as to developing the above further both as the basis of a synthetic vaccine, or as a peptidomimetic, and as to the worth of extending the studies to small organic drug molecules, everything in the above depends on the extent to which gfncyfplqsygfqpt can produce escape mutations which might soon rend such solutions useless. as in the previous paper, we can relate this to variations of the above sequence bother in closer and much more distant relatives. as the following shows, using blastp we do not have to go very far from sars-cov-2 to find matches with only part of this sequence (coverage) and differences within that area of partial match: in the original wuhan seafood market pneumonia virus isolate wuhan-hu-1, genbank id mn908947.3, the subsequence in this regions is fncyfplqsygf, and the following are examples of coverage as found by blastp. the last of the above blastp at https://blast.ncbi.nlm.nih.gov/blast.cgi match results differs in total alignment by clustal omega at https://www.ebi.ac.uk/tools/msa/clustalo/, as follows, but of course this illustrates the high degree of variation that occurs as one proceeds on to coronaviruses less related to the wuhan seafood market isolate that is believed to be associated with the origin of covid-19. phenylalanine (f) commonly immediately precedes many of these matching subsequences ncyfp… ncywp… etc., and the conservative substitution tryptophan (w) substitution for the second phenylalanine (f) is also very common, so it may be worth noting that fnctwp is a subsequence in the mammalian vomeronasal type-2 receptor 1 on sensory cells within the main nasal chamber that detects heavy moistureborne odor particles, and fnctwp is also found in in dynein. many viruses require the minus-end-directed dynein motor complex transport on microtubules from cell surface toward the nucleus, and dynein in addition to kinesins for the transport toward the plasma membrane. however a direct connection to viral infection, while tempting, is far from obvious as to any mechanistic or evolutionary explanation. also, dynein nuclear shuttle transport may be less relevant to the coronavirus (an rna virus), but certainly rna viruses can rely on the dynein system (e.g. hanta virus uses it for endoplasmic reticulum-golgi intermediate compartment). at very least, the above illustrates the kinds of further, perhaps immediately less obvious, functions that the above ace2 binding domain of the spike glycoprotein, and the above motif, might have. within the coronaviruses, there is some degree of conservation that suggests that ncywplndygf is a segment for the virus to conserve, and a hint that fnctwpgf is the key part, but there are soon very clearly significant variations across coronaviruses of different hosts as we depart from the wuhan seafood market isolate compared with the rsfiedllfnkv motif in the s2' cleavage regions [3] . small organic drugs design to mimic this section, or simply designed to designed to antagonize ace2 binding, are thus potentially susceptible to escape mutations, i.e. rapid appearance of drug resistance. binding studies with 11β-hydroxysteroid dehydrogenase type 1 as model pharmacaphore. 11β-hydroxysteroid dehydrogenase type 1, which is inhibited by emodin, was an interim model pharmacophore of choice [3] . at this point in the development of the argument for optimal targets for vaccines and therapeutic antagonists, the above target fits in as follows. while the above regarding ace2 binding must be kept in mind for antagonist development, as noted above the motif is not well conserved, and so could be prone to development of escape mutations, i.e. acquired resistance to vaccines and therapeutic antagonists. because of the dominant theme of an ace2 α-helix interacting with an extended chain loop of the spike glycoprotein, the structure of the interaction region is fairly easy to deduce for various sars strains, and there was as yet no obvious strongly recurrent theme of significant conserved residues that are discontinuous (i.e. not together in the same subsequence) that could be interacting closely with ace2. at the same time, while emodin appears to act at the ace2 binding site [59] , it remains of interest because there are complexities [60, 61] as discussed in introduction section 1.6. notably, the ace2 binding domain of the spike protein and the binding sequence discussed above might bind other human proteins and might have other functions that emodin and related compounds, related in the sense that they are at least consistent with pharmacophore features, might inhibit. a priori, the binding properties of emodin and the choice of 11β-hydroxysteroid dehydrogenase type 1 as model pharmacophore could equally relate to the rsfiedllfnkv site, or some other site, or a mix of several. the case for interaction vomeronasal type-2 receptor 1 and dynein discussed above was at best marginal, but these examples illustrated the diversity other kinds of functions, important to the virus, that might apply. in any event, any relations between emodin and similar and potentially related molecules remains of interest to impeding sars-cov-2 entry and the worse casualty would be the continuity of the story developed above, which is intended to illustrate a flow of reasoning in using the standard tools of bioinformatics. 11β-hydroxysteroid dehydrogenase type 1 is interesting as accommodating a great variety of ligands at the steroid binding site, but not without a degree of specificity as to general features of the ligands, and so far these resemble those of potential sars-cov-2 therapeutics. keeping in mind the refutation principle [3] that a pharmacophore (or contribution to a pharmacophore ensemble) the dehydrogenase is worthy of use until a new ligand or other information proves otherwise. so far pharmacophore validation here, i.e. a demonstration that it is a suitable pharmacophore model until proven otherwise, has been based circumstantially on emodin and compounds looking chemically similar to it, that are known in practice or argued theoretically to interact with sars virus entry in some way and bind at least weakly, experimentally or computationally, to 11β-hydroxysteroid dehydrogenase type 1 [3] . a review of compounds that are known experimentally to inhibit the dehydrogenase and known experimentally inhibit coronavirus entry, replication and maturation is being prepared. however, validation is also extensively based on a weaker but larger body of preliminary binding studies involving a variety of antagonists of coronavirus infection and very often other kinds of virus infection, that also bind at least very weakly to the dehydrogenase (see discussion on "very weakly" below). most of these, emodin-like and otherwise, were first found by q-uel knowledge gathering tools as used in the initial coronavirus study [3] combined with "very early candidate selection rules" based on estimates of the mean binding strength of groups when binding well. note that a hydrogen bond worth about -4 kcal/mole is nonetheless effectively zero when binding well, because it is relative to binding to water. in contrast aromatic and large aliphatic and are worth circa -3 kcal/mole due to hydrophobic interactions which depend on being considered relative to water. there are more complex electrostatic and intramolecular entropic considerations beyond present scope, noting that at least preliminary study of the interaction with 11β-hydroxysteroid dehydrogenase type 1 is the arbitrator. weak and very weak candidates are also considered because there may be multiple binding modes that will take a great deal of computer time to explore but which could yield lower binding fre energies. this produces a fairly "mixed bag" of compounds, based on the argument that viruses and coronavirus in particular may use each of its limited number of exposed or exposable sites for several purposes, and the coronavirus seems to be able to readily adjust to new mechanisms under the selective pressure of drugs and vaccines. the details of these molecules and studies are the subject of a further paper that will also discuss some interesting unifying themes. briefly, they include many names as hopedfor drugs against the coronavirus that appear in the news and internet discussion. it is convenient to see them as dividing into three classes (i) quinone-like. a "quinone" is any of a class of aromatic compounds having two carbonyl or ketone c=o functional groups in the same six-membered ring, though in "quinone-like" the author includes include many compounds resembling steroid fragments that may have many or just one carbonyl groups and several rings. this group includes 9,10anthraquinone and derivatives that relate to many important drugs some with suggestive laxative and antiinflammatory functions, collectively called anthracenediones. they include ubiquinone as coenzyme q, and various shorter aliphatic chain forms hydroxyl-decylubiquinone and shorter aliphatic chain forms, laxatives such as dantron, emodin, and aloe emodin, and some of the senna glycosides, antimalarials such as rufigallol, antineoplastics used in the treatment of cancer, such as mitoxantrone, pixantrone, and the anthracyclines. caution is reuired in reading this list as a list of potential therapeutics, because anthraquinone derivatives rhein, aloe emodin or anthrone that lacks the methyl group, parietin (physcion), to some extent emodin itself, and chrysophanol extracted from cassia occidentalis are toxic and known to cause hepatomyoencephalopathy in children. it is a medical term effectively defined to cover lethargy, jaundice, and altered senses of children in india after consumption of cassia seeds. (ii) steroid-like. this group includes some plant steroid-like compounds such as carbenoxolone itself from liquorish (licorice) and others found in soy and sprouts.17βestradiol (the endogenous ligand responsible for the growth and development of many tissues) diethylstilbestrol (a synthetic estrogen); 7-methyl-benz[a]anthracene-3,9-diol (a possible natural product from a common polyaromatic hydrocarbon) is also of interest. this group resembles group (i), but the concern for this group (ii) is that molecules like emodin that are known to antagonize viral or other infections are generally smaller, so it possible that a more relevant pharmacophore would sterically exclude a large steroid-like ring. (iii) quinine-like. these should not be confused with "quinone-like". quinine is an alkaloid derived from cinchona bark, used to treat malaria and as an ingredient of tonic water. a common feature is, nonetheless the abundance of aromatic and other rings that in the quinine-like case include nitrogen, so variously resembling pyrimidines, purines, histidine and tryptophan. this group is of current considerable interest as potential thereputics for covid-19. of particular interest are chloroquine, theophylline, tavipiravir, baloxavir marboxil. some ace and ace2 inhibitors can be classified in this group. they are weak but not very weak binders as discussed later below. camostat, a serine protease inhibitor that has been considered as a potential therapeutic for covi-19 is convenient to place in this class because of its analogues but it does not itself include a nitrogen atom within a ring. there are several possible intriguing biological connections that will be discussed elsewhere. one might be briefly mentioned when considering combined therapeutic use of a member of each set. ubiquinone-like compounds can inhibit ubiquinone sites that work in concert with nadh and nadph cofactor sites. the latter in turn are often inhibited by the quinine-like members. many other above compounds generally bind "very weakly", though steroid-like compounds are strong binders and many quinine-like compounds are medium binders: these are discussed below. binding strength is of course a matter of degree. rt (where r is the gas constant and t the absolute temperature) is 0.593 at 298 o k, i.e. circa 0.6 at biological temperatures, so 1 kcal/mole is not significant above thermal noise. free energies of 2, 3, 4, and 5 correspond to binding association constants of 5, 148, 786, and 4160. the above free energies are usually expressed as negative, for the perspective from the associated system. considering that absolute values are much less reliable than relative values in this field, one might conservatively consider a binding energy of -3.5 kcal/mole as worthy justification for keeping a compound on a list, if one does not wish to reject prematurely, and this seems reasonable if one still has in mind the refutation principle. this includes the mental picture that a model pharmacophore such as 11β-hydroxysteroid dehydrogenase type 1 has a fairly large cavity which does not provide strong steric inhibition to the candidate ligands, but new evidence might show that a large ligand such as a steroid might be too big to fit the real target which the experimental data is describing. in other words, deficiencies in the pharmacophore model will start to show up when considering larger potential drugs. there is also the benefit of using 11β-hydroxysteroid dehydrogenase type 1 as model pharmacophore that the present author has a data base of experimental and computational studies on compounds that bind to it. it should be stated, nonetheless, that any case for any common evolutionary relationship between this dehydrogenase and the spike protein binding receptor ace2 would be, at best, marginal. 11βhydroxysteroid dehydrogenase type 1 has 292 residues and ace2 has 613. there is a 24% identity match of amino acid residues in the region of best possible match of the dehydrogenase. there is also further 19% conservative substitution (clustal ':', i.e. conservation between groups of strongly similar properties with a score greater than .5 on the pam 250 matrix). if taken alone, this would provide some basis for further exploring a relationship. admittedly, the conventional rule of thumb is that any two sequences are considered homologous if they are more than 30% exact amino acid residue matches, and strictly speaking this should apply over their entire lengths (this is discussed in chapter 8 of ref [12] and a brief review of standard tools is given in refs [2] and [38] ). nonetheless, caution is required because the 30% exact match criterion is well known to miss many easily detected homologs and 15-20% is sometime found supported by evidence of evolutionary and functional relationship. for example, alignments between common cold and sars-cov-2 spike proteins already discussed above are in this range, but there is every good reason to believe a common ancestry, there is an overall conformational similarity, and essential features of some sequence motifs are preserved. there is some sense of comparable fold motifs with ace2 comprising two 11β-hydroxysteroid dehydrogenase type 1 folds. the dehydrogenase is a bundle of some 12 well defined, roughly parallel and antiparallel α-helices of up to about 30 residues, interspersed by 7 short β-pleated sheet strands. ace2 has some 20 well defined, predominantly and very roughly parallel and antiparallel α-helices of up to about 30 residues, interspersed by 6 short β-pleated sheet strands. if there is a common evolutionary origin of 11β-hydroxysteroid dehydrogenase type 1 and ace2 domains, it is distant, but it remains marginally possible and more extensive conformational analysis is underway. there is even less evidence of homology between 11β-hydroxysteroid dehydrogenase type 1 and tmprss2, although a serine residue is highly conserved in the catalytic site in both cases, which arguably makes it worthy of some initial exploration. tmprss2 comprises distinct cystine rich scavenger domain (residues 150-242) and a serine protease domain (residues 255-484). clustal o(1.2.4) multiple sequence alignment gives an exact match of amino acid of only 17.5%. there are some grounds for further investigation in the future. there is also further 17.5% conservative substitution (clustal ':', see above). for tmprss2 there are some suggestive short section matches in same order of appearance, e.g. aqyyys with ayyyys, vvshc with vvshc, lyhsd with lfhdd, and gilrqs with galrqe, which by some arguments slightly increase statistical significance. no significant conformational homology is apparent, so it is even more likely to be a chance match, and any argument for similarity between the proteins would be on the basis of some kind of convergent evolution based on certain common ligands, recalling again that the coronavirus might benefit from inhibiting an inflammatory response. preliminary studies on the panel of ligands discussed below suggest some degree of binding (-4.5 kcal/mole and better, i.e. more negative) to both the above and 11β-hydroxysteroid dehydrogenase type 1, but these studies are still not fully complete and low energies may yet be obtained. the most substantial data base of results that can reasonably be considered final is in large part from the original studies [50] . there carbenoxolone was automatically evolved (by automatic editing of its chemical structure) under the combined selective pressure of improve binding to 11βhydroxysteroid dehydrogenase type 1 while avoiding significant match with compounds covered by all us patents [50] , and subsequent docking and high grade molecular dynamic simulations were carried out on ibm's blue gene [50] . many subsequent studies have, however been carried out on using krunch on a personal computer, because in the initial study it predicted well the blue gene results providing that the krunch binding energies obtained were corrected (or refined) to fit the blue gene results by a linear regression formula [50] . recall again that it is on the basis of similarities between some compounds that antagonize sars virus entry and bind the steroid dehydrogenase, plus a notable commonality in the case of emodin (i.e. it binds both), that this model pharmacophore was chosen. since emodin and many other compounds of interest contain two or three or more aromatic rings, it is reasonable, at least as an initial tactic, that one may regard them as pieces of the steroid ring system and start them in the steroid binding cavity in the same "plane" as the steroid ring. in such a case involving minor variations as sidechains on the original steroid core, the way to make initial fit to using carbenoxolone as guide is obvious. however, the flat view of a steroid is misleading. the steroid ring system can "buckle" in various cis-trans combinations of bonds in the rings, and the longer sidechain conformations preferred on the basis of intramolecular energy are perhaps not obvious. although the rotation barriers for most of the transitions are clearly above the thermal energy (kt) energy conformations (0.6 kcal/mole), the associated energy demands for buckling of parts of the steroid ring system of variously and roughly 2.5 to 5.0 kcal/mole are less that the ligand-receptor binding the associated energy demands are below the gain in energy from ligand-receptor binding to the protein target. this is shown in the high grade quantum mechanical hartree-fock gamess calculations on blue gene in the original study [50] but which have not been described in the literature. minimized energy conformers of steroid-like compounds considered are shown in fig. 3 . calculations. such calculations in vacuo are less reliable for the charged species, but one may obtain a qualitative assessment from relative values and comparative uncharged species. these compounds are also shown more clearly from the chemist's perspective in two dimensional formula format, later below. fig. 4 shows one of early analogues of carbenoxolone (the thioketone derivative cbos1 discussed later below) in the 11βhydroxysteroid dehydrogenase type 1 steroid binding site. the particular interest in this compound is as follows. since in the original study [50] krunch judged this as the strongest binder at -16.8 kcal/mole, this compound was frequently used as a starting template for initial docking configurations when using krunch. this is even though (a) it is probably an unlikely choice for a chemist to use in practice because of likely oligimerization of the thioketone groups, and even though (b) corphos (also known as cortisol 21-phosphate, cortisol, phosphate, hydrocortisone-21-phosphate or 21-hydrocortisonephosphoric acid) was the strongest at -16.8 kcal mole when using instead the amber force field for molecular dynamics on ibm's blue gene [50] . the thioketone still retained a reasonable binding energy of -16.3 kcal/mole in the latter study, however, i.e. effectively the same binding strength within the state of the art. fig. 4 does not of itself give details of any ligand-protein interactions (but see discussion in refs [3, 49] ), although it does illustrate the tightest of fit. that is, except to the lower right of the thioketone ring of the ligand, which does appear to relate to genuine opportunities for additional groups to be added to carbenoxolone at that position. carbenoxolone and initial closely related derivatives derived in that study [50] are shown in fig. 4 , binding in the range, -17 to -14 kcal/mole. accuracy and limited realism of such methods does not really justify more precise statements on binding energy, and the classification of binding below is as strong, medium, and weak, but see ref [50] for more detail on some of the compounds. authors variously consider binding energies -5 to -9 as a safe requirement for significant binding, but again this is subject to considerations of accuracy and almost all agree that it is only the relative values that are significant. note that while they are often interpreteted as estimates of binding free energy, the entropy component, particularly of the aqueous solvent and solute-solvent intercations, is difficult to estimate. experimental binding values of ligands in general in biological systems typically range from -4 to -16 kcal/mole, though over 95% lie in the range -7 to -13 kcal/mole. the thiioketone derivatives are more of theoretical interest in binding studies because in practice they may cause oligmerization organic compounds binding the pharmacophore. strong binders. from the original study [50] . the estimated binding energy is in the range -17 to -14 kcal/mole. these were deigned from carbenoxolone with the intent to have a stronger or comparable strong binding (-16 kcal/mole). corphos, cbonring, and cbos2 bind at -17 kcal/mole. recall that the two peptide analogues of features of the spike protein of interest [3] are as follows. so far, simulations only show these to be binding relatively weakly at -10 and -8 kcal/mole respectively, but these compounds are highly flexible with a theoretical internal in vacuo conformational entropy corresponding to about -19.5 kcal/mole as discussed in theory section 2, show multiple binding modes and conformers on binding, and may not yet be complete. a high performance computer like ibm's blue gene used in the earlier drug design study [50] would certainly help. in fig. 6 is shown a set of compounds from the zinc data base [69] , and most were identified from the original 11β-hydroxysteroid dehydrogenase type 1 study [50] and subsequent studies. these bind significantly by usual criteria, but more weakly. they are in the range found for the synthetic peptides of interest, but have much less conformational freedom. a small few not shown here did appear in the original higher grade studies, but the reasonable binding energies could not be reproduced for reasons that are not as yet clear. organic compounds binding the pharmacophore. medium binders. from the zinc data base. the estimated binding energy is in the range -9 to -11 kcal/mole. fig. 7 shows some weaker binding results using krunch [50] . great caution is required in drawing conclusions from the compounds in fig. 3 . camostat is definitely of interest as an inhibitor of the ace2 protein to which the spike protein initially binds for cell entry and does seem effective in blocking entry [74] , and similarly hepsin results are of related interest, e.g. as it is a potential alternative entry point. the ace inhibitors also looked initially interesting by virtue of certain similarities to the other potential ligands, and of course because of their binding in this theoretical study, but most of the traditional ace inhibitors are commonly viewed as not inhibiting ace 2. taking a drug such as valsartan that acts on ace might up-regulate ace2, so facilitating virus entry, [75] but emerging information is revealing a complicated picture: see discussion and conclusions. there are possible explanations that would still allow for competing with spike protein binding, but these seem somewhat unlikely. most probably, the binding is sufficiently weak that the normal substrate, and also the spike protein, displace it. aromatic group interactions may be important here [76] . organic compounds binding the pharmacophore. weak binders. selected known drugs or proposals (caution: use of ace inhibitors might be counterproductive, see text). the estimated binding energy is in the range -5 to -7 kcal/mole. some consideration has been given to prediction of ligand binding site motifs, but so far these have proven essentially negative as regards interesting results that might shed any further light on the above, although some clues may well have been missed. binding sites are often comprised of conserved residues that are not contiguous (continuous in a sequence), which will require further and more detailed study, although subsequences of 2 to 6 amino acid residues in length are worthy of a quick preliminary study because they are commonly involved in ligand interactions. the matches involved in here as judged by blastp and clustal omega are not statistically significant, but one might think of weak matches as ligand binding site predictions in much the same way that one thinks of epitope predictions. in much of the present paper, the structure of emodin, carbenoxolone and related compounds have involved discussion of aromatic rings and hence phenylananine (f), tyrosine (y) and tryptophan (w) and more generally amino acid residues with hydrophobic character. very polar subsequences are also strong binders of charged ligands, or have a role for charged molecules or inorganic ions in some way. as far as such subsequences in the coronavirus spike protein are concerned, very polar charge-pattern motifs such drets and dreds are common in ligand binding some of the molecules that may be of interest as antagonizing sars entry, activation or replication in some way, in the present author's experience. specifically, motifs like this were of initial interest in the present project because sars-cov) nonstructural proteins have zinc finger motifs, and ret and especially red are common in prosite motifs at https://prosite.expasy.org/cgibin/prosite/prosite_search_full.pl, including zinc-finger motifs. this is not considered directly relevant to the spike protein but, for example respectively in genbank entry aia62240.1 and dreds and drets align with srldkv in three-way clustal omega alignment with srldk of the original wuhan spike protein sequence mn908947.3 and drldt of np_073551.1 spike protein. however, these and many similar alignments also illustrate considerable sequence variation, and the weak matches are not close in the sequence to the subsequences of interest neither for coronavirus spike protein nor human proteins of potential discussed above. as far as ace2 is concerned, the closes match with drets and dregs is drkkps, but this weak match again lays well away from regions of current interest, e.g. in the sequence from the region that interacts with the spike glycoprotein. dteta and drfin do occur in the c-terminal half of human 11β-hydroxysteroid dehydrogenase type 1, but again these are expected to be coincidental matches. like the first vaccines [77] therapeutics too have, of course, been drawn directly or almost directly from nature, until the late 19 th century when chemical synthesis became a science, and only in the 1970s did use begin to made of computers for rational drug design. the advantages of still seriously considering herbal remedies is that they tend to be tolerated by cells because they are produced in cells, they are already subjected to hundreds of years of human trial, are often economic solutions for bulk production, and are leads for further drug development and discovery. the principal non-peptide compounds considered above as possible therapeutics have such convenient and herbal sources. as reviewed previously [3] , the herbal extract emodin is a convenient product extracted from rhubarb, buckthorn, and japanese knotweed, and several fungi. the previous paper [3] also noted that emodin had certain molecular similarities with anti-inflammatory drugs such as carbenoxolone, derived from an extract, glycyrrhizic acid, from liquorish (licorice), that variously inhibit or are believed to inhibit human11β-hydroxysteroid dehydrogenase type 1. the above does not guarantee efficacy of emodin carbenoxolone against sars-cov-2, not least because even the emodin studies concerned sars-cov not sars-cov-2, and the case for the dehydrogenase is circumstantial, but these and related substances are worthy of investigation. indeed, this paper has described a number of compounds that bind the dehydrogenase. importantly, however, recall that the weak binders that are also ace inhibitors may be more dangerous and promote infection because they upregulate ace2 [75] . nonetheless, that situation is not resolved, as follows. the above considerations as to the action and possible usefulness are empirical observations that are largely independent of bioinformatics and molecular computation and they are even independent of whether the correct human protein targets discussed here are correct and relevant; however, it would be valuable to know what might relate ace2 and 11β-hydroxysteroid dehydrogenase type 1, and ideally also understand why both enzymes might "benefit" the coronavirus by interaction with them. also, this paper could not provide any evidence of an evolutionary relationship between these proteins, despite certain similarities, or with tmprss2. so far, there is no obvious relationship with the dehydrogenase, and some other studies by the author on other transmembrane serine proteases do not, as yet, suggest any relationship. without such connections, the dehydrogenase can only be considered as a rather arbitrary model pharmacophore. as such, it is possibly meritorious as correctly representing an ensemble of multiple targets, but that may be fortuitous, and hence only to be used until refuted by evidence. nonetheless, possible clues as to mutual relevance of these human protein targets might come noting their tissue distribution and considering how this may relate to their biological role. as regards ace2, its mrna is known to be present in virtually all organs. studying sars entry into human cells, hamming et al. [78] considered their most remarkable finding to be the substantial surface expression of ace2 protein not only on lung alveolar epithelial cells but also enterocytes of the small intestine, as in arterial and venous endothelial cells and arterial smooth muscle cells in all organ studied (oral and nasal mucosa, nasopharynx, lung, stomach, small intestine, colon, skin, lymph nodes, thymus, bone marrow, spleen, liver, kidney, and brain). there is the attractive prospect that several many herbal remedies considered as laxatives interact with ace2 and inhibit sars-covid-2 entry. recall that emodin is an antagonist of both ace2 [59] [60] [61] and 11β-hydroxysteroid dehydrogenase type 1 [62] . in the past, 11βhydroxysteroid dehydrogenase type 1 has been considered to be distributed mainly in the human liver, with no detectable levels in the intestine or kidney, mostly membranebound and retained in the liver microsomal fraction [79] . this was not however the finding of bruley et al. 80] . they found it to be highly expressed in glucocorticoid target tissues including liver and notably the lung, and modest levels in the brain. it was also found in modest levels in adipose tissue where it is of medical interest that selective increase expression occurs in obese humans and rodents and is likely to be of pathogenic importance in the metabolic syndrome [80] . lung expression appears to be managed differently: a new promotor that the authors discovered and called p1 predominated in lung while the previously known promotor predominated in liver, adipose tissue, and brain [79] . researchers therefore need to sort out an intriguing web of information. it is possible that a complex web of laxative and anti-inflammatory effect may provide clues by somehow relating to the body's attempts to reject and eject viruses of this kind, and the virus's attempts to resist. it is well known that some covid-19 patients complain of stomach upsets and diarrhea. to recapitulate the essential themes in terms of action in the alimentary tract, recall again that emodin had earlier been shown by several groups of researchers (e.g. ref [79] ) to inhibit sars-cov entry into cells (apparently initially by binding ace2), and emodin is taken as a herbal laxative. licorice has, conversely, been sometimes taken as a soother for alimentary disorders, and carbenoxolone has been used commercially in the past specifically to treat peptic ulcers. intriguingly, carbenoxolone is also known to influence the renin-angiotensin system involving ace2, so at least there appears to be a connection in terms of networks of physiological control. as noted above, while traditionally 11β-hydroxysteroid dehydrogenase type 1 has been thought of as a liver enzyme, many researchers have indicated that both ace2 and the dehydrogenase are available in both lung and intestinal tract (e.g. refs [78] [79] [80] ). this all hints also that some of the other laxatives that work in a similar stimulatory way might block viral entry on ace2 and perhaps other targets, and should be explored. of course, absolutely nothing should be done by patients without physician direction, because dosages are difficult matters (not least in herbal products) and there are potentially serious side effects on such as salt balance and blood pressure, and some might cause birth defects, all potentially worse than covid-19 would be, for most people. but more worryingly still, the situation is not settled, and physicians and patients could take action in the wrong direction. gurwitz [81] has emphasized that the picture is even more complex. he examined reports from china suggesting that a mechanism of production of lung injury during the viral infection may be due to excess free angiotensin-ii, which might be displaced from ace2 by the sars virus particles. if so, then increasing the amount of ace-2 could be desirable and administering angiotensin receptor antagonists could beneficially upregulate the production of ace-2. it now becomes important to examine medical records of patients who have, and who have not, been infected by sars-cov-2, with a particular eye on who is, and who is not, taking ace inhibitors. as noted in section 1.4, merrifield developed first solid phase peptide synthesis on crosslinked polystyrene beads in 1963 [12] . somewhat like natural compounds discussed above, peptides and petidomimetics are potentially important first steps in more detailed rational design of small organic molecules convenient as traditional "in a pill" drugs. however, as in the present paper, the ability to propose specific peptides and peptidomimetics does depend on bioinformatics, and benefits from some computational chemistry. note that in this case, one is thinking largely not of screening natural products, but now considering truly novel molecules using theoretical methods because they do not yet exist. the variations in the krsfiedllfnkv motif that might be appropriate to synthetic vaccine and peptidomimetic antagonist design suggest the following where the amino acid residues in square brackets [ ] represent alternatives. (g?) means an optional glycine insertion. the above is also valid as a regular expression, i.e. a match query in operating systems and software. more generally and colloquially, (positive charge)-(optional glycine)-serine-hydrophobic-hydrophobic-glutamate-aspartatehydrophobic-leucine-phenylalanine-(hydrophilic or alanine)-lysine-valine considerations at the n-terminus and c-terminus to design a synthetic vaccine, and the retro-inverso approach for a peptidomimetic agonist, are described in ref [3] . other variations appear as the strain becomes more distant; there is not a universal clear indication of any sharp point of departure, although the above glycine (g) insertion is evidence that a significant jump can happen. one may therefore ask what variations should be included. with the emphasis on sars-cov-2, only closely and medium distance relatives are of interest, with the purpose of prevent mutations that escape from vaccines and antagonists, and elude diagnostics. as far as sars-cov-2 is concerned, krsfiedllfnkv is a satisfactory basis because a large number of coronaviruses significantly different from sars-cov-2 preserve it, or in a few cases have very conservative substitutions. it may well be that the fact that residues are, for example, hydrophobic or positively charged is sufficient to for the approach to be applicable to other mammalian coronavirus diseases, if successful for the above basic motif form. attempting to tackle the common cold is not a priority. in other words, it may well be that an immune response against krsfiedllfnkv will also illicit a response against the motif variants, providing of course that krsfiedllfnkv elicits a response itself. it remains that this motif is one of very few subsequences that still recognizable when moving on to rather distantly related coronaviruses such as those of the common cold. one feature of both figs. 5 to 7 is of course the constant appearance of aromatic rings, and this is also noticeable in many of the studies of antagonist's against sars virus binding and activation. of course, the aromatic (i.e. benzene) ring makes copious appearance in many pharmaceutical agents in any event, because they provide rigid scaffolds for added groups supported by many long-established recipes for synthesis. the compounds in figs. 5 to 7 should be distinguished from those such as lopinavar, ritonar, promazine and particularly niclosamide that have been explored for sars viruses in the past, because these are targeted by drug designers against the sars virus own protease required for maturation of the assembling virus. nonetheless, some of these do have a visual similarity to the compounds in fig. 3 , particularly niclosamide (which is normally a medication used to treat tapeworm infestation). also, in the present case, prevalence of aromatic rings in figs 1 to 3 is hardly surprising, since carbenoxolone and derivatives shown in fig. 1 were the starting point for their evolution or selection from the zinc data base. nonetheless, there is, in principle, nothing to constrain the evolution to aromatic chemistry [50] and later unpublished studies did produce molecules departing from aromatic chemistry. however, these bound relatively weakly. with the possible importance of aromatic rings and avoidance of escape mutations by the coronavirus in mind, a question is whether occasional loss of phenylalanine (f) from the krsfiedllfnkv motif discussed above contests the tentative hypothesis that the peptidomimetic candidates derived from krsfiedllfnkv bind to a similar site as the smaller organic ligands considered here, because of two phenylalanine residues (f) in the original motif and a tendency to several benzene rings in the case of organic ligands. the answer is: perhaps. there seems to be a need to have one aromatic ring present in the motif, and no match with a coronavirus in genebank was detected by the author by blast-p using queries with no phenylalanine (f), e.g. rsaiedllldkv, rsaiedllidkv, rsaiedlladkv, rsaiedllmdkv, rsaiedllwdkv, and rsaiedllydkv as queries, though as also noted above, the search has not been exhaustive. it would not be too contradictory to any of the current main hypotheses if some examples were found. the fact that tyrosine (y) does not seem to readily substitute here for phenylalanine (f) (from which it differs only by a hydroxyl -oh, i.e. phenolic group) suggests an important hydrophobic feature of the pharmacophore at that point. of course, many or most drug-like molecules contain at least one aromatic ring and this is almost certainly because they can form especially strong stacking interactions in the binding site. one very relevant report in the same month of writing the present paper emphasizes that the use of protein and other fragments to characterize binding pocket and determine the strengths of ligand-protein interactions is common in both a computational and experimental approach, and that aromatic interactions are both strong and need special attention [76] . because of resonance and the special nature of the π orbitals, the strength of stacking is best calculated using high level quantum mechanical approaches, not empirical force fields [76] . however, as these calculations are performed in vacuum, solvation properties are neglected, and this led to the proposal of a grid inhomogeneous solvation theory (gist) to describe the properties of individual heteroaromatics and complexes; this gave good correlation for the estimated desolvation penalty and the experimental binding free energy, and prediction of binding sites [76] . a main conclusion is that peptide krsfiedllfnkv remains of special interest as well conserved across coronaviruses. other sites and other proteins of the virus may, of course, emerge as the solutions to this formidable problem. all aspects of the virus must be considered. however, even the ace2 binding domain is significantly more prone to accepted mutations. the recurrence of the 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receptor blockers as tentative sars-cov-2 therapeutics drug discovery using very large numbers of patents. general strategy with extensive use of match and edit operations towards automated reasoning for drug discovery and pharmaceutical business intelligence towards new tools for pharmacoepidemiology the concept of novel compositions of matter. a theoretical analysis suggestions for a web based universal exchange and inference language for medicine hyperbolic dirac nets for medical decision support. theory, methods, and comparison with bayes nets popper, a simple programming language for probabilistic semantic inference in medicine suggestions for a web based universal exchange and inference language for medicine. continuity of patient care with pcast disaggregation split-complex numbers and dirac bra-kets implementation of a web based universal exchange and inference language for medicine. sparse data, probabilities and inference in data mining of clinical data repositories interesting things for computer systems to do: keeping and data mining millions of patient records, guiding patients and physicians, and passing medical licensing exams data-mining to build a knowledge representation store for clinical decision support. studies on curation and validation based on machine performance in multiple choice medical licensing examinations studies of the role of a smart web for precision medicine supported by biobanking studies in using a universal exchange and inference language for evidence based medicine. semi-automated learning and reasoning for pico methodology, systematic review, and environmental epidemiology studies in the extensively automatic construction of large odds-based inference networks from structured data. examples from medical, bioinformatics, and health insurance claims data • this paper "drills down" into the studies of the author's previous covid-19 paper.• designing vaccine and drugs must seek to avoid escape mutations.• subsequence krsfiedllfnkv seems recognizable across many coronaviruses.• the ace2 binding domain is a target, but shows variation.• a steroid dehydrogenase is argued to remain an interesting model pharmacophore.this paper is provided to the community to promote the more general applications of the thinking of professor paul a. m. dirac in human and animal medicine in accordance with the charter of the dirac foundation , to emphasize the advantages and simplicity of the basic form of the hyperbolic dirac net, to encourage its use, and to propose at least some of the principles of the associated q-uel, a universal exchange language for medicine, as a basis for a standard for interoperability. these mathematical and engineering principles are used, amongst many others in an integrated way, in the algorithms and internal architectural features of the bioingine.com, a distributed system developed by ingine inc. cleveland, ohio, for the mining of, and inference from, very big data for commercial purposes. immediately prior to joining ibm in 1998 he was hired as principal scientist at mdl information systems in california to help put together the technology for the multimillion sale of a bioinformatics system to the holding company forming craig venter's celera genomics that produced the first draft of the human genome. prior to that, he was cso of gryphon sciences (later gryphon pharmaceuticals) in south san francisco, california, a bio-nanotechnology ultrastructural chemistry start-up largely held and then acquired by smithkline beecham. before moving to the us, barry was the scientific founder of proteus international plc in the uk, designing and leading the development of the prometheus expert system and its underlying global expert system, bioinformatics and simulation language for drug, vaccine, and diagnostic discovery. it sold for the equivalent of $9.4 million to the pharmaceutical industry in the mid-1990s. at proteus, he also led the team that used the above expert system to invent and patent several diagnostics and vaccines including the mad cow disease diagnostic subsequently marketed worldwide by abbott. he has some 300 scientific publications including some 50 patents and two books: "the engines of hippocrates. from the dawn of medicine to medical and pharmaceutical informatics" robson and baek, 2009, wiley, 600 pages)" and "introduction to proteins and protein engineering" (b. robson and j. garnier, 1984 garnier, , 1988 , elsevier, 700 pages). he has contributed to several reports to governments including panels of the national innovation initiative including "innovate america" published by the council on competitiveness, washington d.c. (2004) as a whitepaper to the president of the united states. for five years, barry was a nature "news and views" correspondent on biomolecules. key: cord-298857-4y5o2p44 authors: zhu, jie; cai, yi title: engaging the communities in wuhan, china during the covid-19 outbreak date: 2020-07-13 journal: glob health res policy doi: 10.1186/s41256-020-00162-3 sha: doc_id: 298857 cord_uid: 4y5o2p44 during the early stage of the covid-19 outbreak in wuhan, the lockdown of the densely-populated metropolis caused panic and disorderly behavior among its population. community governance systems (cgss) were mobilized to lead community engagement to address the challenges and issues brought about by the sudden quarantine measures, still unprecedented in any part of the world during that time. this commentary aims to describe and analyze the roles of the cgss, its implementation of culturally-tailored strategies and the performance of new functions as called for by the outbreak. we will introduce the community governance structure which has two parallel administrative units of government including the branches of the communist party of china (cpc). the pandemic showed that the roles of the cgss evolved and may continue to be improved in the future. it is important to engage the community and to have community-based approaches in addressing issues brought about by lockdowns. this community experience in wuhan provides important lessons for the rest of the world. wuhan is a crowded metropolis with a population of 14 million. the city has come to a halt during a metropolitan-wide quarantine on january 23, 2020 due to the spread of covid-19. major problems erupted in wuhan at the early stage of the quarantine. hospitals were inundated with patients because of the public panic. this resulted in severe shortages of medical supplies placing health care workers at high risk to infection. the epidemic started to overwhelm the health care system. circulating rumors aggravated the situation which led to trust issues on the government. as problems kept on mounting, wuhan initiated strict containment strategies at the community level. this meant restricting the movement of the population and strictly confining them within their homes and communities. as a result, normal daily lives of the residents were disrupted including the celebration of the spring festival. the quarantine and confinement of the millions of population brought about unique emotional and other demands necessitating public service responses. a community approach was initiated by the government to address the need of the communities by mobilizing the community governance systems (cgss), a grassrootslevel unit of governance instituted across the country. the cgss was tasked and given the responsibility to meet the various needs of the community, implement containment strategies, and play multiple roles in engaging with the local residents. this commentary aims to describe and analyze the roles played by the cgss and to show the community dimension of governance during the pandemic in china. a community is a small-scale, kinship-, or neighborhood-based unit as compared to a society which pertains to a "large-scale, and competitive market-based unit" [1] . in the context of china, communities are the cells of the chinese society, usually referred to as "communities" in urban areas and "villages" in rural areas. the chinese society is administered by a top-down hierarchical governance system, which is composed of five levels of governments, from the central government to the grassroots level of urban street/rural township governments (fig. 1) . the grassroots unit of government plays a role in community governance. community governance in china is characterized by the integration of an autonomous governance component juxtaposed with a hierarchical governance component. these components are composed and performed by three types of organizations. the autonomous governance is a function of the homeowner associations. with the development of real estate in china, most urban residents became homeowners. homeowner associations were then established to manage their own communities. property management companies are under the management of the homeowner associations. directors of the homeowner associations are elected by the community residents. the hierarchical governance is performed by the grassroots or local governments and the branches of the communist party of china (cpc). they work hand-inhand and in parallel with each other. the grassroots government takes charge of community governance to maintain social stability. they are deployed governmental staff who work in the homeowner associations. the central cpc requires each homeowner association to establish a cpc branch. members of a cpc branch in the community are residents themselves living in the same community. the cpc branch secretaries are elected by the cpc members within the homeowner associations. the cpc members are deemed to contribute more voluntary work and have to perform their functions and responsibilities to the highest standards as part of the cpc accountability system and code of conduct. on the other hand, there is a lesser demand on the non-cpc members. to illustrate this point, on 16 february, four grassroots government officials who were cpc members were meted disciplinary actions for not being able to meet the standards of work during the containment period [2] . 580,000 cpc members from high-level government offices volunteered for the communities in wuhan. as a prerequisite for community engagement to the covid1-9, the world health organization (who) suggested the use of community influencers. they can be community and religious leaders or health workers [3] . within the chinese society, the cpc members are identified to be the most influential and most trusted. during the emergency situation, the cpc members were logically identified as community influencers. they showed effectiveness in mobilizing the people. in addition, cpc members also performed as role models and servant-leaders, which enhanced their ability to influence. they were the first to contribute to the communities which gradually influenced public engagement and in having more volunteers for community services. these volunteers drastically relieved the shortage of human resources needed within the cgss. most communities were provided with public services since the cpc have branches and a wide network in most of these areas, thus not missing out on any community. because the cpc members share the belief of the cpc members on the same guiding principles, which are consistently followed, made the cooperation among them smooth and the functions were performed efficiently and fast. the cgss faced challenges in implementing some containment strategies such as staying home, which was difficult to follow during the celebration of the chinese lunar new year when the covid-19 first broke out. it is customary to celebrate by sharing a meal with family members during the new year's eve, visiting relatives and friends, and hosting parties. cancelling all festivities, particularly in rural areas, was deemed difficult, if not futile. to address this challenge, the cgss created many culturally tailored initiatives to improve the understanding of the containment strategies. for example, due to the importance of family culture to chinese people, the cgss extended the connotation of "family" from a small-family to a big-family which pertained to the city of wuhan; even encompassing the forty counties within the area. this made the people easily grasp the concept of solidarity in fighting the battle against the covid-19. they were observed to be more understanding and cooperative during the latter part of the outbreak. one of the tasks of the cgss during the lockdown and the community closure was to establish a referral system for patient triage within their communities. before patients are transferred to the hospitals, cgss together with community health workers were tasked to be gatekeepers. they identified and diagnosed suspected patients and transferred confirmed cases to the hospitals. prior to this, since there was no established protocol for hospital referral, patients would directly go to the hospitals upon experiencing fever [4] . this necessitated the establishment of a referral system and patient triage. the cgss became responsible for screening febrile patients in the communities and transferring them to quarantine sites for medical observation or sending them to fever clinics for diagnosis [5] . this made the system efficient. on february 12, 2020, for example, over 13,000 cases including clinically diagnosed cases were screened within the communities in 24 h [6] . the cgss also played a role in health information management by acting as a hub for information transfer. the cgss collected first-hand health information from the residents and reported it to higher authorities who then collected and summarized all information before being reported back to the public. this contributed to risk communication strategies and in the provision of timely response to public concern. ensuring that families remain at home, the cgss had to assist in providing them services and supporting their various needs. the cgss organized online grocery shopping, delivered medications to chronic patients, provided transportation to residents who needed medical emergency care, and assisted the police in persuading and enforcing quarantine procedures for non-compliant residents [7] . engaging the community and having community-based approaches in addressing covid-19 have been shown to play a significant role in addressing the issues brought about by the lockdown in the covid-19 outbreak in wuhan. through the community-centered approaches including the mobilization of cgss, the redefinition of their roles, the use of community influencers, and the employment of culturally tailored strategies, national covid-19 initiatives became more effective and efficient. this experience in wuhan may provide lessons for the rest of the world in addressing their local outbreaks. community and civil society four cases are punished for irresponsible behaviors during the covid-19 prevention and control in wuhan world health organization. risk communication and community engagement (rcce) readiness and response to the 2019-ncov the primary health-care system in china wuhan headquarters for covid-19 epidemic prevention and control (whep c-covid-19). the no. 11 bulletin issued by the whepc-covid-19 wuhan headquarters for covid-19 epidemic prevention and control (whep c-covid-19). the covid-19 epidemic situation on february 12, 2020 in hubei province the novel coronavirus outbreak in wuhan, china we have benefited from valuable comments on earlier versions of the manuscript from anonymous reviewers. particularly, we appreciate dr. don eliseo lucero-prisno iii from the london school of hygiene & tropical medicine, for editing the language and refining key messages. authors' contributions zhu j and cai y discussed, draft and revise the commentary together. the author(s) read and approved the final manuscript. not applicable.availability of data and materials not applicable.ethics approval and consent to participate not applicable. competing interests not applicable. received: 19 february 2020 accepted: 1 july 2020 key: cord-292537-9ra4r6v6 authors: liu, fenglin; wang, jie; liu, jiawen; li, yue; liu, dagong; tong, junliang; li, zhuoqun; yu, dan; fan, yifan; bi, xiaohui; zhang, xueting; mo, steven title: predicting and analyzing the covid-19 epidemic in china: based on seird, lstm and gwr models date: 2020-08-27 journal: plos one doi: 10.1371/journal.pone.0238280 sha: doc_id: 292537 cord_uid: 9ra4r6v6 in december 2019, the novel coronavirus pneumonia (covid-19) occurred in wuhan, hubei province, china. the epidemic quickly broke out and spread throughout the country. now it becomes a pandemic that affects the whole world. in this study, three models were used to fit and predict the epidemic situation in china: a modified seird (susceptible-exposed-infected-recovered-dead) dynamic model, a neural network method lstm (long short-term memory), and a gwr (geographically weighted regression) model reflecting spatial heterogeneity. overall, all the three models performed well with great accuracy. the dynamic seird prediction ape (absolute percent error) of china had been ≤ 1.0% since mid-february. the lstm model showed comparable accuracy. the gwr model took into account the influence of geographical differences, with r(2) = 99.98% in fitting and 97.95% in prediction. wilcoxon test showed that none of the three models outperformed the other two at the significance level of 0.05. the parametric analysis of the infectious rate and recovery rate demonstrated that china's national policies had effectively slowed down the spread of the epidemic. furthermore, the models in this study provided a wide range of implications for other countries to predict the short-term and long-term trend of covid-19, and to evaluate the intensity and effect of their interventions. novel coronavirus pneumonia (coronavirus disease 2019, covid-19) break out firstly in wuhan, hubei province, china in december 2019, then the epidemic became prevalent in the rest of the world. with the research on covid-19 so far, through the comparison of the gene sequence of the virus with that of the mammalian coronavirus, some studies found that its source may be related to bat, snake, mink, malayan pangolins, turtle and other wild animals [1] [2] [3] [4] . covid-19 can also cause severe respiratory diseases such as fever and cough [5] , and there is a possibility of transmission after symptoms of lower respiratory diseases [6] . however, unlike sars-cov and mers-cov, covid-19 is separated from airway epithelial cells of patients [6] , yet the mechanism of receptor recognition is not consistent with sars [7] . therefore, the pathogenicity of covid-19 is less than that of sars [8] , and its transmissibility is higher than that of sars [9] . in addition, this new coronavirus presents human-to-human transmission [10] , and close contact could lead to group outbreaks [11] . as of july 7th, 2020, 85,359 confirmed cases and 4,648 deaths had been reported in china [12] . in addition to china, there are over 200 countries and regions in the world with a total of 11,630,898 of confirmed cases and 538,512 of deaths [12] . the outbreak of covid-19 happened right before the lunar new year, which is typical chinese spring festival transportation period. with a population of over 11 million, wuhan is one of the major transportation hubs in china as well as a core city of the yangtze river economic belt. the time and location of the outbreak further led to the rapid spread of the epidemic in china [13] . since there is still no vaccine or antiviral drug specifically for covid-19, the government's policies or actions play an important role in flatting the epidemic curve [14] . from the perspective of public health, the interventions of wuhan government have achieved the purpose of reducing the flow of people and the risk of exposure to the diagnosed patients, and also effectively slowed down the spread of the epidemic [15] . nevertheless, covid-19 can be transmitted by asymptomatic carriers [16] , and some of the recovered patients may still be virus carriers [17] . in order to implement non-pharmaceutical interventions more effectively, we used a combination of epidemiological methods, mathematical or statistical modeling tools to provide valuable insights and predictions as benchmarks. for the study of infectious diseases like covid-19, sars, and ebola, most of the literature used descriptive research or model methods to assess indicators and analyze the effect of interventions, such as combining migration data to evaluate the potential infection rate [18, 19] , understanding the impact of factors like environmental temperature and vaccines that might be potentially linked to the diseases [20, 21] , using basic and time-varying reproduction number (r 0 & r t ) to estimate changeable transmission dynamics of epidemic conditions [22] [23] [24] [25] [26] [27] , calculating and predicting the fatal risk to display any stage of outbreak [28] [29] [30] , or providing suggestions and interventions from risk management and other related aspects based on the results of modeling tools or historical lessons [31] [32] [33] [34] [35] [36] [37] [38] [39] . some literature only used one kind of model to simulate and predict the course of diseases. for instance, to use relatively common epidemiological dynamics models like seir or sird to forecast epidemic trends and peaks in certain provinces, even the world [9, [40] [41] [42] [43] [44] ; to apply some other types of statistical models such as the logistic growth models or time series approaches to analyze the epidemic situation [45, 46] , or to develop new models to support more complex trajectories of epidemics or to predict the number of confirmed cases and the spatial progression of outbreaks [47] [48] [49] . several studies were further expanded based on the basic epidemic dynamic models. for example, joining the border protection mechanism with the seir model to better identify high-risk groups and infected cases [50] ; adding the effect of media or awareness into basic models to assess whether these outside influences would possible change the transmission mode of infectious diseases [51, 52] ; or according to transmission routes contained in dynamic models, using a multiplex network model or transmission network topology to analyze the outbreak scale and epidemic spread more accurately [53, 54] . a small number of studies combined the analysis capabilities of two types of models, like seir model and the recurrent neural networks model (rnn), to determine whether certain interventions could affect the results of outbreak control [55] . however, we did not find any analysis method using geographically weighted regression (gwr) on covid-19 study based on our literature research. there is also a lack of understanding the model efficacy of predicting the epidemic curve among different algorithms. in this study, an seir's extended model seird was used to simulate the epidemic situation in china and to predict the number of confirmed and cured cases in each province and several major chinese cities. an lstm model combined with traffic data and a gwr model were used to predict the number of confirmed patients. specifically, gwr model showing geographical differences was used to predict the development of epidemic situation and analyze the impact of geographical factors. this paper also compares the characteristics and prediction ability of these models. in the absence of vaccines and drugs for covid-19, it makes sense to use multiple models to show the situation and intensity of non-pharmaceutical interventions needed to simulate and guide the control of outbreaks. daily updated covid-19 epidemiological data used in this study were retrieved from national health commission of china [12] and accessed via https://github.com/wybert/openwuhan-ncov-illness-data. the daily number of outbound from wuhan city and relevant migration indice from january to march were collected from an online platform called baidu qianxi [56] . the demographic data and medical resources data were from china urban statistical yearbook published by the national bureau of statistics as shown in s1 table. this study used seird model and the changes in the status of the susceptible (s), exposed (e), infected (i), recovered (r) and dead (d) population in the total population (n) are shown in fig 1. according to the medical characteristics and clinical trials of covid-19, both confirmed patients and asymptomatic carriers have the ability to transmit the virus. therefore, susceptible people have a certain chance to become infected after they come into contact with exposed or infected individuals [43] . carriers in the exposed status may develop obvious symptoms after the incubation period and become diagnosed or they may be recovered. the final status of individuals can be basically divided into two categories: one is the recovery from the combined effects of treatment in hospital and autoimmunity, and the other is the death without effective treatment. in the model formula, the infectious rate β needs to be adjusted in real time to adapt to the trend of disease development. in the middle and late stages of the epidemic, the number of daily new cases decreased significantly due to the positive influence of government policies. thus, to better fit the model, we added an attenuation factor desc to β. based on the basic seird model formulas [57, 58] , our modified model was shown as eqs (1) (2) (3) (4) (5) (6) . here, the parameter t denotes the time; β is the infectious rate; α is the rate for the exposed to be infected; γ 1 is recovery rate for the exposed; γ 2 is the recovery rate for the infected; k is the mortality rate; "desc" is the attenuation factor for β, so that β decays exponentially when 0<desc<1, and β is a constant when desc = 1. lstm (long short-term memory) architecture for recurrent neural networks was first proposed in 1997 [59] . a lstm block is illustrated in fig 2. it features three gates (input, forget, and output), a block input and an output. the output of the block is recurrently connected to the input of the block. the vector formulas for a lstm layer forward pass are given below in eqs (7) (8) (9) (10) (11) (12) . here, z t , i t , f t , c t , o t and h t denote the block input, input gate, forget gate, cell state, output gate and block output, respectively. and x t represents the input vector at time t, ⊙ is the pointwise multiplication operator of two vectors, the w z , w i , w f , and w o are input weight matrices, is used as the activation function of the gates and relu is used as the activation function of the block input and output. epidemic situations and medical resources in different geographic situations may have different extents of influence on the development of the epidemic. ordinary least squares fitting method for regression may not be applicable in this case. geographically weighted regression model (gwr) was proposed in 1996 [60] , which extended the ordinary linear regression model and embedded the geographic location data into the regression parameters as shown below: where y i is the i th dependent variable, x ik is the k th independent variable in location i, p is the total number of independent variables, β i0 is the intercept parameter in location i, β ik is the regression coefficient for the k th independent variable in location i, which varies with the geographical location, and ε i is the error term in location i. the spatial weight matrix in this study uses the bi-square kernel function shown below: if d ij <b, otherwise w ij = 0, where b is the bandwidth, a non-negative attenuation parameter and d ij denotes the distance between the i th and j th observation points. the bandwidth is calculated by optimizing the root mean square prediction error of cross-validation [61, 62] . in this study, we used the modified seird model to make predictions of the number of cumulative confirmed cases in the next day for all provinces, province-level municipalities and autonomous regions in china as well as wuhan city. the parameters were adjusted daily in our dynamic seird model based on the daily updated epidemic data. the comparison of the actual data on february 14 th and february 25 th with the forecast results of our models is shown in table 1 . the percent error was calculated using the formula: (predicted number-actual number)/ actual number × 100%. on february 14 th , the absolute percent errors of all provinces were < 5%. the percent error for wuhan city, hubei province and china were -3.00%, -1.60% and 1.00%, respectively. on february 25 th , the absolute percent error of prediction of cumulative confirmed cases in china was < 0.10%. the absolute percent errors of most provinces were < 0.10%, among which the absolute percent errors in wuhan city was < 0.10% and that of hubei province was less than 0.10%. regarding the number of recovered cases, wuhan city and hubei province had percent errors of -6.03% and -3.12%, respectively. the overall prediction of recovered of the whole country was consistent with the actual situation with percent error of -2.46%. the predicted number of deaths in hubei province was off by 1.40% (forecast 2,599 vs. actual 2,563). actual and predicted number of confirmed cases using the modified seird model for china, hubei province and wuhan city are shown in fig 4 ( hubei province and wuhan city adjusted the criteria for diagnosis on february 13 th , and the number of confirmed cases increased by about 10,000 on that day [63] . in order to smooth the sudden change, the number of cumulative cases before february 12 th in hubei city and wuhan province was proportionally enlarged according to the new criteria. the same for fig 5) . the actual and calculated values of these three regions provided satisfying fitting curves, indicating that the situation simulated by the model was basically in line with the actual situation of the epidemic development. in this study, the inflection point was defined as the date when the number of existing confirmed cases has the largest slope. according to the seird dynamic model, the inflection points of all provinces appeared generally in february, while the specific time varied from region to region. the results of model simulation revealed that the inflection point in wuhan city and hubei province showed up in early february, and that of the whole country roughly in the first half of february, which basically conformed to the spread of covid-19 in china. using data on march 5 th , the model predicted the long-term trends in the number of confirmed, cured and deaths for china, hubei province and wuhan city (fig 5) . again, the model used adjusted historical data as discussed above. under the various social non-pharmaceutical interventions and not allowing for the imported cases from foreign countries, the cumulative number of confirmed nationwide was expected to reach about 83,000 at the end of the epidemic. hubei province was expected to have a total of about 70,000 confirmed cases and wuhan city about 50,000. data from four regions, zhejiang, guangdong, beijing, and shanghai were selected to train the lstm neural network to predict the number of cumulative confirmed cases of the next day. since the lstm model had a memory function, the first feature included in the model was the number of cumulative confirmed cases on the previous day. considering that the number of migrants from wuhan also affected the studied city, thus the number of migrants from wuhan was also included in the analysis. there was a certain probability that some migrants from wuhan may be patients because of the virus's incubation period, and the inference of this probability was based on the number of confirmed cases in wuhan. therefore, the second feature considered the number of migrants from wuhan on the previous day, and the confirmed number of patients in wuhan on the previous day. the feature was calculated as the cumulative number of immigrants from wuhan multiplied by the incidence of covid-19 in wuhan on the previous day. this lstm architecture was designed into 4 layers: an input layer, an lstm layer (hidden layer), a fully-connected layer and an output. each lstm neuron had 10 hidden features, and the activation function was relu. the loss function was mse, and the optimizer was "adam". the model structure diagram is as fig 6. this study used the grid search method to set different hyperparameters for data in different regions. the model was trained and the predicted results for latest 8 consecutive days as shown in in this study, the data of 220 cities that had confirmed cases on february 2 nd were selected to predict the number of confirmed cases on february 3 rd . the number of confirmed cases, the number of deaths and the number of cured cases are main indicators for the epidemic. among them, the number of confirmed cases was the mostly used and reflected the severity of covid-19 epidemic. therefore, this study used the cumulative number of confirmed cases in different places released by the national health commission as dependent variable. in this study we select the population of each city, the number of hospitals per 10,000 people, the number of doctors per 10,000 people, the number of inpatient beds per 10,000 people, the number of confirmed cases, the number of cured cases, and the number of deaths one day and 2 days ago as independent variables. the gwr model was fitted using the data of february 2 nd , and we further made forecast for the number of the confirmed cases on february 3 rd . the r 2 of gwr regression on february 2 nd was 99.98% and the r 2 of the prediction of the data on february 3 rd was 97.95%. the percent errors of fitting and prediction varied for different cities: for beijing were 11.67% and 3.95%, respectively; for shanghai were 2.24% and -5.88%, respectively, for xiaogan in hubei province were -1.27% and 1.70%, respectively, and for wuhan were 0.00% and 14.57%, respectively. the summary of the intercept and coefficients of the independent variables were listed in table 4 . it shows that the coefficients of the demographic data, and the medical resources data have larger variations than those of epidemic data. the coefficients of population, number of hospitals per 10,000 people, number of doctors per 10,000 people, dead_lag1, confirmed_lag2, cured_lag2 were negative, showing that these factors have negative influence on the dependent variable. while the other independent variables, number of inpatient beds per 10,000 people, confirmed_lag1, cured_lag1, dead_lag2 have positive coefficients, indicating positive influence on the dependent variable as shown in table 4 . as of mid-march 2020, more than 60,000 people had been cured in 31 provinces, provincelevel municipalities, and autonomous regions in china, and new cases of infection were mainly led by overseas imports. although the covid-19 epidemic was not over, the traffic in the low-and medium-risk areas in hubei province had been gradually resuming, indicating that the government's non-pharmaceutical interventions had significantly positive effects. in this study, the modified seird model was used to conduct parameter sensitivity analysis of β, desc, and γ 2 based on data before march 5 th , so as to simulate the impact of prevention and control measures on real-time infections for china, hubei province, wuhan city, and beijing city (fig 9) . the decrease of the infectious rate β would promote the reduction of infections during the entire epidemic stage with other conditions being equal (fig 9a) . the shape of the epidemic curve was basically unchanged, but the duration of the epidemic increase as the infectious rate itself increases. the number of cases increased obviously, and the peak of real-time infections was postponed as the infectious rate increases. when the infectious rate increased to 125%, the epidemic size doubled with the delay of the peak of real-time infections by about 10 days ( fig 9a) . moreover, increasing the attenuation factor of infectious rate could lead to a significant slowdown in the spread of the epidemic and the shape of the epidemic curve changed (fig 9b) . in the beginning, the growth of attenuation factor changed the number of confirmed cases little, but the number had changed dramatically over time, the peak of the epidemic moved forward with the increase in the attenuation factor (fig 9b) . the duration of the epidemic also advanced correspondingly. a combination of the changes in the infectious rate β itself and the changes in the attenuation factor of β could reflect the effects of the measures such as timely isolation of confirmed or suspected patients and reduction of population mobility. coupled with the community containment measure, the number of exposed, infected and susceptible individuals outside were greatly reduced, so that the extent of the epidemic in china had been under control. implemented metropolitan-wide quarantine of wuhan city itself could also interfere with the change of infectious rate. the decrease in the number of daily new confirmed cases since late february showed that the corresponding policies had effectively blocked the spread of the epidemic. the change in the recovery rate of infected γ 2 had little effect in the early stage of the epidemic. as time went by, the growth of recovery rate could significantly raise the number of recovered, thus advancing the peak time of the real-time confirmed cases (fig 9c) . when the recovery rate raised from 75% to 125%, the whole country, hubei province, wuhan city and beijing city could reach the time of maximum real-time infections about 6-15 days in advance, and the scale of the epidemic could be reduced as well (fig 9c) . in fact, china transported advantage medical resources of more than 20,000 people to hubei province [5] in order to achieve the goal of early detection, early reporting, early diagnosis, and early isolation. besides, the measure of "one province helping one city" established provincial counterparts to support the rescue work in hubei province except wuhan [5] , so as to rationally allocate advanced resources. these interventions could improve the treatment and medical level of key provinces and cities, thereby increasing the recovery rate of infected and reducing the mortality rate. by march 13 th , 2020, more than a thousand people each day have been cured and discharged for 29 consecutive days [6] , indicating the effectiveness of related policies. although the covid-19 has been effectively controlled in china, it has spread rapidly in other countries. italy, the united states and spain have become the focused areas of the outbreak. by may 2 nd , 2020, the united states, as the country with the largest number of confirmed cases, has over 1.1 million cases, and spain had 216,582 cases, and italy ranked the third with 207,428 confirmed patients [12] . in order to control the spread of coronavirus, america took measures to reduce the mobility of the population, built hospitals and facilitate the treatment of the coronavirus [64] [65] [66] [67] . similar to the us, italy and spain also tried to limit the movement and gathering of the crowds, improve the protection level and provide more medical resources [64, [68] [69] [70] . in conclusion, all three countries have implemented various interventions to slow down the spread of the covid-19 disease. the measures could be basically divided into two categories: reducing the infection rate and increasing the recovery rate. however, according to the recent large-scale outbreak in the united states and spain, it could be found that a part of the people in these two countries might have insufficient awareness of prevention and control of the epidemic [64] . the supervision of those prevention and control measures needs further improvement. thanks to the joint efforts of the people across the italy, while the number of confirmed cases in italy is still large, this country, which was called "the second hubei province" in the early stage of the epidemic, has a trend of declining new cases of infection and death [12] . in order to test the capability of the seird model in foreign countries, data before june 29 th , 2020 of italy were used to calculate the epidemic curve. the results of the model also fitted well with the actual data as shown in fig 10. although some other countries successfully controlled the epidemic using similar measures with china [71] , they may not always work in other countries because the effect depends on the public attitudes towards the measures and commitment to the intervention as debated in [72] . therefore, in the face of the same epidemic situation and similar crises, our seird dynamics model can be potentially applied to other countries to evaluate the intensity and effect of policies implemented by simulating and forecasting the situation of the epidemic, but the effect may be limited by the attitudes and action of the public. to better understand the spatial distribution of the coefficients of the independent variables in the gwr model, four parameters and their correlations in the model of february 2 nd have been studied to evaluation the heterogeneity of their coefficients in space. there was a strong negative correlation between the number of hospitals per 10,000 people and the number of confirmed cases (fig 11a) . this can be explained as that the isolation of confirmed cases in the hospital can prevent contagion. from the perspective of the spatial distribution of the regression coefficients, it has a trend of gradual decline from the northeast to the southwest and northwest of china (fig 11a) . the most influenced areas are located in the northeast of china, while the least influenced areas are in southwest and northwest of china. there was a negative correlation between the number of doctors per 10,000 people and the number of confirmed cases (fig 11b) . from the perspective of the spatial distribution of regression coefficient, it shows a gradually decreasing trend from the northeast and northwest of china to the south (fig 11b) . the regions that are influenced the most are concentrated in northeast and northwest of china, while the least influenced regions are in the south. there was a positive correlation between the number of confirmed cases and the confirmed cases one day ago (fig 11c) . this suggests that the more cases confirmed the day before, the more confirmed cases would emerge the next day. effective local quarantine measures can be used to prevent a pandemic. from the perspective of the spatial distribution of the regression coefficient, it shows a trend of gradual decline from the northeast to the southwest and northwest of china (fig 11c) . this trend is not significant, which shows a universal pattern across the country. there was a positive correlation between the number of cured case and the number of confirmed cases one day ago (fig 11d) . from the perspective of the spatial distribution of regression coefficient, it shows a gradually decreasing trend from the northeast and northwest of china to the south, with the most influenced areas in the northeast and northwest, and the least influenced areas in the south (fig 11d) . by comparing the prediction capabilities of these three types of models, the modified seird, lstm and gwr model could effectively predict the epidemic data for the next day generally. the percent errors of the seird model to predict confirmed cases were within ±5.0% in all of these four selected regions (beijing, wuhan, hubei and china) shown in table 5 . the lstm model also fit well to the real curve by incorporating traffic big data, indicating good simulation and prediction effects. the average percent error of lstm model predictions for the four selected provinces and cities was within ±1.0% on february 14 th (table 5) . gwr model could reflect spatial heterogeneity but larger percent errors showed than the other two models in some cases ( table 5 ). the mape (mean absolute percentage error) for the seird, lstm and gwr models in the selected areas were 1.70%, 1.51%, 3.44%, respectively. in order to compare the ape (absolute percent error) of the three models, we ran wilcoxon signed rank test for the paired observations in table 5 . the p-values for the hypotheses: the ape of gwr> that of lstm, the ape of gwr > that of seird and the ape of seird> that of lstm were 0.173, 0.187 and 0.459, respectively, thus not significant at the level of 0.05. overall, the prediction efficacy of gwr model was inferior to those of seird and lstm models according to the mape and p-values. in this study, the modified seird model, the lstm model with traffic data and the gwr model reflecting the geographical environment were used to make forecasts for the development of covid-19 in china. these three types of models all showed remarkable prediction capabilities. the parameter sensitivity analysis reflected the effectiveness of nonpharmaceutical interventions. now the epidemic quickly spread abroad, in the absence of targeted pharmaceutical treatment such as vaccines, the interventions implemented in various countries were basically similar to those in china, which were based on the two aspects: reducing the infectious rate and improving the recovery rate. as the number of daily new cases continues to increase globally, models in this study shows potential being used for epidemic curve prediction and prevention of covid-19 in other countries. supporting information s1 full-genome evolutionary analysis of the novel corona virus (2019-ncov) rejects the hypothesis of emergence as a result of a recent recombination event discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin evidence of recombination in coronaviruses implicating pangolin origins of pangolin homology associated with 2019-ncov clinical features of patients infected with 2019 novel coronavirus in wuhan another decade, another coronavirus potent binding of 2019 novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody pathogenicity and transmissibility of 2019-ncov-a quick overview and comparison with other emerging viruses novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions. medrxiv a 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in china under public health interventions mathematical model and prediction of epidemic trend of sars epidemic processes in complex networks long short-term memory geographically weighted regression: a method for exploring spatial nonstationarity a simulation-based study of geographically weighted regression as a method for investigating spatially varying relationships geographically weighted regression: the analysis of spatially varying relationships dxy. 2019-ncov daily 24 coronavirus news active alerts in parks fda will allow doctors to treat critically ill coronavirus patients with blood from survivors italy under lockdown to fight coronavirus italy implements more measures in response to coronavirus epidemic spain has nationalized all of its private hospitals as the country goes into coronavirus lockdown active case finding with case management: the key to tackling the covid-19 pandemic we thank our colleagues of taikang pension & insurance co., ltd. for their support, especially dr. ying han, who helped improve english and ms. jieyu wang, who helped in discussion and material preparation. key: cord-103533-k1lg8c7q authors: jin, c.; chen, w.; cao, y.; xu, z.; zhang, x.; deng, l.; zheng, c.; zhou, j.; shi, h.; feng, j. title: development and evaluation of an ai system for covid-19 date: 2020-03-23 journal: nan doi: 10.1101/2020.03.20.20039834 sha: doc_id: 103533 cord_uid: k1lg8c7q early detection of covid-19 based on chest ct will enable timely treatment of patients and help control the spread of the disease. with rapid spreading of covid-19 in many countries, however, ct volumes of suspicious patients are increasing at a speed much faster than the availability of human experts. here, we propose an artificial intelligence (ai) system for fast covid-19 diagnosis with an accuracy comparable to experienced radiologists. a large dataset was constructed by collecting 970 ct volumes of 496 patients with confirmed covid-19 and 260 negative cases from three hospitals in wuhan, china, and 1,125 negative cases from two publicly available chest ct datasets. trained using only 312 cases, our diagnosis system, which is based on deep convolutional neural network, is able to achieve an accuracy of 94.98%, an area under the receiver operating characteristic curve (auc) of 97.91%, a sensitivity of 94.06%, and a specificity of 95.47% on an independent external verification dataset of 1,255 cases. in a reader study involving five radiologists, only one radiologist is slightly more accurate than the ai system. the ai system is two orders of magnitude faster than radiologists and the code is available at https://github.com/chenwwweixiang/diagnosis_covid19. the new coronavirus disease, now known as covid-19 [1] , was first detected in wuhan, china, in december 2019. outbreaks have now occurred in more than 166 countries. it has infected more than 210,000 people worldwide, killed more than 8,000 and is still spreading rapidly. the world health organization (who) officially announced that this is a global pandemic. it is important to diagnosis covid-19 as quick and accurate as possible for controlling the spread of the disease and treating patients. even though reverse transcription-polymerase chain reaction (rt-pcr) is still ground truth of covid-19 diagnosis, the sensitivity of rt-pcr is not high enough for low viral load present in test specimens or laboratory error [2] , and kits of rt-pcr are in short of supply in many areas [3] . by contrast, chest ct can show early lesions in the lung and, if diagnosed by experienced radiologists, can achieve high sensitivity [4] . in addition, ct scans are widely available and economic. at present, the diagnosis of chest ct depends on the radiologists, which has some problems. firstly, chest ct contains hundreds of slices, which takes a long time to diagnose. secondly, covid-19, as a new lung disease, has similar manifestations with various types of pneumonia4. radiologists need to accumulate a lot of ct diagnostic experience to achieve a high diagnostic performance. in some outbreak areas, many suspected patients are in urgent need of diagnosis and proper treatment, and many ct scans are performed every day. there is an urgent shortage of radiologists with high diagnosis performance for covid19 . artificial intelligence (ai) may be the unique preparation to take up this challenge. powered by large labeled datasets [5] and modern gpus, ai, especially deep learning technique [6] , has achieved excellent performance in several computer vision tasks such as image classification [7] and object detection [8] . recent research shows that ai algorithms can even achieve or exceed the performance of human experts in certain medical image diagnosis tasks [9] [10] [11] [12] [13] . the ai diagnosis algorithm also has the advantages of high efficiency, high repeatability and easy large-scale deployment. the current outbreak of covid-19 is worldwide, and the shortage of specialist radiologists threatens the availability and adequacy of screening services for covid-19 in affected areas. by deploying ai diagnosis algorithms, suspicious patients everywhere, especially in developing countries, will have equal access to right diagnosis, timely treatment and isolation. as a very recent disease, we have not yet found ai studies for covid-19 diagnosis in peer-reviewed publications, but a few reports about covid-19 diagnosis algorithms based on chest ct in preprint form [14, 15] . wang et al. [14] describe a covid-19 diagnosis system with specificity of 67% and sensitivity of 74% on 216 slices extracted from ct volumes of patients (the whole dataset consists of 44 positive and 55 negative cases, but split strategy of dataset is unclear). chen et al. [15] describe a covid-19 diagnosis system with a performance comparable to that of an expert radiologist, however the system is validated based on a quite small dataset with only 19 confirmed covid-19 patients and only one radiologist is compared. clearly, the development and rigorous testing of covid-19 diagnosis algorithms remains an open topic. in this study, we used clinically representative large-scale datasets from three centers in wuhan and two publicly available chest ct datasets to develop and evaluate an ai system for the diagnosis of covid-19. we compared the diagnostic performance of this system with that of five radiologists in a reader study of 200 cases, and the results showed the performance of this system is comparable to that of experienced radiologists in designated hospitals for covid-19 in major epidemic areas. in addition, based on prediction score on every slice, we located the lesion areas in covid-19 patients and statically analyzed lesion position in different subsets. we traced the specific phenotypic basis of the diagnosis output from the system on the original ct images through an interpretation network and apply radiomics analysis of the attentional region to understand the imaging characteristics of covid-19. figure 1 a shows the overall flow of the study. we developed and evaluated a deep learning based covid-19 diagnosis system, using multi-center data, which includes 756 subjects (496 covid-19 positives and 260 negatives) collected in wuhan union hospital, western campus of wuhan union hospital, and jianghan mobile cabin hospital in wuhan, the major epidemic area in china (detailed information is in table 1 ). two international public databases, lidc-idri (1,012 subjects available) [16] and ild-hug (113 subjects available) [17] are also included as negative cases to help develop and evaluate our ai system. negatives from the three centers in wuhan are healthy people and ones from public databases are healthy or suffer from other lung diseases. all ct data was divided into four independent parts with no overlapping subjects, a 312 subjects training cohort, a 104 subjects internal validation cohort, an external test cohort consist of 1,255 subjects, and a reader study cohort with 200 subjects (detailly described in methods). due to some positive subjects have multi-stage cts and different stage cts of one subject might be similar, the subset division was performed on subjects to make sure all multi-stage cts of the same subject are in a same subset. figure 1 : workflows of the whole study and the proposed ai system. a. workflow of the whole study. b. construction and usage of the ai system. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint sists of five key components (figure 1 a) , (1) a 2d convolutional neural network (cnn) model for segmenting the lung, (2) a covid-19 diagnosis model, (3) an abnormal slices locating block to locate abnormal slices in positive cases, (4) a network visualization module for interpreting the attentional region of deep networks, and (5) an image phenotype analysis module for explaining the features of the attentional region. the workflow of deep-learning based diagnosis model is shown in figure 1 b. ct cases were firstly divided to different cohorts and extracted to slices since our model takes 2d slices as input. then after slice level training, our model can accurately predict whether the input slices come from covid-19 subjects. with a top-k average block, our model finally fused slice results into case level diagnosis. the model was implemented in 2d not only because 2d network was easily to train with more training samples, but also because slice-level scores can be used for abnormal slice locating. we fine-tuned our diagnosis model on a training dataset consisting of normal and abnormal slices from covid-19 positive cases and obtained the abnormal slice locating model. other parts of our system are described in methods. the trained ai system was evaluated on the external test cohort. we used the receiver operating characteristic (roc) curves (in figure 2 a) to evaluate the diagnostic accuracy of the proposed ai system. the pr curves of evaluating the prediction accuracy were also illustrated in figure 7 a. on the external test cohort, the roc curve showed auc of 0.9791, sensitivity of 0.9406, and specificity of 0.9547. in the open data set lidc-idri and ild-hug, the false positive rates of ai system were 3.12% and 11.85%, and the system showed good generalization ability (figure 7 c ). the ai system shows good performances and it can be used with different diagnosis thresholds according to different policies or prior probabilities. the performances of the ai system and five readers in covid-19 diagnosis on reader study cohort. c. roc curve for abnormal slice locating. this result was test on 12 covid-19 positives cases from internal validation cohort which have manual lesion segmentation. d. metrics of proposed ai system for different cohorts and tasks. e. discrepancies between the ai system and human readers. l) m) two covid-19 cases identified by the ai system but missed by all five readers. r) a covid-19 case identified by a reader but missed by the ai system. (the yellow circles denote possible lesion area) sensitivity of our system is about 84.76% when specificity is 99.5%, and specificity is 80.02% when sensitivity is 97%. besides, because patients in our external test cohort have multi-stage ct volumes, some of the stages of positive subjects might be in the recovery state whose ct may have no abnormalities but are still regarded as positive in experiments. figure 2 a shows the results after roughly filtering out these cases by only keeping the maximum predicted value of multi-stage cts in the same patient, in which the specificity is about 96.74% at sensitivity of 97%. the decision curve analysis (dca) for the ai system are presented in figure 7 b, which indicated that the ai system adds benefit than the "diagnose all" or "diagnose none" strategies when the threshold is within a wide range 1.82-97.6% in covid-19. abnormal slice locating results are showed in figure 2 c, d. the slice locating block took in covid-19 positive cases and predicted where abnormal slices are with auc of 96.35%, specificity of 90.08% and sensitivity of 82.19%. we conducted a reader study with five board-certified radiologists (average of 8 years clinical experience, range 5-11 years, table 2 a). these radiologists interpreted 200 ct volumes in reader study cohort. all readers were asked to read independently without other information about patients. the ai system performs slightly better than the average of five radiologists. the roc curve had auc of 0. 9805, sensitivity of 0. 9470, and specificity of 0. 9139 on the cohort of reader study (figure 2 b, d). in 46% (6/13) of cases, when the ai system missed, the radiologist also missed (table 2 b), indicating that the diagnosis of these missed cases is challenging. among the five readers, one reader performed better than the ai system, one reader performed worse, and the rest three have similar performance as the ai system at different operating points. performance of the ai system in covid-19 diagnosis compared to five readers is shown in figure 2 b and table 2 c. the left, middle of figure 2 e shows two covid-19 cases that all five radiologists missed but were correctly identified by the ai system. it is hard to notice the evidence of covid-19 in these two cases, but ai system can still identify them. it shows that the ai system may capture the information of subtle and continuous changes in slices and make a comprehensive judgment. the right of figure 2 e shows an example that was detected by all five radiologists but missed by the ai system. these cases show that the ai system and human readers are potentially complementary. for an in-depth understanding of the ai system and characteristics of different populations with covid-19, we evaluated the ai system on subsets of the external test cohort divided by gender, age and number of ct scans. figure 3 a shows the roc curves of these three subsets. to understand the cause for different diagnosis performances, we analyzed the abnormal slice locating results 7 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint table 2 : reader study statistics and results. a. experience levels of the five radiologists involved in the reader study. b. comparison of diagnostic error between ai systems and human readers. notes: wrongs of any of five readers means any one or more readers were wrong, while corrects means no any of five readers were wrong. c. comparison of diagnostic performances between ai system and every human reader. in different subsets (figure 3 b, c). we found that the different performances of different subsets were highly correlated to the number of abnormal slices, which means smaller lesion with fewer abnormal slices are more difficult to diagnose ( part of the patients in the database have multi-stage cts. we compared the diagnostic performance of stage i and stage ii and fusion of stage i, ii in the external test cohort (figure 3 a, b, d) . the experiment suggested that the performance of the ai system is independent of the progress of the disease because of no significant differences between performances of different stages. the statistical results also showed that fusion of stage i and ii could slightly improve the performance of diagnosis, in which the fusion method we adopted is to simply average the scores of two stages. we did not test more complex fusion methods which may overestimate the performance since each negative case has 8 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. after proper training of the deep network, guided gradient-weighted class activation mapping (guided grad-cam) [18] was exploited to explain the "black box" system and extract attentional areas which is connected to the back end of the diagnostic model. figure 5 shows some representative cases for the visualization of guided grad-cam to determine the attentional regions. the original ct slices are in the first column. the second column is the result of pseudo-color display of the feature map. the third column is the gradient map in the region of attention. we found that the spatial distribution of the attentional region, morphology and the texture within it are consistent with the characteristics of covid-19 as reported in previous manual diagnosis studies [4, 19] . in order to further verify our conjecture, we performed radiomics [20] feature extraction on these attentional regions, and obtained a total of 752-dimensional imaging features. the least absolute shrinkage and selection algorithm (las-so) were used to find the most discriminative features ( figure 6 ). a total of 15 features were finally chosen whose absolute values of coefficients are higher than 10-3. the cluster-heatmap and heat map of correlation coefficient matrix before and after lasso show that lasso filtered out redundant and unimportant 10 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint features and the remaining features have better identification ability and lower correlation ( figure 9 , figure 10 ). the selected 15 features were used to explain the imaging characteristics in ct (feature analysis in method). the extracted features show more separable statistical distribution between lesion and normal regions (figure 6 b). we extracted three additional features for the attentional regions, distance feature, 2-d margin fractal dimension, and 3-d grayscale mesh fractal dimension (figure 8 ). according to previous literature [21] on the pathogenesis and morphology of covid-19, we believe that there may be a statistical rule in the pathogenesis (see feature analysis section in methods). in this study, we developed an ai system for diagnosis of covid-19. the system showed good sensitivity (94.06%), specificity (95.47%) and auc (97.91%) in external test cohort. furthermore, in the reader study, the diagnostic accura. cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint cy of the ai system was comparable to that of experienced radiologists from the outbreak center, who achieved higher sensitivity (94.70%), specificity (91.39%) and auc (98.05%). among the five professional readers in the radiology department, only one was able to produce a higher diagnostic accuracy than the ai system. this automatic, high-precision, non-invasive diagnostic system was developed to provide clinicians with easy-to-use tools. given the chest ct of a suspected patient as input, the ai system can automatically output the diagnosis result. in the reader study, the average reading time of radiologists was 6.5 min, while that of ai system was 2.73 s, which can significantly improve the productivity of radiologists. meanwhile, we found that 71% (15/21) of errors made by radiologists could be corrected by ai system. it means that ai system can be used as an effective secondary reader to provide reference suggestions when the radiologist is not sure about the case or when multiple radiologists are inconsistent. in general, ai can be adapted to different requirements. according to the highly sensitive settings, it can screen out suspicious patients for confirmation by doctors; in accordance with the highly specific settings, it can warn possible diagnosis errors made by the doctor; or an optimal threshold value is chosen according to the prior probability of infectious diseases and the local prevention and control strategy. to further understand the performance of the ai system, we evaluated it on subsets divided by gender, age and number of ct scans. in the subsets divided by gender, the diagnostic performance of men was higher than that of women. we noticed an obvious difference in the size of lungs and lesions between men and women. this is consistent with the conclusion of xiong et al. [22] that women have higher antiviral immunity than men, leading to a longer incubation period of covid-19. in the subsets divided by age, the disease developed rapidly in the elderly patients and the ct findings were more obvious than young patients. this suggests that different thresholds should be adopted according to gender and age. the results on the subsets divided by the number of ct scans showed that diagnosis results by the ai system have little correlation with the stages of ct scans. these observations may provide decision-making references for the diagnosis of covid-19 in different populations. further, we provided a visual explanation of the system's decision by performing a radiomics analysis to obtain diagnostically relevant phenotypic characteristics of the attentional regions that are fully traceable on the original ct image. this is important for an in-depth study of pulmonary imaging findings in patients with covid-19. for the ai system, by visualizing the diagnostic results of 200 subjects from the reader study cohort and comparing them with human reader in the reader study, together with the subsequent radiomics analysis, we were able to perform detailed imaging phenotype analysis on the diagnosis of covid-19, and subsequently make pathophysiological and anatomical speculations on the viral infection process (see feature analysis in methods). there are still some drawbacks and future works of this research. first, collecting more data on other types of viral pneumonias or lung lesions can help improve its specificity further. second, based on many chest cts with detailed labelled lesions, a semantic segmentation algorithm can be trained to locate the outline of the lesion more accurately than guided grad-gam, and distinguish the detailed category of the lesion. overall, the proposed ai system has been comprehensively validated on large dataset with diagnosis performance comparable to human experts in diagnosing covid-19. unlike classical blackbox deep learning approaches, by visualizing ai system and applying radiomics analysis, it can decode effective representation of covid-19 on ct imaging, and potentially lead to the discovery of new biomarkers. radiologists could perform an individualized diagnosis of covid-19 with the ai system, adding new driving force for fighting the global spread of outbreak. under insitutional review board (irb) approval , data used in our experiments come from three centers in wuhan, which are wuhan union hospital, western campus of wuhan union hospital, and jianghan mobile cabin hospital, and two public databases, lidc-idri of the american national cancer institute (nci), and ild-hug data of university hospitals of geneva. the datasets from the three centers in wuhan contain both positive (confirmed covid-19) and negative cases. database collected from jianghan mobile cabin hospital in wuhan includes chest ct volumes of patients with confirmed covid-19 from february 5th, 2020 to february 29th, 2020. chest ct volumes from wuhan union hospital, western campus of wuhan union hospital are collected from january 11th, 2020 to february 29th, 2020. data from three centers contain 756 subjects, of which 496 were positives and 260 negatives. some positive subjects have multi-stage cts, so that datasets from three centers consist of 710 ct volumes of positive cases and 260 ct volumes of negative cases. stage i means the first chest ct of a patient, and the intervals to stages ii are 4-10 days. two public databases contain only negative cases since these data were collected before covid-19 outbreak. the lung image database consortium image collection (lidc-idri) is a collaboration between seven academic centers and eight medical imaging companies initiated by the national cancer institute (nci) in the united states. this database contains 1,012 subjects [16] . ild-hug is an international public dataset on interstitial lung diseases (ilds) built at the university hospitals of geneva (hug). the dataset contains 113 chest cts (reported to have 128 but only 113 available) with three-dimensional annotated regions of pathological lung lesions [17] . most of the cases taken from these two public datasets are abnormal cases and some of which are similar in cts as covid-19. all ct data was divided into four independent parts with no overlapping subjects: â�¢ training cohort: 312 subjects were assigned to the training cohort, includ-14 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03. 20.20039834 doi: medrxiv preprint ing 147 positive and 75 negative cases from three centers in wuhan, and 75 cases from lidc-idri and 15 cases from ild-hug). this cohort was used to train parameters of model. â�¢ internal validation cohort: 104 subjects were assigned to the internal validation cohort, including 49 positive and 25 negative cases from three centers in wuhan, and 25 cases from lidc-idri and 5 cases from ild-hug. this cohort was used to validate the performances and turn superparameters of model. the proposed ai system takes as input a whole ct volume and outputs covid-19 diagnosis along with abnormal slices (if diagnosed as positive). the whole system consists of five parts: lung segmentation block, covid-19 classification network, abnormal slice locating block for covid-19 positives, ai system interpreting block using guided grad-cam, and feature analysis block. the first four blocks are deep-learning based blocks and the last one is traditional feature extraction block. the lung segmentation block is implemented based on deeplab v1 [23] , which is a 2d semantic segmentation network. all cts are in 3d, so we trained and tested the segmentation model slice by slice. the training slices were extracted from chest cts in the training cohort and annotations of lung segmentation were obtained manually. the segmentation results were used as masks to determined lung areas, and they were concatenated to the raw ct slices as a different channel before feeding into the next block. we used this input-with-mask method to improve diagnosis results which has better performance according to experiments. our covid-19 diagnosis block is a 2d classification deep network whose backbone is resnet152 [24] , a deep network with 152 convolutional, pooling or fully-connected layers. the parameters of resnet152 are pretrained on a figure 7 : extend performances of proposed ai system. a. pr curves was employed to assess the ai system performance of covid-19 diagnosis. b. decision curve analyses (dca) of ai system in independent external test set for covid-19 diagnosis. c. errors count in external public databases in external test cohort. huge dataset imagenet7 for better and faster convergence. we tested a 3d classification network but this 2d scheme showed much better performance. the input of classification model is lung-masked slices, which means the input slices including training, internal validation and external test cohort, have been segment by segmentation model to get lung masks. the outputs of classification model are two scores respectively representing confidence levels of being normal and covid-19 affected. loss function of this block is cross entropy. the block was trained using 2d slices with batch size 32 for 100 epochs which costed about 5 hours under learning rate 10-5. slices for training this block were extracted from training cohort, and the extraction process is detailed explained in supplementary methods. since the predictions are based on 2d slices, an extra step is done to get a volume-level prediction. because one volume is covid-19 positive when any one of its slices is covid-19 positive, we averaged the top 3 highest scores of all slices of a volume as the volume score. as a result, though training and validation were done on slice level, the block can take the whole ct volumes (with the whole lung segmentation volumes) and output a single prediction on volume level. to measure the performance of classification model, auc and some other metrics are computed on both internal validation and external test cohort. the metrics of internal validation cohort is computed on slice-level because the training is on slice-level and turning of super-parameters will be easier if validation is also done on slice-level. while metrics for external test cohort and reader study cohort are on case level, consistent with clinical application. block to locate abnormal slices is in the same structure of diagnosis block but trained especially on covid-19 positive cases whose lesions have been marked manually. we used 28 cases with slice-level annotations in training cohort to train the block and the rest 12 cases in internal validation cohort with annotations to test performances of locating. we used guided grad-cam to obtain attentional regions as our system interpreting block. guided grad-cam has the advantage that it not only generates a heat map to locate the relevant area, but also produces a coarse localization map highlighting the important regions in the image for predicting the result. generally, the features used for classification judgment can be found, such as edges and spots in specific areas. guided grad-cam is important because the areas it focused on are a secondary output of our system together with diagnosis result, giving more detailed diagnosis suggestions. also, the attentional regions were used in latter feature extraction and analysis to get more detailed information about lesion areas. we extracted region of attention by binarizing output of grad-cam and then some morphological operations were done on binarization map. all the deep learning blocks were implemented using pytorch [25] . features were extracted in the attentional region determined by guided grad-cam. we also extracted the same feature in normal lung in controlled cases for comparison. due to no valid lesions attentional region for controlled cases is computed by guided grad-cam, we used the shape of attentional region of covid-19 cases and randomly choose positions within lung area as the attentional regions of controlled cases. we did not use shape features because the shape of attentional regions between covid-19 and controlled cases are the same. we extracted radiomics features which are widely used in lesion diagnosis these years. these features are composed of different image transforms and feature matrix calculations. we adopted three image transforms: original image, transformed image by laplacian of gaussian (log) operator, and transformed image by wavelet. for each image after the operation of a transform, six series of features are extracted, including first order features, gray level co-occurrence matrix (glcm), gray level size zone matrix (glszm), gray level run length matrix (glrlm), neighboring gray tone difference matrix (ngtdm), gray level dependence matrix (gldm). radiomics analysis was performed using python version 3.6 and the "pyradiomics" package [26] . we designed three other features which are distance feature and fractal features of 2d contour and 3d gray level mesh of attentional region. the distance feature was defined as the distance between the center of gravity of the region of interest (obtained by the classification network after grad-gam) and the edge of the lung (obtained by the edge of the lung automatically segmentation results). besides, 2d contour fractal dimension and 3d grayscale mesh fractal dimension of the attentional region was extracted. the fractal dimension describes the degree of curvature of the curve and surface. these three extra features were only extracted from the ct images of covid-19 patients and were not analyzed and compared on the controlled cases. lasso logistic regression model, heat map of cluster and correlation coefficient matrix were used to extract, select and verify the radiological features of the attentional region in the original ct images, which can interpret ai system. lasso analysis was performed using python version 3.6 and the "scikit-learn" package. first, we located the distribution of the attentional region traced by the ai system, which mainly consisted of the subpleural distribution, the fragmentary distribution of patchy based on the secondary lobules, and the diffuse distribution of the fusing above two. the distances feature shows that the centers 18 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint of attentional region are generally 0-20 pixels (2.5 mm/pixel) from the pleura (figure 8 a) , which is consistent with anatomical findings on covid-19. the sars-cov2 is small (60-140 nm in diameter), and when inhaled through the airways, it mainly invades the deep bronchioles, causes inflammation of the bronchioles and their surroundings to damage alveolar [27, 28] . also, from the pathophysiology and etiology [29] [30] [31] , the sars-cov2 mainly invades the bronchioles and lung parenchyma. lesions tend to occur in the lower and peripheral areas of the lung with abundant capillaries and lymphatics. these areas have well-established immune system and well-developed pulmonary lobules, leading to a strong inflammatory response [32, 33] . secondly, fractal dimensions of most regional contour are between 1.95-2.00, shows a tortuous outline and conforms to the diffuse description, which corresponds to the fact that most of the cases in the dataset are at early or developmental stage. a few distributions are between 1.87-1.89, the overall contour of attentional regions are smoother or sub-parts are flat and narrow. the appearance of partial flatness at the boundary of the attentional region is a sign of consolidation, indicating the lesion is in the mend. finally, we obtained some findings on the texture (homogeneity and heterogeneity) of the attentional regions that features for normal and lesion regions show different distributions (figure 6 b, c) . according to all the extracted features, we can describe in depth the relationship between the medical findings and typical patterns. i) halo pattern and anti-halo pattern were easily formed in the attentional regions. the halo pattern was speculated to be that the lesions (mainly the central node of the lobular) infiltrated into the surrounding interstitium and developed the aggregation of inflammatory cells in the interstitium. anti-halo pattern is of the center of the ground glass shadow, almost completely surrounding by the high-density consolidation. the appearance of this sign may be that the inflammatory repair is dominated by the edge, leading to the formation of a band shadow tending to consolidation at the edge, while the central repair is relatively slow. ii) the attentional region presents pleural parallel signs. the formation mechanism was speculated as follows: when the sars-cov2 invaded the interstitium around the alveoli, the lymphatic return direction was subpleural and interlobular septa, and diffused into pleural side and bilateral interlobular septum [34] . because of the limitation of the pleura at the distal end, the lymph can only cling to the pleura and spread along the reticular structure of the interlobular septal margin on both sides. in addition, the fusion of the subpleural lesions results in the long axis of the lesions parallel to the pleura. iii) vascular thickening was found in the attentional region, which was consistent with the rules of inflammation production, inflammatory stimulation, increased vascular permeability, telangiectasia, further pulmonary artery thickening [33, 35] . iv) the fine mesh feature of large area develops in the attentional region. the sars-cov2 mainly invades the interstitium in the lobules, so it appears as confluent fine mesh (crazy paving). v) the density of the ground-glass opacity (ggo) in the attentional regions increases, transforming to consolidation, the consolidation edges are flat or contracted, and fiber strands appear. these are all signs of disease outcome. in addition, when multiple regions of attention are recognized in the lungs of 20 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.20.20039834 doi: medrxiv preprint some cases, the conditions of some regions will be improved, and that of other regions is lagging. the phenomenon of fluctuation is caused by unsynchronized development of lesions. for this study, data from three centers was used, and negative data from public database is added, after which the reader study cohort statistically consisted of 58.5% positive cases and 41.5% negative cases. all the five readers are professional radiologists in the radiology department of wuhan union hospital, who have rich clinical diagnosis experience and is in the center of the epidemic area with the most patients in this outbreak in china. they have all read over fourhundred cts of covid-19 in the past three months. five radiologists had an average of 8 years of clinical experience in the imaging diagnosis of pulmonary diseases, as detailed in table 2 a. readers can choose any window of gray value and zoom in or out when reading ct volumes using slicer 4.10.2 software while our system used fixed size recased images (224 x 224 x 35) with fixed gray value window (-1200, 700) for all volumes. laboratory testing for coronavirus disease 2019 (covid-19) in suspected human cases: interim guidance performance of radiologists in differentiating covid-19 from viral pneumonia on chest ct correlation of chest ct and rt-pcr testing in coronavirus disease 2019 (covid-19) in china: a report of 1014 cases radiological findings from 81 patients with covid-19 pneumonia in wuhan, china: a descriptive study imagenet: a large-scale hierarchical image database deep learning imagenet classification with deep convolutional neural networks faster r-cnn: towards realtime object detection with region proposal networks corrigendum: dermatologist-level classification of skin cancer with deep neural networks deep learning in medical image analysis a guide to deep learning in healthcare high-performance medicine: the convergence of human and artificial intelligence end-to-end lung cancer screening with three-dimensional deep learning on low-dose chest computed tomography a deep learning algorithm using ct images to screen for corona virus disease (covid-19). medrxiv deep learning-based model for detecting 2019 novel coronavirus pneumonia on high-resolution computed tomography: a prospective study. medrxiv the lung image database consortium (lidc) and image database resource initiative (idri): a completed reference database of lung nodules on ct scans building a reference multimedia database for interstitial lung diseases grad-cam: visual explanations from deep networks via gradient-based localization chest ct findings in 2019 novel coronavirus (2019-ncov) infections from wuhan, china: key points for the radiologist computational radiomics system to decode the radiographic phenotype chest ct findings in coronavirus disease-19 (covid-19): relationship to duration of infection women may play a more important role in the transmission of the corona virus disease (covid-19) than men semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected crfs deep residual learning for image recognition an imperative style, high-performance deep learning library computational radiomics system to decode the radiographic phenotype evaluation and treatment coronavirus (covid-19) dail and hammar's pulmonary pathology lung pathology of fatal severe acute respiratory syndrome origin and evolution of pathogenic coronaviruses epidemiology, genetic recombination, and pathogenesis of coronaviruses lung function: physiology, measurement and application in medicine pulmonary vascular and cardiac impairment in interstitial lung disease lymphatic vessel network structure and physiology inflammatory mechanisms in the lung we would like to acknowledge the radiologists participating the reader study. this study was supported by zhejiang university special scientific research fund for covid-19 prevention and control. key: cord-303799-9hh17k86 authors: huang, ying; yang, rui; xu, ying; gong, ping title: clinical characteristics of 36 non-survivors with covid-19 in wuhan, china date: 2020-02-29 journal: nan doi: 10.1101/2020.02.27.20029009 sha: doc_id: 303799 cord_uid: 9hh17k86 background although the outbreak of coronavirus disease 2019 (covid-19) has caused over 2200 deaths in china, there was no study about death yet. we aimed to describe the clinical characteristics of non-survivors with covid-19. methods for this retrospective, single-center study, we included 36 non-survivors with covid-19 in the fifth hospital of wuhan. cases were confirmed by real-time rt-pcr between jan 21 and feb 10, 2020 according to the recommended protocol. the epidemiological, demographic, clinical, laboratory, radiological and treatment data were collected and analyzed. outcomes were followed up until feb 14, 2020. this study was approved by the ethics commissions of the fifth hospital of wuhan, with a waiver of informed consent due to a public health outbreak investigation. results we included 36 patients who died from covid-19. the mean age of the patients was 69.22 years (sd 9.64, range 50-90). 25(69.44%) patients were males, and 11 (30.56%) female. 26 (72.22%) patients had chronic diseases, mainly including hypertension, cardiovascular disease and diabetes. patients had common clinical symptoms of fever (34 [94.44%] patients), cough (28 [77.78%] patients), shortness of breath (21 [58.33%] patients), and fatigue (17 [47.22%] patient). chest computed tomographic scans showed that 31 (96.88%) patients had bilateral pneumonia. lymphopenia occurred in 24 patients (70.59%), decreased albumin (30.18, [sd, 4.76]) in 25 patients (80.65%), elevated d-dimer (8.64 [iqr, 2.39-20]) in 27 patients (100%), and elevated lactate dehydrogenase (502.5 u/l [iqr, 410-629]) in 26 patients (100%). nearly all of the patients have elevated crp (106.3 mg/l [iqr, 60.83-225.3]), pct (0.61 ng/ml [iqr, 0.16-2.10]) and il-6 (100.6 pg/ml [iqr, 51.51-919.5]). most patients received antiviral therapy and antibiotic therapy, and more than half of patients received glucocorticoid therapy (25 [69.44%]). all the patients had acute respiratory distress syndrome (ards). the median time from onset to ards was 11 days. one (2.78%) patient presented with acute renal injury. the median time from onset to death was 17 days. interpretation lots of patients died from covid-19 till now. the median survival time of these non-survivors from onset to death was about 2 weeks. most patients were older males with comorbidities. they finally progressed to ards. the median time from onset to ards was 11 days. gradually decreased lymphocytes and increased inflammation biomarkers were common, and need to be monitored in the routine treatment. although the outbreak of coronavirus disease 2019 has caused over 2200 deaths in china, there was no study about death yet. we aimed to describe the clinical characteristics of non-survivors with covid-19. for this retrospective, single-center study, we included 36 non-survivors with covid-19 in the fifth hospital of wuhan. cases were confirmed by real-time rt-pcr between jan 21 and feb 10, 2020 according to the recommended protocol. the epidemiological, demographic, clinical, laboratory, radiological and treatment data were collected and analyzed. outcomes were followed up until feb 14, 2020 . this study was approved by the ethics commissions of the fifth hospital of wuhan, with a waiver of informed consent due to a public health outbreak investigation. we included 36 patients who died from covid19 author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the lots of patients died from covid-19 till now. the median survival time of these non-survivors from onset to death was about 2 weeks. most patients were older males with comorbidities. they finally progressed to ards. the median time from onset to ards was 11 days. gradually decreased lymphocytes and increased inflammation biomarkers were common, and need to be monitored in the routine treatment. there is no any funder involved in this study. the outbreak of coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) happened since december 2020 in wuhan 1 . 2 sars-cov-2 has been spreading in china as well as in other countries [3] [4] [5] [6] . the outbreak of sars-cov-2 infection has been declared as a public health emergency of international concern by the world health organization (who) on 30 january 2020. according to the situation report from who, as of 21 february 2020, sars-cov-2 infection has caused 76769 confirmed cases in 27 countries and 2247 deaths globally 7 . severity of covid-19 varied from mild to severe. 8 mortality rate of covid-19 can be reduced, by timely identifying those who are at higher risk of developing into critically ill patients, closely monitoring changes of their disease course, and applying intensive care treatment to these patients. however, reports about dead cases of covid-19 were limited but warranted, considering the large amount of confirmed cases, which is still increasing. in this single-centered study, we retrospectively analysed specific clinical information of 36 non-survivors infected with sars-cov-2. for this retrospective, single-center study, we included 36 non-survivors with covid-19 in the fifth hospital of wuhan. cases were confirmed between jan 21 and feb 10, 2020 according to all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint the recommended protocol. this study was approved by the ethics commissions of hospital, with a waiver of informed consent due to a public health outbreak investigation. covid-19 was confirmed by real-time rt-pcr using the same protocol described previously 9 . additionally, all patients were given chest computed tomography (ct). we obtained epidemiological, demographic, clinical, laboratory, treatment and outcome data from patients' medical records. clinical outcomes were followed up to feb 14, 2020. we analysed epidemiological, demographics, exposure history, smoking history, chronic medical illness, signs and symptoms on admission, comorbidity, chest ct findings, laboratory findings and treatment measures. categorical variables were described as count (%). continuous variables were described using mean (sd) if they are normally distributed, median (iqr) if they are not. all statistical analyses were performed using r (version 3.6.1). all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint we included 36 patients who died from covid-19 in the fifth hospital of wuhan. one (2.78%) patients had a history of exposure to the huanan seafood market in wuhan. the mean age of the patients was 69.22 years (sd 9.64, range 50-90). twenty-five (69.44%) patients were males, and 11 (30.56%) female. four (11.11%) patients have smoking history. twenty-six (72.22%) patients had chronic diseases. the most common chronic diseases were hypertension (21, 58.33%), cardiovascular (8, 22 .22%) and diabetes (7, 19.44%) ( table 1 ). on admission, most patients had fever, cough and more than half of them had shortness of breath (table 2 ). other symptoms included fatigue, dyspnea, sputum production, disturbance of consciousness, diarrhea, hemoptysis and myalgia. (table 2) according to chest ct scan, 31 (96.88%, n=32) patients showed bilateral pneumonia (75%). on admission, leucocytes were below the normal range in 5 (14.71%) patients and above the normal range in 11 (32.35%) patients (table 3 ). neutrophils showed above the normal range in 16 (47.06%) patients. lymphocytes and hemoglobin were below the normal range in many patients (table 3) . twelve (35.39%) patients' platelets were below the normal range. 22 patients had varying degrees of liver function abnormality, with alanine aminotransferase (alt) or aspartate aminotransferase (ast) rose above the normal range ( table 3) . elevation of lactate dehydrogenase were showed in 26 (100%, n=26) patients. about 30% of these patients had different degrees of renal function damage, with elevated blood urea nitrogen or serum creatinine. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint regarding the infection index, procalcitonin (pct) rose above the normal range in 28 (100%) patients. 11 patients were tested for il-6, most of whose index were above the normal range (table 3) . 32 patients had increased c-reactive protein (crp). thirty-five (35, 97.22%) patients received antiviral treatment, including oseltamivir, ganciclovir, ribavirin or umifenovir hydrochloride. all patients were given antibiotic treatment ( table 2) table 2 ). the median time from onset to death was 17 days (figure 1 ). we reported on 36 patients who died from sars-cov-2 infection in a single hospital of wuhan. all these patients had ards and 28 (77.78%) patients needed mechanical ventilation. bilateral pneumonia was detected in most patients on admission. previous studies have shown that elder patients and males who were confirmed with coronavirus infection are at higher risk of ards, 10 all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint which was consistent with our study. antibiotic treatment was used to prevent secondary infections since these patients were critically ill. antiviral regimes were also used in most patients which we hoped may have roles but still need more data. however, there were no specific remedies for sars-cov-2 yet 11, 12 . therefore, most patients were treated with supportive treatment and intensive care. unfortunately, due to restrictions of hospital's conditions and the heavy burden of covid-19 in wuhan city, neither were we able to provide patients in need with advanced life support systems like extracorporeal membrane oxygenation (ecmo), nor were able to transport all serious patients to superior hospital for better medical treatments in time. the median survival time of the patients in our study was only 2 weeks approximately, which was shorter compared to previous reports 13 will decrease as the clinical capacity improves. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint as reported in previous studies, patients who are male, elder or have a history of cerebrovascular disease are at higher risk of sars-cov-2 infection 2,14,15 . in our study, we found that the majority of coronavirus non-survivors were male patients, elder patients and patients with chronic diseases, which indicated that these patients might be also at increased risk of becoming critically ill or death. cerebrovascular diseases were the most common comorbidities. twentytwo (61.11%) non-survivors had cerebrovascular diseases in our report, and the percentage of cerebrovascular diseases among non-survivors was higher than that reported by yang et al 13 . besides, there were 4 (11.11%) non-survivors who had smoking history and 4 (11.11%) had preexisting copd. according to previous studies on middle east respiratory syndrome coronavirus (mers-cov), smokers and copd patients might be susceptible to mers. further, compared to non-smokers, smokers and copd patients had a higher dipeptidyl peptidase iv (dpp4) expression, which was inversely correlated with lung function and diffusing capacity parameters 16 . although the relationship between smoking history and susceptibility as well as worse outcomes in covid-19 remains unclear, we cautioned that the prognosis of covid-19 in patients with smoking history might be more severe. in our cohort, lymphocytopenia occurred in more than 70% of patients at admission, which is a main laboratory feature in covid-19 patients 15, 17 . lymphocytopenia have been identified in the critically ill patients with sars-cov and mers infection 18, 19 . as mentioned in previous studies, the severity of lymphocytopenia might indicate the severity of covid-19, under the assumption of sars-cov-2 viral could attack and destroy the lymphocyte targetedly 2 . further studies are warranted to confirm these findings. increased levels of serum crp, pct, il-6 were also found. it indicated the obvious inflammatory response among these patients. in addition, we noticed that all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint the increased crp, pct concentration and decreased lymphocyte count from admission to death (supplementary figure 2) , which may represent more prominent inflammation in severe patients. therefore, intravenous glucocorticoids therapy, intravenous immunoglobulin therapy and interferon-alpha (α-ifn) aerosol inhalation were also used to restore homeostasis, without solid evidence. to our knowledge, there is still no specific medicine for covid-19 till now. clinical trials on promising regimens for covid-19, such as remdesivir, lopinavir, and chloroquine phosphate are ongoing, which shed light on conquering the covid-19 epidemic 12 . this study has several limitations. first, only 36 dead cases were included. however, this is the largest cohort about the non-survivors of covid-19 up to now. second, some specific clinical information was insufficient, such as mechanical ventilation settings, oxygen concentration, and detailed medication history. third, this is a retrospective, single-centered study. it may be limited to the hospital critical care resources. further studies are still needed. in conclusion, most non-survivors are older men with comorbidities (especially cardiovascular diseases). they finally progressed to ards. the median time from onset to ards was 11 days. the mean survival time in our cohort of covid-19 non-survivors was about 2 weeks. gradually decreased lymphocytes and increased inflammation biomarkers were found in these patients, and need to be monitored in the routine treatment. early detection and intervention of patients are especially important which can delay the development from mild to severe cases. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint yh, ry,yx collected the epidemiological and clinical data. yh summarised all data. yh, ry, yx, and pg drafted the manuscript. yh and pg revised the final manuscript. we declare no competing interests. the data will be made available to others on reasonable requests to the corresponding author. deidentified participant data will be provided after approval from the corresponding author and the fifth hospital of wuhan. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.20029009 doi: medrxiv preprint a novel coronavirus from patients with pneumonia in china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study covid-19 in singapore-current experience: critical global issues that require attention and action journey of a thai taxi driver and novel coronavirus first case of 2019 novel coronavirus in the united states transmission of 2019-ncov infection from an asymptomatic contact in germany presumed asymptomatic carrier transmission of covid-19 covid-19) sars and mers: recent insights into emerging coronaviruses therapeutic options for the 2019 novel coronavirus (2019-ncov) more than 80 clinical trials launch to test coronavirus treatments clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical characteristics of 138 hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china dpp4, the middle east respiratory syndrome coronavirus receptor, is upregulated in lungs of smokers and chronic obstructive pulmonary disease patients clinical characteristics of 2019 novel coronavirus infection in china multiple organ infection and the pathogenesis of sars t-cell immunity of sars-cov: implications for vaccine development against mers-cov we thank all patients and their families involved in the study. we thank all the doctors and key: cord-293831-28ddm9um authors: qian, mengcen; wu, qianhui; wu, peng; hou, zhiyuan; liang, yuxia; cowling, benjamin j; yu, hongjie title: psychological responses, behavioral changes and public perceptions during the early phase of the covid-19 outbreak in china: a population based cross-sectional survey date: 2020-02-20 journal: nan doi: 10.1101/2020.02.18.20024448 sha: doc_id: 293831 cord_uid: 28ddm9um objective: to investigate psychological and behavioral responses to the threat of sars-cov-2 infections and their associations with public perceptions in china design: cross sectional population-based telephone survey via random digital dialing between 1 and 10 february, 2020 setting: wuhan (the epicentre and quarantined city), and shanghai (a typical major city with close transportation link with wuhan) participants: random sample of 510 residents in wuhan and 501 residents in shanghai aged above 18 main outcome measures: anxiety (measured by the 7-item generalized anxiety disorder [gad-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out). results: the prevalence rates of moderate or severe anxiety (score ≥10 on gad-7) were 32.7% (n=167) among wuhan participants and 20.4% (n=102) among shanghai participants. 78.6% (n=401) of wuhan participants and 63.9% (n=320) of shanghai participants had carried out all six precautionary behaviors. for both measures, wuhan participants were more responsive to the outbreak (p<0.001). controlling for personal characteristics, logistic regression results suggested that risks of moderate or severe anxiety were positively associated with perceived susceptibility (odds ratio 1.6, 95% confidence interval 1.3-1.8) and severity of the disease (1.6, 1.4-1.9) and confusion about information reliability (1.6, 1.5-1.9). having confidence in taking measures to protect oneself against the disease was associated with a lower risk (0.6, 0.5-0.7). the strongest predictor of behavioral change was perceived severity (1.2, 1.1-1.4), followed by confusion about information reliability (1.1, 1.0-1.3). conclusions: psychological and behavioral responses to covid-19 have been dramatic during the rising phase of the outbreak. our results support efforts for timely dissemination of accurate and reliable information to address the high anxiety level. in december 2019, coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) emerged in wuhan city, china. 1 as of feb 16, 2020, a total of 70,548 covid-19 cases with 1,770 deaths had been reported in mainland china. 2 the outbreak has now spread to twenty-five countries outside of china. 3 on jan 31, 2020 (beijing time), the world health organization (who) declared the coronavirus outbreak a public health emergency of international concern (pheic). since jan 23, 2020, the chinese government has put wuhan and several nearby cities under quarantine, hoping to stop the disease from spreading to other parts of the country. however, millions of people had left wuhan before the lockdown because of the approaching spring festival holiday. containment measures in the covid-19 outbreak have focused on identifying, treating, and isolating infected people, tracing and quarantining their close contacts, and promoting precautionary behaviors among the general public. therefore, the psychological and behavioral responses of the general population play an important role in the control of the outbreak. previous studies have explored on this topic in various culture settings with sars, 4, 5, 6 pandemic influenza a(h1n1), 7, 8, 9, 10 and influenza a(h7n9). 11, 12, 13 cultural differences are evident in public responses. 14, 15 behavioral changes are also associated with government involvement level, perceptions of diseases, and the stage of the outbreak, and these factors vary by diseases and settings. 4, 5, 8, 16 the current covid-19 outbreak provides a unique platform to study behavioral changes for two main reasons. first, government engagement in the control of the outbreak has been unprecedented, for example, locking down wuhan and surrounding cities, building new hospitals to treat infected patients in wuhan within two weeks, extending holidays and school closure, deploying thousands of medical staff to heavily affected areas, and running intense public messaging campaigns. second, the public are faced with rather mixed information, partly because knowledge of the newly emerging disease is evolving with the course of the outbreak. for example, the national technical protocols for covid-19 released by the national health commission have been updated five times within a month. both features might result in different public responses towards the outbreak. in this study, we aimed to investigate psychological and behavioral responses to the threat of covid-19 outbreak and to examine public perceptions associated with the response outcomes in mainland china. a population-based telephone interview was carried out between 1 and 10 february, 2020. the cities of wuhan and shanghai were selected to represent diverse exposure intensities to the threat of sars-cov-2 infection. wuhan is the hardest-hit city to date, the city where the virus originated, and the earliest city put under quarantine. by contrast, shanghai is one of the largest cities in china, and was estimated to have received the largest number of infected travelers from wuhan. 17, 18 before our survey, wuhan confirmed 3,215 cases, 19 accounting for 27.3% of all cases across china; 20 shanghai reported 153 cases, 68 (44.4%) of them from nonlocal residents. 21 figure 1 illustrates the timeline of the outbreak progression compared with our survey dates. the survey was conducted by well-trained interviewers with 1,011 residents of wuhan (n=510) and shanghai (n=501) using a computerized random digital dialing system. the sample size provided us with a sample error of 5%. proportional quota sampling based on age and sex was used to ensure a demographically representative sample of the general population in each city. calls were placed three times at different hours on the same day before being classified as invalid. local residents who were aged 18 years and above and were currently living in the selected cities were eligible to participate. verbal informed consent was obtained from all participants. figure s1 presents the flow chart of participant recruitment. ethical approval was obtained from the institutional review board at school of public health, fudan university (irb#2020-tysq-01-1). anxiety was assessed using the 7-item generalized anxiety disorder scale (gad-7). the tool is a brief self-reported scale that has demonstrated good reliability and validity in the general population. 22, 23 participants were asked to answer how frequently they had been bothered by various symptoms over the past two weeks. the scale accordingly produced a summary gad scores ranging from 0 to 21. respondents that scored 10 and above were identified as having moderate or severe level of anxiety. 22 participants were asked three questions about recent avoidance behaviors (avoided eating out, avoided taking public transportation, and reduced visits to public places) and another three about recommended behaviors (rescheduling travel plan, increasing surface cleaning, and maintaining better indoor ventilation) in response to the outbreak. all questions were phrased as "during the past week, did you ever … because of the novel coronavirus outbreak". possible responses for each question were yes or no. three sets of questions were asked to collect information about preventive behaviors in usual days before 31 december 2019 when an unknown pneumonia outbreak related to the later identified sars-cov-2 was firstly reported, and then in the past week. the first two sets of questions regarding the frequency of wearing a face mask when going out and the frequency of handwashing immediately when returning home. response options were never (scored as 1), rare (2), sometimes (3), usually (4), always (5), or did not go out. the top reasons for wearing a face mask in usual days and in the past week were collected. respondents who did not always wear a face mask in the past week were also required to provide a most possible reason. the third set of question concerning handwashing duration with five responses categories from short to long (1 score to 5 scores), for less than 10 seconds, [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] seconds, 20-39 seconds, 40-59 seconds, or 60 seconds and above, respectively. respondents whose answers for behaviors in the past week scored higher than those in usual days were categorized as increased frequency or duration of the aforementioned behaviors. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint to capture possible over-reaction of the public, a supplementary question was asked "in the past week, have you ever purchased or tried to purchase goggles for the purpose of protection against infection with sars-cov-2?" with two possible responses (yes or no). five items were used to assess whether participants believed that certain measures would reduce their risk of catching covid-19, with possible response options being ineffective (1), even (2), or effective (3). the first three items (frequent handwashing, wearing a face mask, and avoiding going out) were consistent with the advertising campaign run by the government. the last two items (washing mouth with salty water, and taking vitamin c or a product of the traditional chinese medicine, isatis root) were considered as misinformation by medical experts. participants answered effective in all first three items and ineffective in both of the last two items were categorized as having correct perceived efficacy of behaviors. four items assessed perceived threats of the novel coronavirus. participants were asked "how likely do you think you will contract novel coronavirus infection over the next month" with five responses from very unlikely (1) to very likely (5), and "how serious do you think the novel coronavirus infection would be if you contracted it" with five options from very mild (1) to very serious (5) . participants were also required to report relative transmissibility and severity compared with sars in 2003 with five response categories being much lower (1), lower (2), similar (3), higher (4), or much higher (5) . three items assessed how well informed were the public. participants were asked "whether you have received and read the information brochure about the novel coronavirus from the government and medical experts" with two response options (yes or no). they were then required to provide response to the statement "information that i received about the novel coronavirus outbreak is sufficient" with five options from strongly disagree (1) to strongly agree (5) . to assess the impact of mixed information during the outbreak, participants were asked to report the frequency that they felt confused or bothered about the reliability of the information that they received. response options ranged from never (1) to always (5). all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint the confidence of the public was assessed by asking if they agreed with the statement "i believe that i can take measures to protect myself against the novel coronavirus" with five response options from strongly disagree (1) to strongly agree (5). personal characteristics were collected in the following dimensions: sex, age, working status, perceived household income level, whether experienced symptoms (cough and fever) during the past two weeks, whether has friends or relatives with symptoms in the past two weeks, and whether there had been confirmed or suspected cases of novel coronavirus infections in their neighborhood. analyses were carried out in stata version 14 for windows. descriptive analysis of the aforementioned responses was performed to report the counts and frequencies, stratified by cities. differences across cities were examined using t tests for dummy variables and chisquare or fisher's exact tests (when applicable) for variables measured by a likert scale. the primary outcomes were moderate or severe anxiety (gad-7 score ≥10), and whether respondents engaged in all recommended and avoidance behaviors. multivariate logistic regression models were first used to estimate associations between personal characteristics and primary outcomes. these models adjusting for personal characteristics were then used to investigate associations between perception variables and primary outcomes. perception variables were included in the form of continuous scores. public were involved in this study as participants of the telephone survey. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint overall, 18,576 randomly generated digital numbers were selected and called. of these, 7,341 calls answered; of these, 5,650 declined the participation invitation, 505 were ineligible, 185 dropped before completion, leaving 1,011 respondents successfully completed the interview. the response rate was 13.8% (1,011/7,341) ( figure s1 ). participants in wuhan (34.5%) reported a much higher rate of living in neighborhood with confirmed or suspected novel coronavirus cases than those in shanghai (6.4%) ( table 1 ). a total of 167 (32.7%) respondents in wuhan and 102 (20.4%) respondents in shanghai were identified to have moderate or severe anxiety (panel a table 2 ). the prevalence was significantly higher in wuhan (p<0.001). the mean gad-7 scores were 7.1 and 5.1 in wuhan and shanghai, respectively (p<0.001). in total 401 (78.6%) wuhan participants and 320 (63.9%) shanghai participants engaged in all six recommended and avoidance behaviors due to the novel coronavirus outbreak (panel b table 2 ). a high compliance rate of above 90% was observed in all other behaviors in both samples, except for increased surface cleaning, which was driving the significant observed differences in behavioral responses between the two cities (table s1 ). frequencies of washing hands immediately when returning home, wearing a face mask when going out, and duration of handwashing significantly increased in both cities during the outbreak (panel b table 2 ; figure 2 ). we found no statistically significant differences in changes of the first two aforementioned behaviors. by contrast, more respondents reported longer duration of handwashing in wuhan (p<0.001). moreover, a significantly higher proportion of wuhan respondents reported purchasing or trying to purchase goggles for prevention purpose (p=0.009). overall, 12.7% wuhan participants responded with correct perceived efficacy of behaviors. the proportion was significantly higher (p=0.004) in the shanghai sample (19.4%) (panel c table 2 ). generally, wuhan respondents reported significantly higher self-perceived risk (p=0.033) of contracting novel coronavirus than their counterparts in shanghai; however, all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint their perceived severity and relative transmissibility to sars were significantly lower (p<0.001). no differences were found between the two cities in terms of perceived harm to body compared with sars. moreover, respondents aged 40 and above, who presumably have clearer memory of sars, had higher (p<0.001) perceived relative severity than those aged 18-39 in shanghai; similar findings were not found in wuhan (table s2) . around 96.1% wuhan respondents had received and read the information brochures of the novel coronavirus from the government or medical experts. the proportion was significantly lower (p<0.001) but still very high in shanghai (89.0%). the majority of the respondents in both cities thought that the information that they received was sufficient, without discernable differences. by contrast, the wuhan respondents were significantly more often confused about the reliability of the information that they received (p=0.003); only 31% respondents in wuhan never felt bothered about this issue, while the corresponding figure in shanghai was 42.9%. the majority of the participants agreed or strongly agreed with having confidence on taking measures to protect themselves. we detected no statistically significant differences across cities in this domain. the largest positive and significant effects on moderate or severe anxiety were from participants with confirmed or suspected cases in their living neighborhood (odds ratio 1.9, 95% confidence interval 1.3-2.8) ( table 1 ). compared to low income individuals, those with median income were less likely to suffer moderate or severe anxiety (odds ratio 0.6, 0.4-0.9). furthermore, shanghai participants were significantly less likely to report moderate or severe anxiety (odds ratio 0.6, 0.5-0.8) or carry out all recommended and avoidance behaviors (odds ratio 0.4, 0.3-0.6) than wuhan participants. we found no evidence that sex, age, educational attainment, working status and marital status were closely associated with psychological and behavioral responses during the novel coronavirus outbreak. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint we found that higher perceived risk and severity of contracting the novel coronavirus, higher perceived relative transmissibility and harm to body to sars, and more confusion about information reliability were all significantly and positively associated with reported moderate or severe anxiety during the outbreak (table 3 ). in contrast, stronger self-confidence was significantly associated with lower risks of moderate or severe anxiety. for behavioral responses, increases in anxiety levels, perceived risks and harms to body relative to sars, and confusion about information reliability were significantly associated with higher probability of carrying out all recommended and avoidance behaviors during the outbreak (table 3 ). for increases in frequencies of immediate handwashing behavior when returning home, the factor that exerted the largest impact was having received and read information brochures from the government, followed by having correct perceived efficacy of behaviors (table s3 ). higher perceived harm to body compared with sars was the only factor with significant explanatory power for goggles purchase behavior. we found no evidence that perceptions and anxiety levels were associated with changes in frequencies of wearing face masks during the outbreak (table s3 ). we conducted a population-based telephone survey via random digital dialing to investigate anxiety levels, changes in precautionary behaviors and public perceptions among wuhan and shanghai residents during the early phase of 2019 novel coronavirus. around of 32.7% wuhan and 20.4% shanghai participants reported moderate or severe anxiety; 78.6% wuhan and 63.9% shanghai respondents carried out all six precautionary behaviors due to the outbreak. wuhan residents were significantly more responsive than their shanghai counterparts in the two aforementioned outcomes. our results suggested that perceived risk and severity of the disease as well as information reliability were important factors associated with the psychological and behavioral responses. our study provides new evidence on psychological and behavioral response to disease outbreaks by comparing public response in two cities under various exposures to the early all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is second, our results suggest that more responsive behavioral changes observed in this study were associated with the strong involvement from the chinese government during the control and prevention of coronavirus than voluntary avoidance behaviors reported previously. 5,9,26,27, measures such as temporary closing down public transportation in wuhan and imposing punishment for passengers not wearing a face mask on metro in shanghai have fueled the high compliance rates with government recommendations (table s1 ) and perceived efficacy of these behaviors (table s4 ). these polices are also responsible for the limited observed heterogeneity in uptake and changes of precautionary behaviors. for example, we find that no perception variables exerted a statistically meaningful effect on increased face mask wearing frequency (table s3) . third, we provided evidence for unwarranted precautionary behavior in coping with a novel disease, which was less documented in the literature. 5 around 28% wuhan and 21% shanghai respondents reported having purchased or having tried to purchase goggles for infection prevention. according to the national health commission experts, goggles are unnecessary protective equipment for people other than medical staff on the front line of coronavirus outbreak. however, goggles were sold out nationwide shortly after a doctor wrote on social media and suspected that lack of eye protection in early investigation of the outbreak all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint might have led to his infection. our results showed that the irrational behavior was mainly driven by perceived higher severity than sars and the over-reaction was more prevalent in wuhan (table s3) . fourth, perceived susceptibility and severity of the coronavirus were higher compared with studies regarding other diseases. after translating our results into comparable scales, we found that the perceived chance of infection (12.5-18.6%) was higher than that during h7n9 in urban china (1.0-2.6%), 11 and sars in hong kong (3.9-14.3%); 4 and the relative severity to sars was four times higher than that of h7n9 in urban china (8.9-11.4%). 11 though higher perceived risk and harm of coronavirus positively associated with favorable responses in behaviors, it also led to significantly higher anxiety levels among the general public. our findings also yield several important public implications. first, providing the public with reliable and accurate information is crucial for addressing the psychological effects of contagious disease outbreaks. public confusion about the reliability of information that they received might have led to significantly sustained anxiety. about 57.1-69.0% individuals were ever bothered by this issue, and the prevalence of this issue was significantly more common among people subject to quarantine in wuhan, suggesting stronger desire for facts. 28 second, consequences of misinformation could be long-lasting and should not be underestimated in health crisis management. 7, 29 although efficacy of behaviors supported in advertising campaign was well received, rumors that have been proved wrong earlier during the sars outbreak, for example, washing mouth with salty water, or having vitamin c or radix isatidis, still found their audience. only 24.6-37.9% respondents in our study correctly considered these measures as ineffective (table s4) ; the correct rate was significantly lower in wuhan. finally, awareness of hand hygiene in china has been low, which calls for more handwashing education in the community. we found that the proportion of handwashing duration over 40 seconds as recommended by who only slightly increased from 17.3% to 37.6% during novel coronavirus outbreak. 30 fortunately, having received and read information brochures was positively associated with longer handwashing duration (table s3) , suggesting education programs will be effective for addressing this issue. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint our study has a number of limitations. first, in order to investigate public response rates in the immediate aftermath of the major public health crisis, we shortened our survey questionnaire and chose to use random digital dialing with quota sampling to obtain demographically representative samples for both selected cities. we deliberately selected out times of handwashing as a key behavior measure, although it is widely discussed in the literature. because people have largely reduced going out during the extended national holidays while embracing remote work, resulting in less times of handwashing than in usual days, which makes this measure less valid. second, we asked respondents to recall some of their behaviors in usual days before december 2019. their answers might suffer recall bias. in conclusion, it is seen that psychological and behavioral responses to covid-19 had been dramatic during the rising phase of the outbreak. prevalence of moderate or severe anxiety were 4-5 times of its normal level in urban china. the majority engaged in all six recommended and avoidance behaviors. wuhan, the epicentre and quarantined city, was significantly more responsive in the aforementioned domains than shanghai. tremendous government efforts in control and prevention of the disease were associated with sizable changes in face mask wearing. however, confusion about information reliability significantly fueled the public anxiety levels, and public awareness of hand hygiene was less optimal. our results support efforts for timely dissemination of accurate and reliable information and to focus more on handwashing education. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is a statement that the lead author, h.y., affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted. ethical approval was obtained from the institutional review board at fudan university school of public health (irb#2020-tysq-01-1). the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is notes: the first two columns report counts and frequencies of each variable value. the last two column present multivariate regression results. * for significance at the 5% level; ** for significance at the 1% level. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. 1 the total number of respondents was 386 in the wuhan sample and 432 in the shanghai sample because 124 and 69 participants reported "never went out last week" respectively in the above samples. 2 the total number of respondents was 457 in the wuhan sample and 473 in the shanghai sample because 43 wuhan participants and 28 shanghai participants refused to answer. 3 the total number of respondents was 398 in the wuhan sample and 403 in the shanghai sample because 112 wuhan participants and 98 shanghai participants refused to answer. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint table 3 . perception factors associated with anxiety and behavioral responses table 1 are controlled for. * for significance at the 5% level; ** for significance at the 1% level. all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 18.20024448 doi: medrxiv preprint a novel coronavirus from patients with pneumonia in china latest situation of new coronavirus pneumonia as of world health organization. coronavirus disease 2019 (covid-19) situation report -26 monitoring community responses to the sars epidemic in hong kong: form day 10 to day 62 sars risk perception, knowledge, precautions, and information sources, the netherlands the psychological impact of the sars epidemic on hospital employees in china: exposure, risk perception, and altruistic acceptance of risk public perceptions, anxiety, and behaviour change in relation to the swine flu outbreak: cross sectional telephone survey population responses during the pandemic phase of the influenza a(h1n1)pdm09 epidemic measured voluntary avoidance behaviour during the 2009 a/h1n1 epidemic avoidance behaviors and negative psychological responses in the general population in the initial stage of the h1n1 pandemic in hong kong human exposure to live poultry and psychological and behavioral responses to influenza a(h7n9), china live poultry exposure and public response to influenza a(h7n9) in urban and rural china during two epidemic waves in 2013-2014 responses to threat of influenza a(h7n9) and support for live poultry markets the psychology behind the masks: psychological responses to the severe acute respiratory syndrome outbreak in different regions all rights reserved. no reuse allowed without permission the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is perceived threats, risk perception, and efficacy beliefs related to sars and other (emerging) infectious diseases: results of an international survey nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions update on the outbreak of novel coronavirusinfected pneumonia as of 31 update on the outbreak of novel coronavirus-related pneumonia as of 31 shanghai municipal health commission, shanghai municipal administration of traditional chinese medicine. 18 new confirmed cases of novel coronavirus-infected pneumonia in shanghai a brief measure for assessing generalized anxiety disorder validation and standardization of the generalized anxiety disorder screener (gad-7) in the general population meta-analysis of the prevalence of anxiety disorders in mainland china from generalized anxiety disorder in urban china: prevalence, awareness, and disease burden skip the trip: air travelers' behavioral responses to pandemic influenza precautionary behavior in response to perceived threat of pandemic influenza coronavirus: the psychological effects of quarantining a city confirmatory bias in health decisions: evidence form the mmrautism controversy hand hygiene: why, how & when? all rights reserved. no reuse allowed without permission. the author/funder, who has granted medrxiv a license to display the preprint in perpetuity.the copyright holder for this preprint (which was not peer-reviewed) is . key: cord-288432-n2y9cunc authors: liu, kun; ai, siqi; song, shuxuan; zhu, guanghu; tian, fei; li, huan; gao, yuan; wu, yinglin; zhang, shiyu; shao, zhongjun; liu, qiyong; lin, hualiang title: population movement, city closure in wuhan and geographical expansion of the 2019-ncov pneumonia infection in china in january 2020 date: 2020-04-17 journal: clin infect dis doi: 10.1093/cid/ciaa422 sha: doc_id: 288432 cord_uid: n2y9cunc background: the unprecedented outbreak of 2019-ncov pneumonia infection in wuhan city caused global concern, the outflowing population from wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the chinese new year. methods: based on the daily reported new cases and the population movement data between january 1 and 31, we examined the effects of population outflow from wuhan on the geographical expansion of the infection in other provinces and cities of china, as well as the impacts of the city closure in wuhan in different scenarios of closing dates. results: we observed a significantly positive association between population movement and the number of the 2019-ncov cases. the spatial distribution of cases per unit outflow population indicated that some areas with large outflow population might have been underestimated for the infection, such as henan and hunan provinces. further analysis revealed that if the city closure policy was implemented two days earlier, 1420 (95% ci: 1059, 1833) cases could have been prevented, and if two days later, 1462 (95% ci: 1090, 1886) more cases would be possible. conclusions: our findings suggest that population movement might be one important trigger for the transmission of 2019-ncov infection in china, and the policy of city closure is effective to control the epidemic. in december 2019, an unprecedented pneumonia outbreak caused by a novel coronavirus, namely 2019-ncov, emerged in wuhan, the capital city of hubei province in china [1] . similar with severe acute respiratory syndrome (sars), the outbreak was highly suspected to be linked to the wild animals in the seafood market, although the definitive source was not clear yet [2] . as of january 31, 2020, the infection has been transmitted to all the provinces in china and a few other countries. epidemiology evidence showed that most of the cases outside wuhan had a history of living or travelling to wuhan, and human-to-human transmission route was possible [3] , which might be the reason for a rapid increasing rate of infection across the country and globally [4] . considering the person-to-person transmission and the large travel volume during the traditional chinese new year (the largest annual population movement in the world), it is expected that the population movement would lead to further expansion of the infection, so the government imposed a lockdown on wuhan city at 10:00 am on january 23, as well as some other cities later on [5] . however, an estimated 5 million individuals had already left wuhan for the holiday or travelling, some of which rushed out after the lockdown announcement [6] . in addition, the novel coronavirus is infectious during the incubation period and when the symptoms are not obvious, which is likely to make the huge floating population potential sources of infection [7] . therefore, it is reasonable to hypothesize that the population transported a c c e p t e d m a n u s c r i p t 6 from wuhan may have a significant impact on the potential outbreaks in other parts of china. recent studies on the novel coronavirus pneumonia focused more on its etiology [8, 9] , transmission route [10, 11] , and epidemiological characteristics [12, 13] , there is still a lack of investigating the relationship between the migrating population and the outbreak, which is of great importance for making intervention policies. thus, we conducted this study with the following objectives: 1) to evaluate the impacts of the population movement on the spatial transmission of the 2019-ncov cases at the provincial and city levels in china; 2) to estimate the potential outbreak risk at areas with the population outflowed from wuhan; 3) to evaluate the effectiveness of the city closure measures on the epidemic control. the data on the daily number of 2019-ncov pneumonia cases from january 1 to 31 were derived from the real-time update of the china health commission (http://www.nhc.gov.cn/), 2019-ncov epidemic report on the websites of phoenix and dingxiangyuan. the diagnosis and definition of the case have been described elsewhere [2, 3] . in brief, a confirmed case was defined as a pneumonia case that was laboratory confirmed 2019-ncov infection with related respiratory symptoms and a travel history to wuhan or direct contact with patients from wuhan. a c c e p t e d m a n u s c r i p t 7 as the city closure took place at 10:00 am on january 23, 2020, and the incubation period of the infection was considered to be about 3-7 days [14] , we obtained the daily index of population outflow from wuhan and the proportion of the daily index from wuhan to other provinces and top 50 cities, from january 1 to 31 in 2020, the information was retrieved through the spring festival travel information of china released by baidu qianxi. the data came from baidu location based services (lbs) and baidu tianyan based on location and traffic information systems, which could provide real-time dynamic information on regional population outflow. data of baidu qianxi was freely available to the public (http://qianxi.baidu.com). the daily index of population outflow from wuhan to other provinces and top 50 cities was obtained by multiplying the daily index of population outflow within c is the cumulative 2019-ncov cases in each province from january 1 to 31: d is the total index of population inflow from wuhan to other provinces: we finally calculated the average number of cases per unit outflow population for each province in china: the net loss index of outflow population caused by advanced wuhan city closure for each province: 11 a c c e p t e d m a n u s c r i p t 10 similarly, we evaluated the impacts of one-day and two-day delayed city closure. we took the average index of the population outflow between january 21 and 23 as the daily index of population outflow before the city closure, and used the same calculation method to estimate the index of population outflow within wuhan increased by the delayed city closure on january 24 and january 25 (the delayed outflow index). we multiplied the delayed outflow index by the average proportion and one corresponding unit to estimate the increased number of cases caused by one-day and two-day delayed city closure of wuhan for each province in china. (table 1) . on the contrary, if the closure measures was delayed for one to two days, the number of cases would increase by 722 and 1462, respectively. our study provided timely evidence for the formulation of efficient strategies to prevent diseases from spreading out. on the one hand, the result could help assess the effectiveness of the prevention and control efforts. for example, the cases in zhejiang and guangdong are apparently more than estimated, which indicated a better health emergency response system (i.e. higher detection efficiency) or inadequate isolation, whereas the cases reported in henan were much lower than expected. two possible explanations should be considered: (1) strong prevention and control measures had been adopted in henan; (2) the epidemic in henan has been underestimated and enhanced screening efforts should be enforced. on the other hand, exploring the association was expected to help identify high-risk areas and guide health strategy a c c e p t e d m a n u s c r i p t 15 formulation [19, 20] . take henan as an example, great difference between estimated and reported data may imply a great increase of cases in the future, which required enhancement of the surveillance system and rational allocation of resources [17] . the medicine supply, personal protective equipment, hospital supplies, and the human resources necessary to respond to an outbreak should be always ensured [21] . in addition, this study could be used to guide the assessment of the risk of disease transmission and help raise public awareness. as a large number of infected people had transported to all of 31 provinces, epidemics across the country may be inevitable. to halt the spread of the epidemic, harsh measures including quarantine and isolation of exposed persons, cancellation of mass gatherings, school closures, and travel restriction were needed to reduce transmission in affected areas. furthermore, screening of people who have been to wuhan recently was of crucial importance, especially cities with close ties to wuhan. considering the impact of population movements on the outbreak, the wuhan government announced the suspension of public transportation on january 23, 2020, with a closure of airports, railway stations, and highways, to prevent further disease transmission [22] . despite inconsistent reports on the role of the lockdown in halting the disease transmission across china [11, 20, 21] , the unprecedented measure might play an important role in slowing the epidemic spread, especially when an effective vaccine was developed [23, 24] . in addition, to explore the impact of date selection, we estimated the changes of cases when the measure was implemented on different a c c e p t e d m a n u s c r i p t 16 date. the results varied significantly, 1420 cases could be prevented with the measure implemented two days earlier, and the number of cases will increase by 1462 with the lockdown implemented two days later, suggesting that the effect of the lockdown depending on the choice of date greatly, which could provide a reference for the future outbreaks. since the political and economic effects were not considered, further studies on secondary impacts of the measure, like socioeconomic impacts, were also warranted. though we estimated that some cases would possibly be prevented if the policy was implemented earlier, it was actually hard to make such a huge decision given the whole picture of the infection was not clear at that stage. the authors believe that the current policy was appropriate at this complex situation. there were a few limitations of our study. firstly, we used the index of population outflow to reflect the general real-time magnitude of population movements, so it was not an accurate representation of the actual population flow data. secondly, some possible influencing factors, such as socio-economic factors and demographic characteristics, were not included in the analysis because of data inaccessibility. thirdly, it is assumed that the infected travelers in the population were randomly distributed [25] and that there was no significant difference in the surveillance capability between cities [17] , which would result in some difference between the estimated value and the actual situation. in addition, daily data used in this study was reported infection data, rather than the actual number of incident cases. in summary, our study indicates that the population outflow from wuhan might m a n u s c r i p t we appreciated the support by national key r&d program of china (grant no: 2018yfa0606200). we thank our colleagues for their careful reading and editing of this manuscript. the funder had no role in study design, data collection, data analysis, data interpretation, or writing of the report. the corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication. the authors declare they have no 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-uganda forecast and control of epidemics in a globalized world nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study commission cnh. announcement from the headquarter for novel coronavirus pneumonia prevention and control delaying the international spread of pandemic influenza empirical evidence for the effect of airline travel on inter-regional influenza spread in the united states predicting the international spread of middle east respiratory syndrome (mers) a c c e p t e d m a n u s c r i p t 20 a c c e p t e d m a n u s c r i p t 22 key: cord-290758-kz0qfy3r authors: hui, david s.; i azhar, esam; madani, tariq a.; ntoumi, francine; kock, richard; dar, osman; ippolito, giuseppe; mchugh, timothy d.; memish, ziad a.; drosten, christian; zumla, alimuddin; petersen, eskild title: the continuing 2019-ncov epidemic threat of novel coronaviruses to global health — the latest 2019 novel coronavirus outbreak in wuhan, china date: 2020-02-29 journal: international journal of infectious diseases doi: 10.1016/j.ijid.2020.01.009 sha: doc_id: 290758 cord_uid: kz0qfy3r nan the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china the city of wuhan in china is the focus of global attention due to an outbreak of a febrile respiratory illness due to a coronavirus 2019-ncov. in december 2019, there was an outbreak of pneumonia of unknown cause in wuhan, hubei province in china, with an epidemiological link to the huanan seafood wholesale market where there was also sale of live animals. notification of the who on 31 dec 2019 by the chinese health authorities has prompted health authorities in hong kong, macau, and taiwan to step up border surveillance, and generated concern and fears that it could mark the emergence of a novel and serious threat to public health (who, 2020a; parr, 2020) . the chinese health authorities have taken prompt public health measures including intensive surveillance, epidemiological investigations, and closure of the market on 1 jan 2020. sars-cov, mers-cov, avian influenza, influenza and other common respiratory viruses were ruled out. the chinese scientists were able to isolate a 2019-ncov from a patient within a short time on 7 jan 2020 and perform genome sequencing of the 2019-ncov. the genetic sequence of the 2019-ncov has become available to the who on 12 jan 2020 and this has facilitated the laboratories in different countries to produce specific diagnostic pcr tests for detecting the novel infection (who, 2020b) . the 2019-ncov is a β cov of group 2b with at least 70% similarity in genetic sequence to sars-cov and has been named 2019-ncov by the who. sars is a zoonosis caused by sars-cov, which first emerged in china in 2002 before spreading to 29 countries/regions in 2003 through a travel-related global outbreak with 8,098 cases with a case fatality rate of 9.6%. nosocomial transmission of sars-cov was common while the primary reservoir was putatively bats, although unproven as the actual source and the intermediary source was civet cats in the wet markets in guangdong . mers is a novel lethal zoonotic disease of humans endemic to the middle east, caused by mers-cov. humans are thought to acquire mers-cov infection though contact with camels or camel products with a case fatality rate close to 35% while nosocomial transmission is also a hallmark (azhar et al., 2019) . the recent outbreak of clusters of viral pneumonia due to a 2019-ncov in the wuhan market poses significant threats to international health and may be related to sale of bush meat derived from wild or captive sources at the seafood market. as of 10 jan 2020, 41 patients have been diagnosed to have infection by the 2019-ncov animals. the onset of illness of the 41 cases ranges from 8 december 2019 to 2 january 2020. symptoms include fever (>90% cases), malaise, dry cough (80%), shortness of breath (20%) and respiratory distress (15%). the vital signs were stable in most of the cases while leucopenia and lymphopenia were common. among the 41 cases, six patients have been discharged, seven patients are in critical care and one died, while the remaining patients are in stable condition. the fatal case involved a 61 year-old man with an abdominal tumour and cirrhosis who was admitted to a hospital due to respiratory failure and severe pneumonia. the diagnoses included severe pneumonia, acute respiratory distress syndrome, septic shock and multi-organ failure. the 2019-ncov infection in wuhan appears clinically milder than sars or mers overall in terms of severity, case fatality rate and transmissibility, which increases the risk of cases remaining undetected. there is currently no clear evidence of human to human transmission. at present, 739 close contacts including 419 healthcare workers are being quarantined and monitored for any development of symptoms (who, 2020b; center for health protection and hksar, 2020). no new cases have been detected in wuhan since 3 january 2020. however the first case outside china was reported on 13th january 2020 in a chinese tourist in thailand with no epidemiological linkage to the huanan seafood wholesale market. the chinese health authorities have carried out very appropriate and prompt response measures including active case finding, and retrospective investigations of the current cluster of patients which have been completed; the huanan seafood wholesale market has been temporarily closed to carry out investigation, environmental sanitation and disinfection; public risk communication activities have been carried out to improve public awareness and adoption of self-protection measures. technical guidance on novel coronavirus has been developed and will continue to be updated as additional information becomes available. however, many questions about the new coronavirus remain. while it appears to be transmitted to humans via animals, the specific animals and other reservoirs need to be identified, the transmission route, the incubation period and characteristics of the susceptible population and survival rates. infection and data are missing in regard to the age range, animal source of the virus, incubation period, epidemic curve, viral kinetics, transmission route, pathogenesis, autopsy findings and any treatment response to antivirals among the severe cases. once there is any clue to the source of animals being responsible for this outbreak, global public health authorities should examine the trading route and source of movement of animals or products taken from the wild or captive conditions from other parts to wuhan and consider appropriate trading restrictions or other control measures to limit. the rapid identification and containment of a novel coronavirus virus in a short period of time is a reassuring and a commendable achievement by china's public health authorities and reflects the increasing global capacity to detect, identify, define and contain new outbreaks. the latest analysis show that the wuhan cov cluster with the sars cov.10 (novel coronavirus -china (01) whilst several important aspects of mers-cov epidemiology, virology, mode of transmission, pathogenesis, diagnosis, clinical features, have been defined, there remain many unanswered questions, including source, transmission and epidemic potential. the wuhan outbreak is a stark reminder of the continuing threat of zoonotic diseases to global health security. more significant and better targeted investments are required for a more concerted and collaborative global effort, learning from experiences from all geographical regions, through a 'one-human-enivronmental-animal-health' global consortium to reduce the global threat of zoonotic diseases (zumla et al., 2016) . sharing experience and learning from all geographical regions and across disciplines will be key to sustaining and further developing the progress being made. the middle east respiratory syndrome (mers) severe acute respiratory syndrome: historical, epidemiologic, and clinical features pneumonia in china: lack of information raises concerns among hong kong health workers pneumonia of unknown origin -china. disease outbreak news pneumonia of unknown origin -china. disease outbreak news world health organization. sars (severe acute respiratory syndrome) world health organization. mers situation update taking forward a' one health' approach for turning the tide against the middle east respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential novel coronavirus -china (01): (hu) who, phylogenetic tree all authors have a specialist interest in emerging and reemerging pathogens. fn, rk, od, gi, tdmc, cd and az are members of the pan-african network on emerging and re-emerging infections (pandora-id-net) funded by the european and developing countries clinical trials partnership the eu horizon 2020 framework programme for research and innovation. az is a national institutes of health research senior investigator. all authors declare no conflicts of interest. key: cord-280786-944pn0k9 authors: wang, chaolong; liu, li; hao, xingjie; guo, huan; wang, qi; huang, jiao; he, na; yu, hongjie; lin, xihong; pan, an; wei, sheng; wu, tangchun title: evolving epidemiology and impact of non-pharmaceutical interventions on the outbreak of coronavirus disease 2019 in wuhan, china date: 2020-03-06 journal: nan doi: 10.1101/2020.03.03.20030593 sha: doc_id: 280786 cord_uid: 944pn0k9 background we described the epidemiological features of the coronavirus disease 2019 (covid-19) outbreak, and evaluated the impact of non-pharmaceutical interventions on the epidemic in wuhan, china. methods individual-level data on 25,961 laboratory-confirmed covid-19 cases reported through february 18, 2020 were extracted from the municipal notifiable disease report system. based on key events and interventions, we divided the epidemic into four periods: before january 11, january 11-22, january 23 february 1, and february 2-18. we compared epidemiological characteristics across periods and different demographic groups. we developed a susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions. results the median age of the cases was 57 years and 50.3% were women. the attack rate peaked in the third period and substantially declined afterwards across geographic regions, sex and age groups, except for children (age <20) whose attack rate continued to increase. healthcare workers and elderly people had higher attack rates and severity risk increased with age. the effective reproductive number dropped from 3.86 (95% credible interval 3.74 to 3.97) before interventions to 0.32 (0.28 to 0.37) post interventions. the interventions were estimated to prevent 94.5% (93.7 to 95.2%) infections till february 18. we found that at least 59% of infected cases were unascertained in wuhan, potentially including asymptomatic and mild-symptomatic cases. conclusions considerable countermeasures have effectively controlled the covid-19 outbreak in wuhan. special efforts are needed to protect vulnerable populations, including healthcare workers, elderly and children. estimation of unascertained cases has important implications on continuing surveillance and interventions. the coronavirus disease 2019 (covid-19) is an emerging respiratory infectious disease caused by sars-cov-2 (also known as 2019-ncov), which first occurred in early december 2019 in wuhan, china. until march 1, covid-19 has affected more than 79,900 individuals and caused 2873 deaths in china, and quickly spread to over 55 countries worldwide. 1 although some studies with varying sample sizes have described the clinical characteristics of patients with covid-19, 2-7 and a previous study has reported the early transmission dynamics of the first 425 confirmed cases in wuhan, 8 most recent data are required to illustrate the full spectrum of the epidemiological characteristics of the outbreak in wuhan. during the outbreak, the chinese authorities have implemented a series of non-pharmaceutical interventions to control the epidemic (details in fig. 1 several modelling studies have used the international cases exported from wuhan to extrapolate the severity of epidemic in wuhan, which estimated much larger numbers of infected cases than those officially reported, implying a substantial amount of unascertained cases. 9, 10 while the huge discrepancy remained unexplained, these early models can no longer be applied since january 23 due to the intensive intra-city and inter-city traffic restriction, social distancing measures, and improvement of medical . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint resources within wuhan city. these interventions would inevitably affect the model parameters such as the transmission rate across time. in addition, many previous modeling studies have used the date of laboratory confirmation in the analysis without considering the long lag between onset and confirmation date for the early cases. [11] [12] [13] moreover, several recent studies have reported a nonnegligible proportion of asymptomatic cases [14] [15] [16] and transmissibility of the asymptomatic or presymptomatic cases, 17-19 which were not considered by previous models. in this study, we described the epidemiological characteristics of the laboratory-confirmed patients with covid-19 in wuhan till february 18, 2020. we developed a novel susceptible-exposed-infectious-recovered (seir) model to study the epidemic by accounting for time-varying population movement, ascertainment rate, transmission rate, and duration from illness onset to hospitalization. we compared model prediction under different scenarios and the actual reported cases to evaluate the overall impact of the city quarantine and subsequent interventions on the epidemic in wuhan. covid-19 cases from december 2019 till february 18, 2020 were extracted on february 19 from the municipal notifiable disease report system, including the general information of birth date, sex, occupation, residential district, date of illness onset (the self-reported date of symptoms such as fever, cough, or other respiratory . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint symptoms), and date of confirmed diagnosis (the laboratory confirmation date of sars-cov-2 in the bio-samples). the identifiable personal information was removed for privacy protection. a case was recorded as a healthcare worker if reported to work in a hospital or clinic. cases were diagnosed and the severity status was categorized as mild, moderate, severe, and critical according to the diagnosis and treatment scheme for covid-19 released by the national health commission of china. 20 a laboratory-confirmed case was defined if the patient had a positive test of sars-cov-2 virus by the real-time reverse-transcription-polymerase-chain-reaction (rt-pcr) assay or high-throughput sequencing of nasal and pharyngeal swab specimens. we only included laboratory-confirmed cases in our analyses for consistency of case definition throughout the periods. to better reflect the dynamics of the covid-19 epidemic and corresponding interventions, we classified the outbreak into four periods based on important dates that could affect the virus transmission (fig. 1) . the time before january 11, 2020, the first date of chunyun (massive migration for the chinese new year), was considered as the first period when no intervention was imposed. the second period referred to the chunyun of january 11-22, 2020, when massive population movement occurred . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint and was expected to accelerate the spread of covid-19. no strong intervention was imposed except for the announcement of human-to-human transmission and infections in healthcare workers on january 20. the hospitals started to be overcrowded with people with fever or respiratory symptoms. during the third period between january 23 and february 1, the local government first blocked all outbound transportations on january 23 and subsequently suspended public transit and banned all vehicular traffic within the city. other social distancing measures were also implemented, including compulsory mask-wearing in public places and cancellation of social gathering. due to severe shortage of medical resources in this period, many confirmed or suspected cases could not receive timely treatment and were self-quarantined at home. on february 2, with improvement in medical resources, the government implemented the policy of centralized quarantine and treatment of all confirmed and suspected cases, those with fever or respiratory symptoms, as well as close contacts of confirmed cases in designated hospitals or facilities. meanwhile, temperature monitoring and stay-at-home policies were implemented to all residents in the city. taken together, we divided the outbreak in wuhan into four periods (before january 11, january 11-22, january 23-february 1, and february 2-18, 2020, respectively) with specific intervention activities provided in fig. 1 . we calculated the daily onset numbers of confirmed covid-19 cases from december 2019 till february 18, 2020. we estimated the attack rate, defined as the . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint number of infections per day per 10 6 people, by age, sex, healthcare occupation, and residential districts, with the subtotal population size in each stratum from the wuhan statistical yearbook 2018. logistic regression was used to evaluate the association of age, sex, time period and healthcare occupation with the disease severity (mild/moderate versus severe/critical). odds ratios (ors) were reported along with the 95% confidence intervals (cis) and p values. we extended the classic seir model to account for population movement, unascertained cases, and quarantine by hospitalization ( fig. 2 and supplementary methods). we chose to analyze data from january 1, 2020, when the huanan seafood market was closed. we assumed a constant population size of 10 million of wuhan with equal daily inbound and outbound travelers (500,000 for january 1-10, 800,000 for january 11-22 due to chunyun, and 0 afterwards due to cordon sanitaire since january 23). 9 we divided the population into six compartments including susceptible individuals, latent cases, ascertained cases, unascertained cases, hospitalized cases, and removed individuals. here, unascertained cases included asymptomatic cases and those with mild symptoms who could recover without seeking medical care and thus were not reported to authorities. we assumed only those seeking medical care would be reported and quarantined by hospitalization. dynamics of these six compartments across time were described by ordinary differential equations (supplementary methods), along with the key parameters. the daily case data were assumed to the poisson regression under the seir model. considering the impacts of major interventions, we assumed that the transmission rate and ascertainment rate were the . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . same in the period 1 and 2, while the two parameters were different for the period 3 and 4. the effective reproductive number r t , defined as the expected number of secondary cases infected by a primary case, was computed for each period. initial states of the seir model and parameter settings for the main and methods).we used the fitted model to predict the trend from february 11 to 18 and compared that with the observed data to assess the accuracy of the model. the ethics approval was considered exempt because all date collection and analyses belong to a part of continuing public health outbreak investigation determined by the national health commission of china. our analyses included a total of 25,961 confirmed cases, among whom 49.7% were men and 50.3% were women ( table 1 ). the epidemic curve according to the onset date and key interventions is shown in the fig. 1 . most cases occurred between january 20 and february 6, with a spike on february 1. there was a substantial delay . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint between the onset date and confirmation date in early periods, with the lag decreasing over periods (median 22, 14, 10 and 5 days for the four periods, respectively; fig. s1 ). the outbreak started from the urban districts and gradually spread to the suburban and rural areas across the four periods, leading to strong geographic differences with the highest attack rates in the urban districts (fig. s2) . the average daily attack rate per 10 6 people dramatically increased from 2.2 (95% ci, 2.0 to 2.4) before january 11, to 44.9 (43.6 to 46.2) between january 11 and 22, and to 150.9 (148.3 to 153.5) between january 23 and february 1, while dropped to 54.1 (52.9 to 55.3) after february 2 (fig. 3a) . similar patterns were observed for men and women, with slightly higher attack rate in women (fig. 3a) . a total of 1316 healthcare workers were infected, representing 5.1% of the total cases ( table 1) the median age of the patients was 57 years, with the majority (n=19，693, 75.9%) aged 40 to 79 years ( table 1) . the attack rate peaked in the third period then declined in the fourth period for those older than 20 years, while it continued to increase throughout the periods for children (age <20 years) (fig. 3b) , particularly for the infants below 1 year old (fig. 3c) . the clinical severities of the confirmed cases (n=25,727) were classified into . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint fig. 3d ). the proportion of severe/critical cases decreased gradually over time, accounting for 53.9%, 34.8%, 22.0% and 14.7% of the classifiable cases in the four periods, respectively, while the proportion of mild cases increased dramatically (fig. 3d) . compared to cases aged 20 to 40, children younger than 10 were less likely to be severe/critical (or, 0.33; 95% ci, 0.14 to 0.82), while (table s1 ). in addition, females were at lower risk of severity than males (or, 0.89; 0.84 to 0.95), while there was weak evidence that healthcare workers were at higher risk of severity (or, 1.12; 0.96 to 1.31). our seir model fit the observed data well, except for the outlier on february 1 (fig. 4a ). the slight overprediction for the last five days (february 14-18) was likely due to the delay in laboratory confirmation of recent cases. the transmission rate decreased from 1.75 (95% cri, 1.71 to 1.80) before january 23 to 0.58 (0.56 to 0.60) and 0.15 (0.13 to 0.17) after january 23 and february 2, respectively (table s2) , which could be translated into r t of 3.88 (3.77 to 3.99), 3.86 (3.74 to 3.97), 1.26 (1.21 to 1.31), and 0.32 (0.28 to 0.37) for the four periods, respectively (fig. 4b) . we estimated the number of cumulative ascertained cases till february 18 to be 49,943 (95% cri, 43,577 to 56,635) if the trend of the third period was assumed (fig. 4c) , or . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint 474,897 (410,660 to 537,448) if the trend of the second period was assumed (fig. 4d) , both were much higher than the current ascertained case number of 25,961. these numbers were translated to a total of 48.0% (40.7 to 54.3%) and 94.5% (93.7-95.2%) prevented cases by the interventions. strikingly, we estimated that the overall ascertainment rate was 0.21 (95% cri, 0.18-0.24), and similar across the periods ( (fig. 4e) . if the trend remained unchanged, we predicted the number of ascertained cases to become zero by april 22 (95% cri, april 5 to may 19), 2020, and the total number of both ascertained and unascertained cases would become zero around may 4 (april 17 to may 30), 2020. we performed a series of sensitivity analyses to test the robustness of our results by considering the outlier data point on february 1, and varying incubation and infectious periods, transmission ratio between unascertained and ascertained cases, and initial values of the model (fig. s4-s12, tables s2-s4 ). our major findings of remarkable decrease in r t in response to interventions and the existence of a large proportion of unascertained cases remained in all sensitivity analyses. in particular, we noticed that the estimated ascertainment rates increased with decreasing initial number of unascertained cases (fig. s9-s11, table s2 ). if we assumed an extreme . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint scenario with no unascertained cases initially (fig. s11) , the overall ascertainment rate would be 0.41 (0.36-0.47), which would be the upper bound of the ascertainment rate. we also tested a simplified model assuming no unascertained cases anytime, but this simplified model performed significantly worse than the full model in fitting the data (fig. s12) . here we provide a comprehensive assessment of the epidemiological characteristics of the laboratory-confirmed covid-19 cases in wuhan, the epicenter of outbreak. the virus affected equally to men and women and most cases were middle-aged and elderly adults. the attack rate continued to increase before february 2 while dramatically declined thereafter for all groups, except for children (age <20 years). consistent with early analyses, younger people were less likely to be affected, 8, 11 ,21 but we found that the attack rate continued to increase over time for those aged under 20 years. in particularly, infants under the age of 1 year had the highest attack rate than the other age groups of children, probably because they cannot wear masks and have low immunity. 22 children had a lower chance of getting infected probably because they had less frequent social activities during the school winter break starting in early or middle january, but the attack rate increased when all people were required to stay at home and risk of familial clustering of infection started to increase. 11 our results also indicated that healthcare workers and elderly people had higher attack rates and the . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint severity increased significantly with age. therefore, special attention and efforts should be applied to protect and reduce transmission and progression in vulnerable populations including healthcare workers, elderly people and children. despite that the outbreak started in early december, no strong interventions were taken before january 20 when the human-to-human transmission was officially announced. the outbreak quickly spread from the urban areas to the suburban and rural areas. the attack rate in the healthcare workers was substantially higher between january 11 and february 1, indicating a high risk of nosocomial infections. this was probably due to lower awareness of protection before january 20, and later severe shortage of medical resources including designated wards and personal protective equipment in hospitals confronting overwhelmed patients. we compared our model prediction with published modeling studies using independent datasets. based on early international exported cases, wu et al. 9 estimated that 75,815 (95% cri, 37,304 to 130,330) individuals had been infected in greater wuhan as of january 25, 2020. for comparison, we estimated the number to be 36,798 (95% cri, 30,898 to 43,390) by the same day, including both ascertained and unascertained cases. the discrepancy was mainly due to different assumptions of population size, which was 19 million for the greater wuhan area including surrounding cities by wu et al. 9 versus 10 million for the wuhan city in our analysis. after accounting for the population size, the estimates of prevalence were indeed highly consistent (0.40% versus 0.37%). another study, 10 which was also based on international exported cases but used a different model with an assumed population . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint size of 11 million, estimated the number of infected cases in wuhan to be 29,500 (14, 300 to 85,700) on january 23, 2020, closely matching our prediction of 26, 144 cases (21,936 to 30,748) on the same day. these studies supported the validity of key assumptions made in our main analysis, including the initial ascertainment rate of 0.5. for example, if we assumed no unascertained cases in the initial state (fig. s10) , our estimated cumulative number of cases would be 13,441 (10,853 to 16,356) on january 23 and 18,826 (15, 115 to 23,039) on january 25, much lower than those estimated by these two studies. our finding of substantial unascertained cases has important implications for the evaluation and control of the covid-19 epidemic. 23 these unascertained cases were likely asymptomatic or with mild symptoms, who could mostly recover without seeking medical care. there is accumulating evidence on the existence of many asymptomatic or presymptomatic cases. for example, asymptomatic cases were estimated to account for 34.6% of the virus positive cases onboard the princess cruise ship. 14 several recent reports also highlighted the difficulty to detect covid-19 cases: about two thirds of the cases exported from mainland china remained undetected worldwide, 24 and the detection capacity varied from 11% in low surveillance countries to 40% in high surveillance countries. 25, 26 consistent with these studies, our analyses and extensive simulations also indicated an ascertainment rate of 14%-41% in wuhan (table s2) . increasing evidence also suggested that the asymptomatic and presymptomatic cases can be infectious to the susceptible population, 17-19 imposing a substantial challenge to the epidemic control. 27 there would be about two weeks . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint delay in the predicted ending date of the epidemic when taking the unascertained cases into account (table s4) . therefore, understanding the proportion of unascertained cases and the rate of asymptomatic spread will be critical for pandemic prevention of covid-19, including prioritization the surveillance and control measures. 23, 28 we demonstrated that the series of interventions has been highly effective in controlling the epidemic in wuhan. our estimate of r t =3.88 for the first period reflected the basic reproductive number r 0 as few interventions had been implemented by then. some previous studies have reported varied r 0 (range 1.40 to 6.49 with a mean of 3.28) due to different data sources, time periods and statistical methods. 29 even using the same dataset of the first 425 patients in wuhan, an early study reported a r 0 of 2.20 based on the growth rate of the epidemic curve and the serial interval, 8 while a recent analysis based on a transmission network model reported a r 0 of 3.58, similar to our estimate. the transmissibility was higher than that for the sars-cov in 2003 (from 2.2 to 3.6), 30 and was consistent with the rapid spreading of covid-19. nevertheless, by taking drastic social distancing measures and policies of controlling the source of infection, with the tremendous joint efforts from the government, healthcare workers, and the people (fig. 1) , r t was substantially reduced to 0.32 in wuhan after february 2, which was encouraging for the global efforts fighting against the covid-19 outbreak using traditional non-pharmaceutical measures. 31 some limitations of this study need to be noted. first, while our model prediction . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint aligned well with the observed data, we set the values of several parameters based on earlier epidemiological studies without accounting for the uncertainty, 8, 9 which might reduce the accuracy of our results. second, we need field investigations and serologic studies to confirm our estimate of the ascertainment rate, and the generalizability to other places is unknown. this may depend on the detection capacity in different locations. 26 third, due to the delay in laboratory tests, we might have missed some cases and therefore underestimated the ascertainment rate, especially for the last period. finally, the impact of the interventions should be considered as a whole and we could not evaluate individual strategies by the epidemic curve. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint we are grateful for all staff at the national, provincial and municipal center for disease control and prevention for providing the data and all medical staff members and field workers who are working on the front line of caring for the patients and collecting the data. we also thank the government at all levels and all citizens in wuhan for their sacrifice and enormous efforts in battling with the covid-19. we declare no competing interests. cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint activities that could appear to have influenced the submitted work. the sponsors have no role in the study design; the collection, analysis, or interpretation of data; the writing of the report; or in the decision to submit the article for publication. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint . it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint two key parameters in the model are r (ascertainment rate) and b (transmission rate). the details of the model assumptions and dynamics of these six compartments across time are described in the supplementary methods. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint world health organization. novel coronavirus (2019-ncov) situation report-41 clinical characteristics of coronavirus disease 2019 in china clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan february 8 (epub ahead of print) epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with 2019 novel coronavirus in wuhan, china epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan, china february 8 (epub ahead of print) clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia doi: medrxiv preprint ahead of print) nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study early dynamics of transmission and control of 2019-ncov: a mathematical modelling study. medrxiv covid-19) 2020 modified seir and ai prediction of the epidemics trend of covid-19 in china under public health interventions tracking and predicting covid-19 epidemic in china mainland estimating the asymptomatic ratio of 2019 novel coronavirus onboard the princess cruises ship clinical characteristics of 24 asymptomatic infections with covid-19 screened among close contacts in nanjing relative sensitivity of international imperial-college---covid-19---relative-sensitivity-international-cases using predicted imports of 2019-ncov cases to determine locations that may not be identifying all imported cases quantifying bias of covid-19 prevalence and severity estimates in wuhan, china that depend on reported cases in international travelers a novel coronavirus emerging in china -key questions for impact assessment escaping pandora's box -another novel coronavirus the reproductive number of covid-19 is higher compared to sars coronavirus february 13 (epub ahead of print) transmission dynamics and control of severe acute respiratory syndrome . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity.is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity.is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint figure 4 . four-period susceptible-exposed-infectious-recovered modeling of the parameters were fitted based on data from january 1 to february 10. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity.is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.03.20030593 doi: medrxiv preprint key: cord-275853-fym8qze2 authors: yang, juan; chen, xinhua; deng, xiaowei; chen, zhiyuan; gong, hui; yan, han; wu, qianhui; shi, huilin; lai, shengjie; ajelli, marco; viboud, cecile; yu, hongjie title: disease burden and clinical severity of the first pandemic wave of covid-19 in wuhan, china date: 2020-09-01 journal: medrxiv doi: 10.1101/2020.08.27.20183228 sha: doc_id: 275853 cord_uid: fym8qze2 the pandemic of novel coronavirus disease 2019 (covid-19) began in wuhan, china, where a first wave of intense community transmission was cut short by interventions. using multiple data source, we estimated the disease burden and clinical severity of covid-19 by age in wuhan from december 1, 2019 to march 31, 2020. we adjusted estimates for sensitivity of laboratory assays and accounted for prospective community screenings and healthcare seeking behaviors. rates of symptomatic cases, medical consultations, hospitalizations and deaths were estimated at 796 (95%ci: 703–977), 489 (472–509), 370 (358–384), and 36.2 (35.0–37.3) per 100,000 persons, respectively. the covid-19 outbreak in wuhan had higher burden than the 2009 influenza pandemic or seasonal influenza, and that clinical severity was similar to that of the 1918 influenza pandemic. our comparison puts the covid-19 pandemic into context and could be helpful to guide intervention strategies and preparedness for the potential resurgence of covid-19. as of 26 july 2020, 188 countries have been affected by the novel coronavirus disease 42 2019 , with 15,745,102 covid-19 cases and 644,661 deaths reported 43 worldwide 1 . covid-19 has a broad spectrum of severity. the bottom of the severity 44 pyramid includes serological-confirmed infections, of which only a fraction will 45 develop symptoms. a fraction of symptomatic cases may seek medical care, when 46 they can be identified via surveillance systems, require hospitalization and die. 47 hospitalization is an important metric as it determines the strain exerted by an 48 epidemic on the health care system. further, deaths are highly relevant to planning 49 pandemic response, as mortality is an outcome that health authorities typically aim to 50 minimize. (fig.1a ) 51 52 estimates of disease burden and clinical severity of covid-19 are critical to identify 53 appropriate intervention strategies, plan for healthcare needs, and ensure the 54 sustainability of the health system throughout the duration of the pandemic. however, 55 quantifying these estimates based on surveillance data is challenging due to changes 56 in health seeking behaviors during the pandemic, as well as underdiagnoses. for 57 instance, the detection of a novel pathogen may give a high rate of false negatives. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https: //doi.org/10.1101 //doi.org/10. /2020 typically considered as the worst-case pandemic scenario for pandemic planning. in 62 contrast, the 2009 influenza pandemic is considered mild but provides a benchmark 63 for a pandemic in modern times, as the health systems, supportive care, and wuhan is a particularly well-suited location to assess the health burden of firstly, wuhan experienced intense community transmission of severe acute 73 respiratory syndrome coronavirus 2 (sars-cov-2); secondly, the first wave has 74 ended, with only seven sporadic cases reported between march 24 and may 18 3 . 75 therefore, the first epidemic wave in wuhan (for the period december 1, 2019-march 76 31, 2020) is an opportunity to comprehensively quantify the disease burden and 77 clinical severity of covid-19. here we used multiple data sources to estimate age-78 specific rates of symptomatic sars-cov-2 infections, medically attended cases, 79 hospitalizations, and deaths, accounting for health seeking behaviors and 80 underdiagnoses. we also estimated rates of medically attended influenza-like-illness 81 (ili) associated with sars-cov-2 infections; hospitalizations with severe acute 82 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https: //doi.org/10.1101 //doi.org/10. /2020 6 respiratory infection (sari), and pneumonia hospitalizations associated with sars-83 cov-2 infections by dividing the number of ili consultations, sari hospitalizations 84 and pneumonia hospitalizations by the number of symptomatic sars-cov-2 85 infections. moreover, we estimated the clinical severity of covid-19 including the 86 symptomatic case-fatality risk (scfr), medically attended case-fatality risk (mcfr), 87 hospitalization-fatality risk (hfr), symptomatic case-hospitalization risk (schr), and 88 medically attended case-hospitalization risk (mchr). the rates of symptomatic cases, 89 medically attended cases, hospitalizations, and deaths with sars-cov-2 were 90 calculated by dividing the number of cases at each level of severity by population 91 size. clinical severity was obtained by dividing the numbers of cases in the 92 corresponding severity pyramid. (fig.1a is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint 7 symptoms, and radiographic evidence of pneumonia. severe cases refer to cases with 104 any breathing problems, finger oxygen saturation, and low pao2/fio2 (pao2 denotes 105 partial pressure of oxygen in arterial blood; fio2 denotes fraction of inspired oxygen), 106 etc. critical cases refer to cases having any respiratory failure, shock, and any other 107 organ failure that requires icu admission. clinically-diagnosed cases included 108 suspected cases with pneumonia as indicated by chest radiography, but without 109 virological confirmation of infection 6 . (supplementary information file 1) these 110 clinically-diagnosed cases were included in our study, recognizing the value of a 111 clinical definition at the peak of a pandemic and in the context of limited laboratory 112 testing capacity. a total of 50,333 covid-19 cases were reported in the four-month 113 epidemic in wuhan. of them, 32,968 (65.5 %) were laboratory-confirmed cases. as 114 of july 20, 3,869 cases have died, and all others recovered. these cases were recorded 115 from passive surveillance which was launched at the start of the outbreak in late 116 december 2019 in wuhan 9 , and from active door-to-door and individual-to-individual 117 screenings for fever (supplementary information file 2) 10, 11 . 118 119 estimated disease burden of covid-19 120 rt-pcr sensitivity for sars-cov-2 detection varies based on the interval between 121 symptom onset and laboratory testing, which was highest (97.9%) at an interval of <7 122 days 12 . a population-based telephone and online survey conducted in wuhan found 123 that 35.4% (95%ci 28.4%-43.9%) of patients with acute respiratory infections (i.e., 124 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint 8 fever with any symptoms of cough, and/or sore throat) sought medical care during the 125 epidemic of covid-19 13 . all cases from passive surveillance were considered as 126 medically attended cases. in the baseline analysis, we assumed that a proportion of 127 mild cases, and all moderate-to-critical cases (had radiographic evidence of 128 pneumonia) captured by active screening in the community would eventually seek 129 medical care given that the health system was not overwhelmed. it was assumed that 130 the cases from passive surveillance had the same health seeking behavior as those 131 captured by active screening in the community. laboratory-confirmed cases 132 (moderate-to-critical) and clinically-diagnosed cases had radiographic evidence of 133 pneumonia, and thus were considered as requiring hospitalization. (fig.1b per 100,000 individuals respectively. a consistent increasing trend with age was 143 observed across all metrics, with the highest rates occurring in adults aged 60 years 144 and over (fig.2a, fig.3a, fig.4a and supplementary information file 3) . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. the hospitalization rates of covid-19 in wuhan were 3.1-fold higher than that of the 155 2009 influenza pandemic, and 1.8-2.6 times that of seasonal influenza 16, 17, 18, 19 . the overall scfr of covid-19 was 4.54% (95%ci 3.70-5.14%), which is 165 comparable, if not higher, than that of the 1918 influenza pandemicfrom the 166 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 analysis of data from eight us localities, the scfr was estimated at 1.61% and 1.98% 167 for the first and second wave, respectively 23, 24 . such a figure is substantially higher 168 than that of the 2009 influenza pandemic (<0.1% in the us) 25 . the scfr of covid-169 19 was higher for adults aged ≥60 years than for the other age groups (9.09% vs. affected during seasonal influenza epidemics 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 . to assess the robustness of our findings, we conducted four sensitivity analyses: in 182 scenario i) we assumed that moderate cases had the same health seeking behavior as 183 mild cases, i.e., only a proportion of moderate cases sought medical assistance; in 184 scenario ii) we excluded clinically-diagnosed cases; in scenario iii) we used the upper 185 limit of 95%ci of the probability of seeking medical care; and in scenario iv) we used 186 the lower limit of 95%ci of the probability of seeking medical care. compared to the 187 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint baseline analysis, the mean rates of symptomatic cases for covid-19 increased from 188 796 to 935 per 100,000 persons in scenario i) and 960 per 100,000 persons in scenario 189 iv), while rates decreased to 634 per 100,000 persons in scenario ii) and 719 per 190 100,000 persons in scenario iii). the scfr decreased from 4.54% to 3.87% in 191 scenario i) and 3.77% in scenario iv), while it increased to 5.38% in scenario ii) and is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 this study uses multiple sources of data to estimate different levels of the covid-19 208 severity pyramid. we find that the mean rates of symptomatic cases, medical 209 consultations, hospitalizations and deaths were respectively 796, 489, 370, and 36.2 210 per 100,000 persons in wuhan from december 2019 to march 2020. all burden 211 metrics increased with age, with adults ≥60 years of age most affected. similarly, the 212 highest scfr and hfr were found in older adults. 213 214 our study is strengthened by adjustment for several potential biases. first, rates of 215 medical consultations were adjusted by the sensitivity of rt-pcr assays 12 . 216 sensitivity was only 30-40% before january 23 due to delayed detection, which could 217 lead to important underdiagnoses and has not been considered in previous studies. 218 second, we accounted for the health seeking behaviors among the wuhan population 219 during the epidemic 13 . the probability of seeking medical treatment conditionally on 220 symptoms of acute respiratory diseases is a critical parameter to estimate the true 221 number of covid-19 cases in community. accordingly, our estimates of disease 222 burden may be the most accurate for wuhan so far. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint 13 affected province of canada. variation in testing strategies likely contribute to the 229 difference in rate of symptomatic cases, in addition to true difference in epidemic 230 dynamics. unlike in wuhan, only individuals with signs or symptoms consistent with 231 covid-19, and asymptomatic individuals with suspected exposure were 232 preferentially tested in the us. moreover, in contrast to our study, the us and 233 canadian estimates were not adjusted for the sensitivity of rt-pcr assays and health 234 seeking behavior, and thus may be underestimated. 235 our estimated hospitalization rate for a four-month covid-19 outbreak was much 237 higher than that for a three-to-six-month covid-19 outbreak in the us and qué bec 238 (370 vs. 47-114 per 100,000 persons) 27, 28, 29, 30 . we estimated that 76% of medically-239 attended cases were hospitalized in wuhan, while only 18% were hospitalized in the 240 us 30 . the difference between these estimates could be explained by the potential 241 different clinical thresholds for hospitalization. we assumed that moderately ill cases 242 with radiographic evidence of pneumonia and more severe cases would be 243 is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. our estimates of scfr (4.54% vs. 1.2-1.4%) and mcfr (7.40% vs 5.91%) for wuhan 263 are higher than in prior modeling studies 35, 36 . this is likely explained by the addition 264 of revised statistics on cases and deaths, and a more complete dataset with no right-265 censored outcomes in our study. large variations in mcfr were observed between 266 countries, which have not been systematically analyzed. qualitatively, these 267 variations could be explained by differences in the sensitivity of surveillance systems 268 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 to detect cases at different levels of the severity pyramid, differences in clinical care 269 of severe and critical patients, and in age structure and underlying conditions of the 270 population. 271 our hfr estimate (9.77%) is higher than the estimate obtained by wang et al. in a 273 highly censored sample in wuhan in the very early stages of the epidemic (4.3%) 37 . 274 however, it is much lower than the 28% estimate obtained in two covid-19-275 designated hospitals for severe covid-19 cases in wuhan, probably due to the 276 particularly high proportion of severe and critical patients hospitalized in these 277 facilities (64% vs. 28%) 38 . our hfr estimate was lower than the 18.1% estimate in 278 france 39 , probably due to aforementioned loose threshold for hospital admissions in 279 china and preference of seeking care in hospitals rather than outpatient settings. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint burden and clinical severity of seasonal and pandemic influenza using wuhan age 290 profile as a reference (supplementary information file 5 and file 8). comparison of 291 severity estimates between pandemics was difficult to standardize, particularly for 292 1918 influenza pandemic 23 . the 1918 scfr is based on data from a single us study 293 from more than a 100 years ago, at a time when awareness of viral diseases was 294 inexistent, case ascertainment and disease surveillance were limited, and definition of 295 clinical outcomes varied. therefore, our comparison was not intended to quantify the 296 absolute value of differences, but to put the covid-19 pandemic into perspective. 297 to put our results in perspective, it is important to stress that our covid-19 estimates 299 refer to the first epidemic wave in wuhan -a four-month long period. the epidemic 300 was controlled by intense interventions 4 . if the epidemic rebounds, as one would 301 expect if the infection was reintroduced in a population with low immunity, the 302 disease burden would rise. moreover, given that the epidemic lasted only four months, 303 the stress on the healthcare system was tremendous, as severe cases and 304 hospitalizations were concentrated over a relatively short period of time. furthermore, 305 neither seasonal nor pandemic influenza outbreaks were controlled, as vaccination 306 was either low or delayed until after the main wave had passed, and no social 307 distancing was put in place. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint using a simple data-driven approach, we quantitatively assessed the impact of 310 covid-19 on the healthcare sector using the local number of ili consultations and 311 sari/pneumonia hospitalizations in the absence of covid-19 as a reference. the 312 number of covid-19 hospitalizations was several folds higher than that of baseline 313 sari hospitalizations and 25-132 folds higher than that of pneumonia 314 hospitalizations among adults ≥20 years of age. this indicates that during this time 315 period, the wuhan healthcare system considerably exceeded surge capacity, 316 highlighting the importance and necessity of preparedness for sufficient healthcare 317 resources. moreover, there is a winter peak of consultations and hospitalizations 318 related to respiratory diseases such as seasonal influenza and respiratory syncytial 319 virus 14, 40, 41 , which may have contributed to overwhelm the healthcare sector during 320 the first wave of the covid-19 epidemic. 321 our study has some limitations. firstly, health seeking behavior maybe not constant 323 throughout the epidemic. in this survey, study participants in wuhan were asked to 324 review their history of ari between december 2019 and march 2020, and whether 325 they sought medical assistance for these symptoms 13 . however, since we did not 326 obtain the onset date of these symptoms, and hence we could not stratify health-327 seeking behavior by covid-19 epidemic phase. instead, we calculated the overall 328 proportion of aris cases who sought medical care during the epidemic. if the 329 distribution of onset dates of aris cases in our sample was skewed towards the early 330 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. triage, and treatment, and health seeking behavior over time and across locations. a 360 modelling study has revealed that containment has proved to be successful to control 361 the local covid-19 epidemic in wuhan. without containment efforts, the number of 362 covid-19 cases would have been an estimated 67-fold higher than that has been thus 363 far 46 . therefore, our estimates in wuhan could represent the disease burden and 364 clinical severity in a region with 1) wide-spread community transmission of sars-365 cov-2; 2) strict non-pharmaceutical interventions, referred as to "wartime measures" 366 in the study by leung et al. 47 ; 3) extensive detection of all outpatients with fever 10 ; 4) 367 is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https: //doi.org/10.1101 //doi.org/10. /2020 exceeded that in wuhan by far, the pandemic in other countries is still ongoing and 373 any estimate is bound to be revised. our estimates represent the full impact of a short 374 but intense first wave, and could be considered as benchmarks to plan intervention 375 strategies for a potential second wave of the pandemic. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint 26 methods 454 case definitions for laboratory-confirmed-cases were issued by the national health 456 commission of china, and included mild, moderate, severe, and critical cases. cases 457 were confirmed by real-time reverse transcription polymerase chain reaction (rt-458 pcr) or by viral sequencing indicating genomes highly homologous to sars-cov-459 2 5, 6, 7, 8 . clinically-diagnosed cases included suspected cases with pneumonia as 460 indicated by chest radiography, but without virological confirmation of infection 6 . 461 the "clinical" definition was only used for one week in hubei province as laboratory 462 testing capacity was insufficient, and led to a large number of clinical cases to be 463 isolated and treated without delay. these clinically-diagnosed cases were included in 464 our study, recognizing the value of a clinical definition at the peak of a pandemic and 465 in the context of limited laboratory testing capacity. the laboratory-confirmed cases 466 include mild-to-critical cases, while the clinically-diagnosed cases include moderate-467 to-critical cases. definitions are presented in detail in supplementary information file 468 our study aimed to account for underdiagnosis associated with the sensitivity of 473 laboratory assays, which is strongly dependent on the time lag between symptom 474 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020 . . https://doi.org/10.1101 /2020 27 onset and diagnostic test 12 . the distribution of lags varied at different phases of the 475 epidemic in wuhan due to laboratory testing capacity 4 . accordingly, the daily number 476 of covid-19 cases by symptom onset date was preferred to the aggregated 477 cumulative data. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020 . . https://doi.org/10.1101 /2020 all of these datasets were registered through a surveillance system, which was 496 launched to record information on covid-19 cases in china at the start of the 497 outbreak in late december 2019 in wuhan 9 . these data were collected from passive 498 surveillance, and active door-to-door and individual-to-individual screenings for 499 fever. the active screening was implemented twice in wuhan on a daily basis from 500 january 24-february 10, and february 17-19 10, 11 . a total of 16,781 laboratory-501 confirmed cases were identified through active screening (d7, details shown in 502 supplementary information file 2) 10, 11 . 503 504 a study retrospectively analyzed the rt-pcr assays of 301 patients with 1,113 506 specimens in wuhan, and found that rt-pcr sensitivity varied at different phases of 507 the epidemic due to the difference of interval between symptom onset and laboratory 508 testing (pse) (supplementary information file 9). the sensitivity of rt-pcr assays 509 was highest (97.9%) at an interval of <7 days 12 . 510 511 a population-based telephone and online survey was conducted to understand the 513 health seeking behaviors of patients suffering from acute respiratory infections (i.e., 514 fever with any symptoms of cough, and/or sore throat) during the epidemic of 515 covid-19 in wuhan. of patients with acute respiratory infections, 35.4% (95%ci 516 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020 . . https://doi.org/10.1101 /2020 28.4%-43.9%) sought medical care, by adjusting for the age structure of wuhan 517 population. children had a higher probability of medical attendance than adults 518 (pmed.care) 13 . 519 520 a total of 10.7 million persons lived in wuhan during the epidemic 52 . the age profile 522 of the wuhan population was obtained from the china statistic yearbook 53 . to 523 compare the burden of covid-19 to baseline activity of acute respiratory infections, 524 we obtained refence historical data on ili surveillance in hubei province and sari 525 surveillance in jingzhou city, hubei province 14, 17, 21 . additionally, we collected the 526 annual number of consultations in pediatric and internal medicine departments in 527 hubei, and the national number of pneumonia hospitalization rates from the chinese 528 health statistics yearbook 54 . all these data were collected from publicly available 529 sources and did not contain any personal identifiable information. summary of data 530 were presented in supplementary information file 10. 531 532 statistical analysis 533 is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint in the baseline analysis, we considered covid-19 cases in wuhan as those with 539 laboratory-confirmation or with a clinical diagnosis (for the brief period where the 540 clinical definition was in place) and tabulated data by symptom onset date. the 541 interval between symptom onset and diagnosis was obtained from data d1 4 . then, we 542 randomly simulated 10,000 draws from a gamma distribution representing these time 543 intervals to estimate onset dates for laboratory-confirmed cases reported between 544 march 9-april 3 (data d3), and added laboratory-confirmed cases (data d5). this 545 allowed us to impute onset dates for cases that did not have this information. 546 547 all cases from passive surveillance were considered as medical attendance (data 549 d1+d3+d5, and d2). in the baseline analysis, we assumed that a proportion of mild 550 cases, and all moderate-to-critical cases captured by active screenings in the 551 community (data d7) would eventually seek medical care given that the health system 552 was not overwhelmed (assumption 1). the health seeking behavior of mild cases was 553 assumed to be the same as aforementioned patients with acute respiratory infections 554 during the covid-19 epidemic (pmed.care) 13 . hence, to estimate medically attended 555 cases, we only excluded a proportion of (1-pmed.care) mild cases identified by 556 community screening from the total reported covid-19 cases. moreover, the number 557 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint of laboratory-confirmed cases from official reports (data d1+d3+d5, and d7) was 558 divided by the sensitivity of rt-pcr (pse) to account for underdiagnoses. 559 560 in the baseline analysis, we assumed the cases from surveillance system (data 562 d1+d3+d5, and d2) had the same health seeking behavior as those captured by 563 active screenings in the community (data d7) given that the health system was not 564 overwhelmed (assumption 1). accordingly, the number of mild symptomatic cases 565 was estimated by dividing reported mild covid-19 cases by the probability of 566 seeking medical care, conditionally on self-reported acute respiratory infection 13 . 567 adjustment of sensitivity of rt-pcr was considered as well. 568 569 moderate-to-critical covid-19 cases had radiographic evidence of pneumonia, while 571 mild cases were defined as those without radiographic evidence of pneumonia 5, 6, 7, 8 . 572 chest x-ray confirmed pneumonia is a threshold for hospital admissions in china. 573 accordingly, in our study, estimates for sars-cov-2 related hospitalizations 574 excluded patients defined as mild cases in the baseline analysis. (assumption 2) 575 576 in above analyses, to account for the uncertainty of two parameters (rt-pcr 577 sensitivity and probability of seeking medical care), we conducted a monte carlo 578 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 simulation by drawing 10,000 samples on the basis of binomial distributions. we 579 generated 10,000 estimates for the number of covid-19 cases, based on which we 580 calculated the median, and 95% cis (the 2.5th and 97.5th percentiles) for the 581 outcomes of interest in this study. 582 583 additionally, below sensitivity analyses were conducted: in scenario i) for above 584 assumptions 1) and 2), we assumed moderate cases had the same health seeking 585 behavior as mild cases, i.e., only a proportion of moderate cases sought medical 586 assistance (pmed.care); and in scenario ii) we excluded clinically-diagnosed cases. chi-587 square tests were used to compare the estimates of baseline and sensitivity analyses. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 moreover, for comparison with historical outbreaks, we conducted a narrative review 599 on estimates of disease burden and clinical severity for the 1918 and 2009 influenza 600 pandemics, as well as seasonal influenza in china and usa (summary of studies 601 shown in supplementary information file 4-5) . the age profile of covid-19 cases 602 was obtained from data d1 4 , in which covid-19 cases were broken down into 20-603 year age categories. we could not generate disease burden and clinical severity 604 estimates for influenza using the same age stratification because numerators and 605 denominators were not available from the literatures. 606 607 the funder of the study had no role in study design, data collection, data analysis, data 609 interpretation, or writing of the report. the corresponding author had full access to all 610 the data in the study and had final responsibility for the decision to submit for 611 publication. 612 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint 695 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 coronavirus (covid-19) information and updates health commission of hubei province. daily report on epidemic situation of covid-19 619 in hubei province association of public health interventions with the epidemiology of the 623 covid-19 outbreak in wuhan, china evolving epidemiology and transmission dynamics of novel coronavirus 625 disease 2019 outside hubei province in china: a descriptive and modeling study national health commission of china. the diagnosis and treatment scheme of novel 628 coronavirus diseases 2019 (trial version 5th) national health commission of china. the diagnosis and treatment scheme of novel 632 coronavirus diseases 2019 (trial version 6th) national health 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and characteristics of patients hospitalized with 692 coronavirus disease 2019 -covid-net, 14 states 321 individuals residing in california 696 and washington, united states: a prospective cohort study analysis and suggestion on the factors leading to the difficulty in the 701 construction of hierarchical diagnosis system response team. preliminary estimate of excess mortality during the covid-19 estimation of excess deaths associated with the covid-19 pandemic in the united states estimating clinical severity of covid-19 from the transmission dynamics 710 in wuhan, china an investigation of transmission control measures during the first 50 days 712 of the covid-19 epidemic in china clinical characteristics of 138 hospitalized patients with coronavirus-infected pneumonia in wuhan, china clinical course and risk factors for mortality of adult inpatients with 716 covid-19 in wuhan, china: a retrospective cohort study estimating the burden of sars-cov-2 in france genetic variability of 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management: the key to tackling the covid-19 745 pandemic the novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases 748 (covid-19) -china health commission of hubei province. the 20th press conference on prevention and 750 control of pneumonia caused by novel coronavirus china health commission. chinese health statistical yearbook. china peking union 756 the r project for statistical computing . cc-by-nc-nd 4.0 international license it is made available under a perpetuity.is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprintthe copyright holder for this this version posted september 1, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprintthe copyright holder for this this version posted september 1, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprintthe copyright holder for this this version posted september 1, 2020. supplementary information is available for this paper. 785correspondence and requests for materials should be addressed to j.y., and h.y. 786. cc-by-nc-nd 4.0 international license it is made available under a perpetuity.is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprintthe copyright holder for this this version posted september 1, 2020 . . https://doi.org/10.1101 /2020 . cc-by-nc-nd 4.0 international license it is made available under a perpetuity.is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprintthe copyright holder for this this version posted september 1, 2020. . https://doi.org/10.1101/2020.08.27.20183228 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a perpetuity.is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprintthe copyright holder for this this version posted september 1, 2020. . https://doi.org/10. 1101 /2020 key: cord-285772-4xt4anq5 authors: huang, rui; zhu, li; xue, leyang; liu, longgen; yan, xuebing; wang, jian; zhang, biao; xu, tianmin; ji, fang; zhao, yun; cheng, juan; wang, yinling; shao, huaping; hong, shuqin; cao, qi; li, chunyang; zhao, xiang-an; zou, lei; sang, dawen; zhao, haiyan; guan, xinying; chen, xiaobing; shan, chun; xia, juan; chen, yuxin; yan, xiaomin; wei, jie; zhu, chuanwu; wu, chao title: clinical findings of patients with coronavirus disease 2019 in jiangsu province, china: a retrospective, multi-center study date: 2020-05-08 journal: plos negl trop dis doi: 10.1371/journal.pntd.0008280 sha: doc_id: 285772 cord_uid: 4xt4anq5 limited data are available for clinical characteristics of patients with coronavirus disease 2019 (covid-19) outside wuhan. this study aimed to describe the clinical characteristics of covid-19 and identify the risk factors for severe illness of covid-19 in jiangsu province, china. clinical data of hospitalized covid-19 patients were retrospectively collected in 8 hospitals from 8 cities of jiangsu province, china. clinical findings of covid-19 patients were described and risk factors for severe illness of covid-19 were analyzed. by feb 10, 2020, 202 hospitalized patients with covid-19 were enrolled. the median age of patients was 44.0 years (interquartile range, 33.0–54.0). 55 (27.2%) patients had comorbidities. at the onset of illness, the common symptoms were fever (156 [77.2%]) and cough (120 [59.4%]). 66 (32.7%) patients had lymphopenia. 193 (95.5%) patients had abnormal radiological findings. 11 (5.4%) patients were admitted to the intensive care unit and none of the patients died. 23 (11.4%) patients had severe illness. severe illness of covid-19 was independently associated with body mass index (bmi) ≥ 28 kg/m(2) (odds ratio [or], 9.219; 95% confidence interval [ci], 2.731 to 31.126; p<0.001) and a known history of type 2 diabetes (or, 4.326; 95% ci, 1.059 to 17.668; p = 0.041). in this case series in jiangsu province, covid-19 patients had less severe symptoms and had better outcomes than the initial covid-19 patients in wuhan. the bmi ≥ 28 kg/m(2) and a known history of type 2 diabetes were independent risk factors of severe illness in patients with covid-19. during december 2019, severe acute respiratory syndrome coronavirus 2 (sars-cov-2) emerged in wuhan, china and spread among humans in china and other countries [1, 2] . global attention was soon focused on this virus due to the rapidly increasing number of confirmed cases [3] . sars-cov-2 infection may result in severe and even fatal respiratory diseases [4] . as of march 13, 2020, 132,536 confirmed cases have been reported in 123 countries with 4,947 deaths [5] . despite the rapid spread of the disease worldwide, the clinical characteristics of coronavirus disease 2019 (covid-19) remain largely unclear. furthermore, there are no directly antiviral drugs for covid19 . several studies have reported the clinical characteristics of covid-19 patients who were hospitalized in wuhan (the outbreak center of the infection) [4, 6, 7] . huang et al. first reported 41 cases of covid-19 and most patients had a history of exposure to huanan seafood market in wuhan [6] . fever and cough were the most common symptoms [6] . 13 (32%) patients were admitted to an intensive care unit (icu) due to the severity of disease and six (15%) patients died [6] . chen et al. conducted a retrospective, single-center study which included 99 confirmed cases of covid-19 in wuhan and found that the virus was more likely to infect older men with comorbidities, and the mortality rate was as high as 11% [4] . another single-center study which analyzed 138 hospitalized patients with confirmed covid-19 in wuhan, found that 26% of patients received icu care and the mortality rate was only 4.3% [7] . although several studies have reported the clinical manifestations and short-term prognosis of covid-19, the source of cases in majority of these studies was from a single center in wuhan. the characteristics of the disease and risk factors of severe illness among inpatients in other parts of china outside wuhan were still lacking. chang et al. reported early clinical features of 13 patients with confirmed covid-19 who were admitted to hospitals in beijing, china [8] . in their study, all the patients recovered indicating milder clinical presentation caused by infections [8] . however, the sample size was very small with only inclusion of 13 patients and the study was limited by the lack of detailed data since patients were transferred to the designated hospitals after diagnosis [8] . xu et al. summarized the clinical characteristics of 62 patients in zhejiang province, which revealed that the symptoms of patients were relatively mild [9] . however, only 62 patients were included in the study and risk factors for severe illness could not be analyzed due to the limitation of sample size [9] . nevertheless, these studies provide important evidence that the clinical characteristics of patients outside wuhan may differ from those initially reported in wuhan. in this multi-center study, we aimed to describe the clinical characteristics of covid-19 and to identify the risk factors of severe illness among inpatients with confirmed covid-19 in jiangsu province, which is located in the east of china. 1) . data of the confirmed covid-19 patients were collected from january 22, 2020 to february 10, 2020. the 8 designated hospitals are responsible for the treatment of covid-19 clinical findings of covid-19 patients in jiangsu patients in jiangsu province, china, assigned by the chinese government. all confirmed patients were diagnosed based on the criterion of world health organization (who) interim guidance [10] . the study was approved by the institutional ethics board of these hospitals, with a waiver of informed consent. all the medical records of confirmed cases were reviewed by more than two health care workers in each medical center. the data of epidemiology, clinical laboratory, radiology, treatment, and prognosis were collected from medical records. the demographic characteristics, comorbidities, exposure history, symptoms, signs, laboratory data, radiological data, treatment data, and outcomes were collected. all data were entered into a computerized database for further analysis. different researchers preformed the cross check of the data to avoid errors. unclear information was further clarified by directly contacting the specific clinicians who were responsible for the patients. the diagnostic criteria of acute respiratory distress syndrome (ards), acute cardiac injury, acute renal injury and acute liver injury were based on the corresponding guidelines [11] [12] [13] [14] . additionally, treatment medication and outcomes of the enrolled cases were also collected based on the medical records. the criteria for discharge was based on the guidelines for the diagnosis and treatment of novel coronavirus infection by the chinese national health commission (trial version 5) [15] . patients were grouped into severe and non-severe covid-19 according to the same guidelines [15] . all patients were confirmed by throat swab sample obtained from the upper respiratory tract and detected by a real-time reverse transcriptase polymerase chain reaction (rt-pcr) in accordance with the protocol by the world health organization [16] .the positive throat swab samples were confirmed by both hospitals and local centers for disease control and prevention. these routine laboratory tests were detected according to the state of disease, including blood routine tests, liver function, renal function, coagulation function, inflammatory biomarkers and myocardial enzymes. radiological assessments including chest x-ray or chest computed tomography (ct) were performed for each patient. continuous variables were described as medians (interquartile range (iqr)), and categorical variables were presented as the counts and percentages. continuous variables were compared by the independent group t tests (normal distribution) and mann-whitney u (non-normal distribution). categorical variables were compared by chi-square or fisher exact test. the risk factors for severe illness were analyzed by binary logistic regression. variables having p values <0.05 in the univariate analysis were further used for a multivariate logistic regression analysis. p<0.05 was regarded to be statistically significant. the data analysis was performed by spss version 22.0 software (spss inc., chicago, il, united states). distribution map was plotted by qgis version 3.10.2 (qgis development team, open source geospatial foundation project). a total of 202 admitted patients who were identified as covid-19 were included in the study. the median age of the patients was 44.0 (iqr 33.0-54.0) years ( although only 3 (1.5%) patients had direct exposure to huanan seafood market, 84 (41.6%) patients visited hubei province and 92 (45.5%) patients had contact with people who visited hubei province after the onset of the covid-19 epidemic. 98 (48.5%) patients had known contact with suspected or confirmed cases. however, 32 (15.8%) patients did not report any known contact with hubei. the median time from symptom onset to admission was 5.0 days (iqr 2.0-7.0 days). age ( 23 (11.4%) of the patients developed severe illness in our study. the age of severe patients was comparable with non-severe patients (median age 49.0 yr vs. 44.0 yr, p = 0.066) and the bmi index of severe patients was higher than non-severe patients (median bmi, 26.4 kg/m 2 vs. 24.2 kg/m 2 , p = 0.004). nearly half (44.4%) of the severe patients were obese (bmi � 28 kg/ m 2 ) compared to only 10.4% of the non-severe patients. furthermore, more severe patients had history of type 2 diabetes (34.8% vs. 6.1%, p<0.001). more non-severe patients contacted with suspected or confirmed patients than severe patients (51.4% vs. 26.1%, p = 0.022). the most common symptoms at onset of illness were fever (156 [ compared to non-severe patients, severe patients presented higher percentage of shortness of breath (7.3% vs. 26.1%, p = 0.004), lower lymphocytes (median 0.8 ×10 9 /l vs. 1.2×10 9 /l, p<0.001) and albumin (alb) levels (median 38.1 g/l vs. 41.1 g/l, p = 0.002). however, prothrombin time was not significantly different between severe patients (median 12.3 s) and non-severe patients (median 12.8 s, p = 0.089). the proportion of patients with crp < 10mg/ l, 10-50mg/l, and � 50mg/l were 40.0%, 30.0%, and 30.0% in severe patients, while patients with crp < 10mg/l, 10-50mg/l, and � 50mg/l account for 65.3%, 30.6%, and 4.0% in nonsevere patients, respectively. more patients showed elevated crp in severe patients than nonsevere patients (p<0.001). furthermore, severe patients had higher fasting blood glucose (median 6.5 mmol/l) as compared with non-severe patients (median 5.7 mmol/l, p = 0.009). on admission, abnormalities of chest ct examinations were detected in 193 (95.5%) patients. out of 193 patients, 158 (78.2%) had bilateral involvement, and 149 (73.8%) had ground glass opacity (table 2) . bilateral pneumonia was more commonly observed in severe patients (95.7%) than non-severe patients (76.0%, p = 0.031). representative chest ct findings for a 30-year-old man on admission to the hospital were shown in fig 2. bilateral ground-glass opacities were observed in both lungs on admission (fig 2) . oxygen therapy was required in 109 (54.0%) patients and non-invasive mechanical ventilation was required in 9 (4.5%) patients. none of the patients required intubation and invasive mechanical ventilation. 196 (97.0%) patients received antiviral therapy (lopinavir/ritonavir, 89.1%; interferon α-2b, 59.9%; arbidol, 29.2%; oseltamivir, 15.8%). 149 (73.8%) patients were administered with empirical antibiotic treatment. additionally, sixty-four (31.7%) patients were given corticosteroids and 31 (15.3%) patients were given gamma globulin. (table 4 ). our study provides a comprehensive description of the clinical characteristics of laboratoryconfirmed cases of covid-19, and the risk factors for severe covid-19 in 202 cases from 8 designated hospitals in 8 cities of jiangsu province, china. consistent with the study by wang et al., about half of the patients in our study were male [7] . these data differ from the recent report by huang et al. and chen et al. which showed sars-cov-2 is more likely to infect male [4, 6] . one possible explanation is that more covid-19 patients in the previous report had an exposure history of the huanan seafood market in wuhan, and most of patients tended to be male workers [7] . however, only 1.5% of patients in our study had known contact with huanan seafood market. the median age of the patients was 44 years and only 12.9% of the patients aged over 60 years. 27.2% of the patients had chronic comorbidities. several studies suggested that sars-cov-2 is more likely to infect elder adult males with chronic comorbidities [4, 7, 17] . however, our study indicated that patients at a wide age range can be infected by sars-cov-2. recently, wei et al. even reported nine infants infected by sars-cov-2 [18] . although 15.8% of the patients did not report any known contact with wuhan-related people, the majority of patients in our study were wuhanrelated which indicated the epidemiology are important for the diagnosis of covid-19 for patients outside wuhan. consistent with two recent reports, fever and cough were the common symptoms whereas other symptoms such as diarrhea were much rare [4, 6] . however, our study found that 22.8% of the patients were afebrile on admission. the percentage of patients with fever was lower than the previous study which was ranged from 83% to 98.6% [7] . thus, the afebrile patients with an epidemiological link of the disease should be also suspected for covid-19. compared with symptoms of non-severe patients, shortness of breath was more common in severe patients. the most common laboratory abnormalities observed in this study were decreased white blood cells and lymphocyte counts as well as increased crp and ldh levels. compared to non-severe patients, severe patients had laboratory abnormalities such as lower lymphocytes and alb levels as well as higher ldh and cpr levels. the onset of symptoms and laboratory abnormalities on admission may help the physicians identify the covid-19 patients who likely develop severe illness and provide better supportive care. currently, except for meticulous supportive care, no specific treatment has been recommended for covid-19. although antibacterial agents are ineffective for covid-19, over 70% of the patients in this study still receive antibacterial agents. about 90% of the patients received antiviral therapy, such as atomized inhalation of interferon α-2b, lopinavir/ritonavir, arbidol, and oseltamivir. the benefit of the antiviral agents for covid19 is not yet clear and deserves further investigation. 31.7% of the patients used corticosteroids during the treatment, especially for severe patients (78.3%). although some experts recommend the prudently use of short courses of corticosteroids at low-to-moderate doses for critically ill patients with covid-19, the use of corticosteroids remains controversial in covid-19 [19] . moreover, the optimal time, dose and duration of corticosteroids for patients with covid19 are not yet clear and need to be evaluated by randomized controlled trials to provide a more solid evidence for treatment recommendations in the future. gamma globulin was also used for the treatment of covid-19 and severe patients were more likely to receive gamma globulin treatment. however, the efficacy of gamma globulin for covid-19 remains controversial. 23 (11.4%) patients were identified as severe illness cases in our study which is lower than the previous study (15.7%) [20] . the icu admission (5.4%) was also lower as compared with the previous studies which ranged from 26.1% to 32% [6, 7] . as of february 10, 2020, no patients died in our study. the mortality rate in our study is significantly lower than patients in wuhan as previously reported which ranged from 4.3% to 15% [6, 7] . wu et al. also reported only 1 of 62 patients was transferred to an icu and no patient died in zhejiang province [9] . the possible interpretation of the mild disease and better outcomes in our study may be that the patients were younger than previous reports. the elderly people may have an increased risk of coexisting disorders and are more susceptible to developing severe forms of disease than younger people [21, 22] . indeed, less patients had comorbidities (27.2%) in our study as compared with the previous reports (32.0%-46.4%) [4, 6, 7] . the median time from symptom onset to admission was 5.0 days which is also shorter than the previous studies (7.0 days) [6, 7] . thus, early diagnosis and prompt care of the covid-19 patients might also together contribute to the significant reduction in mortality rate in our study [20] . early identification of patients with severe illness is important for the management of patients with covid-19. we conducted univariate and multivariate analysis for risk factors of covid-19 patients with severe illness on admission. for the first time, we identified the obesity (bmi over 28 kg/m 2 ) and a history of type 2 diabetes as two independent risk factors of severe illness, suggesting that the metabolic conditions was associated the severity of covid-19. in the previous study, metabolic syndrome-related conditions such as diabetes and obesity were also demonstrated to be etiologically linked to middle east respiratory syndrome coronavirus (mers-cov) pathogenesis [23] . these disorders were reported to down regulate some key mediators of host immune response to pathogenesis [23, 24] . previous study found that a known history of type 2 diabetes was also an independent predictor of death and morbidity in patients with severe acute respiratory syndrome (sars) [25] . whether the obesity and known history of type 2 diabetes could predict the fatal outcome of patients with covid-19 deserves further investigation. this study has several limitations. first, only 202 patients with confirmed covid-19 were included from eight cities of jiangsu province. it would be better to include as many as possible patients in jiangsu province to get more comprehensive understanding of covid-19 outside wuhan. moreover, we only included patients with laboratory confirmed cases. the suspected but undiagnosed cases were not included in the present study. as of february 10, 2020, 515 confirmed cased have been reported in jiangsu province [5] . in fact, about a half of the confirmed cases were included in our present study. thus, our study is very representative. second, clinical outcomes of the remaining 165 hospitalized patients were not available at the time of analysis. thus, we could not assess the risk factors for poor outcomes of patients. however, this multicenter study provides an early assessment of the epidemiological and clinical characteristics of covid-19 outside wuhan, china. in conclusion, covid-19 patients in jiangsu province were less severe and have improved prognosis than the initial covid-19 patients as previously reported in wuhan indicating that mild cases might already have occurred. a bmi > 28 kg/m 2 and a history of type 2 diabetes are independent risk factors for severe illness of covid-19. sustained intensive control efforts remain urgently needed to minimize the risk of covid-19. a novel coronavirus from patients with pneumonia in china severe acute respiratory syndrome-related coronavirus: the species and its viruses-a statement of the coronavirus study group a novel coronavirus outbreak of global health concern epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study novel coronavirus (covid-19) situation clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan, china clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance acute respiratory distress syndrome: the berlin definition kdigo clinical practice guidelines for acute kidney injury acute liver injury and failure association between cardiac injury and mortality in hospitalized patients infected with avian influenza a (h7n9) virus guidelines for the diagnosis and treatment of novel coronavirus (2019-ncov) infection by the national health commission (trial version laboratory diagnostics for novel coronavirus early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia novel coronavirus infection in hospitalized infants under 1 year of age in china on the use of corticosteroids for 2019-ncov pneumonia clinical characteristics of 2019 novel coronavirus infection in china severe human influenza infections in thailand: oseltamivir treatment and risk factors for fatal outcome motivational strategies to prevent frailty in older adults with diabetes: a focused review prevalence of comorbidities in the middle east respiratory syndrome coronavirus (mers-cov): a systematic review and meta-analysis connecting type 1 and type 2 diabetes through innate immunity. cold spring harb perspect med plasma glucose levels and diabetes are independent predictors for mortality and morbidity in patients with sars conceptualization: rui huang, chuanwu zhu, chao wu. key: cord-269453-30l6rzgo authors: yang, po; qi, jun; zhang, shuhao; wang, xulong; bi, gaoshan; yang, yun; sheng, bin; yang, geng title: feasibility study of mitigation and suppression strategies for controlling covid-19 outbreaks in london and wuhan date: 2020-08-06 journal: plos one doi: 10.1371/journal.pone.0236857 sha: doc_id: 269453 cord_uid: 30l6rzgo recent outbreaks of coronavirus disease 2019 (covid-19) has led a global pandemic cross the world. most countries took two main interventions: suppression like immediate lockdown cities at epicenter or mitigation that slows down but not stopping epidemic for reducing peak healthcare demand. both strategies have their apparent merits and limitations; it becomes extremely hard to conduct one intervention as the most feasible way to all countries. targeting at this problem, this paper conducted a feasibility study by defining a mathematical model named semcr, it extended traditional seir (susceptible-exposed-infectious-recovered) model by adding two key features: a direct connection between exposed and recovered populations, and separating infections into mild and critical cases. it defined parameters to classify two stages of covid-19 control: active contain by isolation of cases and contacts, passive contain by suppression or mitigation. the model was fitted and evaluated with public dataset containing daily number of confirmed active cases including wuhan and london during january 2020 and march 2020. the simulated results showed that 1) immediate suppression taken in wuhan significantly reduced the total exposed and infectious populations, but it has to be consistently maintained at least 90 days (by the middle of april 2020). without taking this intervention, we predict the number of infections would have been 73 folders higher by the middle of april 2020. its success requires efficient government initiatives and effective collaborative governance for mobilizing of corporate resources to provide essential goods. this mode may be not suitable to other countries without efficient collaborative governance and sufficient health resources. 2) in london, it is possible to take a hybrid intervention of suppression and mitigation for every 2 or 3 weeks over a longer period to balance the total infections and economic loss. while the total infectious populations in this scenario would be possibly 2 times than the one taking suppression, economic loss and recovery of london would be less affected. 3) both in wuhan and london cases, one important issue of fitting practical data was that there were a portion (probably 62.9% in wuhan) of self-recovered populations that were asymptomatic or mild symptomatic. this finding has been recently confirmed by other studies that the seroprevalence in wuhan varied between 3.2% and 3.8% in different sub-regions. it highlights that the epidemic is far from coming to an end by means of herd immunity. early release of intervention intensity potentially increased a risk of the second outbreak. a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 throughout human history, infectious diseases (id), also known as transmissible diseases or communicable diseases, are considered as serious threats to global public health and economics [1] . from the 1918 influenza pandemic in spain resulting in nearly 50 million deaths in 1920s, to recent ongoing global outbreaks of corona-virus disease 2019 (covid-19) killing over 11 thousands people in all over the world [2] , infectious disease is a leading contributor to significant mortality and causes huge losses to society as well as personal family burden. among a variety of factors leading to emergence and outbreaks of id, the key issues are population density and human mobility where in these cities with developed transportation systems, pathogens can be spread to large geographic space within a short period of time. for instance, the ongoing global epidemic outbreak of covid-19 has spread to at least 146 countries and territories on 6 continents in 2 months. in order to give an accurate prediction of outbreaks, many researchers have been working in traditional id propagation models [3] [4] [5] [6] [7] like sir, seir, etc, for understanding covid-19 transmission with human mobility and predicting outbreak process of epidemics. meanwhile, as realizing a long period of this battle against covid-19, many of them recently focus on intervention strategies [8] [9] [10] that can balance a trade-off between limited human mobility and potential economic loss in covid-19 control. it poses an important research area that explores how and when to take what level of interventions in light of multiple natures and capabilities of countries. in traditional compartmental models paradigm in epidemiology, sir (susceptible-infectious-recovered) [3] and seir (susceptible-exposure-infectious-recovered) [4] are two popular approaches to simulate and predict how infectious disease is transmitted from human to human. these two models have defined several variables that represent the number of people in each compartment at a particular time. as implied by the variable function of time, these models are dynamic to reflect the changes and fluctuations of these numbers in each compartment over time. for covid-19 control in wuhan, zhong, et.al [11] introduced a modified seir model in prediction of the epidemics trend of covid-19 in china, where the results showed that under strong suppression of "lockdown hubei", the epidemic of covid-19 in china would achieve peak by late february and gradually decline by the end of april 2020. some other extended models [8] [12] are also proposed for predicting the epidemics of covid-19 in wuhan and give some similar forecasts. while above methods demonstrate good performance in prediction of covid-19 outbreak by taking strong public intervention, also named as suppression strategy [13] that aims to reverse epidemic growth, one important challenge is that taking suppression strategy only is to treat disease controls as single-objective optimization of reducing the overall infectious populations as soon as possible, and require strategic consistency in a long term. in real-world, taking public health intervention strategies is actually a multiple-objective optimization problem including economic loss and society impacts. thus, most countries have taken different intervention strategies, like enhanced surveillance and isolation to affected individuals in singapore [14] , four-stage response plan of the uk [15] [16] , mitigation approaches [13] and even multiple interventions taken in many eu countries [17] [18] [19] [20] [21] . due to the fact that standalone intervention strategy has apparent merits and limitations, it becomes highly necessary to study the feasibility of intervention strategies to certain country in light of its multiple natures and capabilities. targeting at this problem, this paper conducts a feasibility study that analyses and compares mitigation and suppression intervention strategies for controlling covid-19 outbreaks in wuhan and london. as shown in fig 1 with wuhan as a simulated case using data from [6] , we demonstrated performance of taking different intervention strategies: a) no interventions: the peak of daily infections would be up to 2.1 million, but will be completed in 150 days. the epidemics lasts a relatively shorter period of 140-150 days, but lead to more death. b). mitigation intervention from the 32 nd day: the peak of daily infectious populations increased to 27.7 thousand, but the period of maintenance extended to 150 days. it implied there would be growing death, but less economic loss compared to suppression. c). suppression intervention from the 32 nd day: the peak of daily infections greatly reduced to 16 thousand, but it had to be followed at least 200 days. nearly 3 months suppression may potentially lead to economic loss even crisis. d). hybrid intervention of taking both suppression and intervention every 2 weeks: the epidemics of covid-19 appeared a long-term multimodal trend where the peaks of daily infectious populations were within a range of 40-60 thousand. this might lead to less daily critical cases and offer more time to hospital for releasing their resources. e) contain phase: taking 90% effectiveness of surveillance and isolation from the 2 nd day of confirmed case potentially enables controlling a new outbreak of covid-19, but it needs to be maintained over 300 days. above analysis demonstrates the complexity of controlling covid-19 outbreaks that how and when to take what level of interventions. in this paper, we proposed a mathematical model: semcr to study this problem. the model extended traditional seir (susceptible-exposed-infectious-recovered) model [3, 4] by adding one important fact: there has been a direct link between exposed and recovered population. we found that the number of confirmed diagnoses reported by governments of various countries is actually much smaller than the actual number of infected persons. although many exposed people have been infected, they will not show symptoms and transformed into infected people after the incubation period of the virus, and directly become recovered people after a certain self-healing cycle [22] [23] . because they are asymptomatic, they will not take the initiative to go to the hospital for treatment testing, so they will not be counted as the actual number of infected people. if we make a statistic on the cumulative number of cured people and the cumulative number of infected people, the difference between them is the number of asymptomatic patients who are directly transformed into cured people without going through the infection stage. then, it defined parameters to classify two stages of covid control: active contain by isolation of cases and contacts, passive contain by suppression or mitigation. the model was fitted and evaluated with public dataset containing daily number of confirmed active cases including wuhan, london, hubei province and the uk during january, 2020 and march 2020. for each point, we design and set up experimental protocols for comparison and exploration, highlighting following contributions: • immediate suppression taken in wuhan significantly reduced the total exposed and infectious populations, but it has to be consistently maintained at least 90 days (by the middle of april 2020). its success heavily relied on sufficiently external support from other places of china. this mode was not suitable to other countries that have no sufficient resources. • in london, it is possible to take a hybrid intervention of suppression and mitigation for every 2 or 3 weeks over a longer period to balance the total infections and economic loss. while the total infectious populations in this scenario would be possibly 2 times than the one taking suppression, economic loss and recovery of london would be less affected. • both in wuhan and london, one important issue of fitting practical data was that there were a large portion (probably 62.9% in wuhan) of self-recovered populations that were asymptomatic or mild symptomatic. these people might think they have been healthy at home and did not go to hospital for covid-19 tests. early release of intervention intensity potentially increased a risk of the second outbreak. • one limitation of our model was that our prediction of infections and deaths depended on a parameter estimation of intervention intensity that presented by average-number contacts with susceptible individuals as infectious individuals in a certain region. it assumed that each intervention had equivalent effects on the reproduction number r in different regions over time. the measures of strong intervention in different countries and regions are similar, so the culture or other issues of different countries will not change the impact of strong intervention on the basic regeneration number. the remainder of this paper is arranged as follows. section 2 introduces the model. in the section 3, the materials and implementation of experiment are reported. section 4 provides detailed experimental evaluation and discussion. the conclusion and future directions are given in section 5. we modified a seir model to account for a dynamic susceptible fig 2. here, we assume that susceptible population e represents susceptible population of a certain region; and β represents effectiveness of intervention (strict isolation) in contain phase. if effectiveness of intervention in contain phase is not sufficiently strong, susceptible individuals may contract the disease with a given rate when in contact with a portion of exposed population (asymptomatic but infectious) e. after an incubation period, the exposed individuals become the infectious population i (symptomatic) at a ratio α 1 . notably, infectious population starts from mild cases m to critical cases c at a ratio α 2 . finally, a portion d of critical cases lead to deaths; the rest of infectious population will be recovered. there are two enhanced features in our model in comparison to popular seir models [6, 8, 11] . the first one is a straightforward relationship between exposed and recovered population. we find that in the early outbreaks of covid-19, some portion of exposed people may have no obvious symptoms or only develop as mild cases, but they cannot get a test due to lack of testing kits. this group of populations might be self-recovered in some days, but will not realize they were infected. and we can calculate the approximate proportion of the number of asymptomatic or mild symptoms in the total number of infected people by counting the cumulative number of each population. the second feature in our model is that we separate infectious population into mild and critical cases in light of their symptoms. according to the curve of the number of critical cases and the number of deaths, we can make a certain explanation for the relatively high mortality rate of early outbreaks of covid-19 after wuhan city took immediate inhibitory interventions on january 23, 2020. introducing above two features, it is helpful for evaluating real effects of different interventions. if we assumed the overall population of a certain region is n, the number of days is t, the dynamic transmissions of each components of our model are defined as follow: regarding mild cases, critical cases and death, the dynamic transmission is as below: lastly, we define a benchmark in semcr model to reflect the strength of intervention over time, as m t . it is presented by average number of contacts per person per day in a region. we estimated changes in covid-19 transmissibility over time via the effective reproduction number(r t ), which represents the mean number of secondary infections that result from a primary case of infection at time t. values of r t exceeding 1 indicate that the epidemic will tend to grow, whereas values below 1 indicate that the epidemic will tend to decline. we estimated the time-varying reproduction numbers from serial intervals and incidence of covid-19 cases over time. in practical cases, it also needs to estimate the defined parameters including α 1 , α 2 , β, and γ 1 , γ 2 , γ 3 , b, where β is the product of the people exposed to each day by confirmed infected people (k) and the probability of transmission (b) when exposed (i.e., β = r t /γ = kb) and σ is the incubation rate which is the rate of latent individuals becoming symptomatic (average duration of incubation is 1/α 1 ). according to recent report [24] , the incubation period of covid-19 was reported to be between 1 to 14 days, we chose the midpoint of 6 days. preliminary data suggests that the time period α 2 from onset to the development of severe disease, including hypoxia, is 1 week [24] . γ is the average rate of recovery or death in infected populations. using epidemic data from [11] , we used semcr model to determine the probability of transmission (b) which was used to derive β and the probability of recovery or death (γ). the number of people who stay susceptible in each region was similar to that of its total resident population. other transmission parameters were estimated with early prediction of hubei cases in [11] on january 23 2020 using monte carlo simulation, as shown in the table 1 notably, as for the strength of intervention m, it was related to the population density in a region. we used a benchmark reported in [11] that assumes hubei province with no intervention as m = 15, and after suppression intervention, m reduced to 3. when applying semcr model into other simulated cases, m was initialized according to the population density and human mobility in these places. also, after taking any kind of interventions, the change of m would follow a reasonable decline or increase over few days, not immediately occur at the second day. following previous assumptions, the implementation of dynamic transmission of semcr model follows steps as below: in order to utilize our proposed semcr model into practical cases, we design an evaluation protocol to access multiple effects of taking different intervention strategies to control outbreak of covid-19 in 4 typical cases, including hubei province, wuhan city, the uk and london, as shown in feasibility study of mitigation and suppression strategies for controlling covid-19 outbreaks the first stage is initial parameters estimation using covid-19 data from four cases: hubei, wuhan, uk and london. in this stage, a preliminary qualitative assessment of each case is performed, by comparing their similarity and dissimilarity on area, transportation, population density, migration flows, date of the first confirmed case, etc. we would determine value of initial parameters in the semcr including n, m t , and date of the first confirmed case. notably, in wuhan, the date of the first confirmed case is not officially released. the work [8] estimates the first confirmed case is by the end of nov 2019; and zhong [11] points out the first confirmed case in wuhan is on 23 nd december 2019. here, we take the same settings of first confirmed case on 23 nd december 2019. the next step is to estimate and normalize other parameters in the model. assuming that covid-19 has similar transmission ratio and incubation rate in all four cases, we use parameter values fitted from [11] , where incubation rate is 1/6; the rate of transmission for the i to s is 0.157; the rate of transmission for the e to s is 0.787. as for estimation of other parameters, we follow the covid-19 official report from who [24] , including the proportion of mild, severe and critical cases, the probability of death, etc. thirdly, how to take intervention strategies needs to be evaluated by tuning parameters in semcr model. the key tuning operation is to adjust the level of m t over a period. for instance, we assume that no intervention strategies result in unaltered internal mobility of a region, taking suppression strategy in wuhan means a reduction of m to 3. but in other cases with larger area, it is extremely difficult to take a complete suppression strategy. so the reduction of m will be relatively adjusted to 4 or 5. final stage, we perform quantitative analysis of effectiveness of different intervention strategies, including: strict surveillance and isolation, suppression strategy, mitigation strategy, and multiple intervention. the evaluation metric of cross-validation is employed to evaluate the performance of covid-19 progression model. the final two evaluation indicators are the length of intervention and the peak time. the length of intervention is calculated due the date that confirmed cases are nearly clear to zero. the most recent epidemiological data in hubei province, china based on daily covid-19 outbreak numbers reported by the national health commission of china were retrieved [25] . the dataset used to analyse several european countries comes from the statistics of worldmeters [26] . specifically, we used confirmed cases, new cases, recovery cases and deaths since 22nd january 2020 to 25th march 2020. all the datasets used in this paper are anonymised. also regarding the daily update from world meter, we record the number of confirmed cases and death each day in four cases. in order to simulate four cases, we require the exact confirmed cases in the first 2-5 days to initialise parameters of our model. we simulated four cases that predict covid-19 outbreaks without taking any interventions. the initial populations were given as london (9.3 million), wuhan (14.18 million), uk (66.49 million) and hubei (58.9 million). the parameter m representing average number of contacts per person per day was given as 15 to london, wuhan and hubei; 12 to the uk. the simulation results were given in fig 4. the results showed that in the peak time, there would be up to 1.16 million, 2.1 million, 4.5 million and 8.7 million exposed population (infection but no symptoms) at london, wuhan, uk and hubei. this implied that: 1) the total infectious population of these four cases would be 7.76 million in london, 12.27 million in wuhan, 50.95 million in hubei and 48.46 million in the uk. 2) the total death of these four cases would be 76 thousand in london, 120 thousand in wuhan, 493 thousand in hubei and 475 thousand in the uk. it equalled to about over 80% of total population of each region will be infectious, with the mortality rate nearly 1%. it showed that without intervention, the outbreak of covid-19 would lead to huge infections and deaths. the main reason was that covid-19 was estimated as relatively high production number r 0 up to 2-2.5 [24] , where the transmission ratio β 2 from susceptible to exposed is up to 78%. thus, in some regions with high migration and dense population, it would easily lead to an outbreak. but, one notable issue was that the initialization of parameter m seems to impact on the occurrence of peak time and the length of overall period. in the cases of london, wuhan and hubei with m = 15, their peak date were all roughly on the 60 th day from the date of first confirmed case; but uk with m = 12, their peak time was delayed to the 100 th day from the date of first confirmed case. that meant to regions with similar total population, low population density potentially reduced overall infectious population, but delayed the peak time of outbreak as a result of longer period. as for the strategy of taking surveillance and isolation intervention in the contain phase, recent study [15] developed a stochastic transmission model parameterised to the covid-19 outbreak. it proved that highly effective contact tracing and case isolation can control a new outbreak of covid-19 within 3 months, where for a production number r 0 of 2-2.5, more than 90% contacts had to be traced. we transferred this finding as a tuning parameter β 2 to evaluate if the outbreak of covid-19 could be controlled. considering that 98% of contacts had to be traced, it implied that the surveillance and isolation was effective to scale down the group of contacts. in other words, we simulated a situation that from the second day of receiving confirmed case, only 5% of the overall population would be possible to contact the infectious ones. then, the β 2 = 0.05. the results were shown in the fig 5. the results show that in all four cases, the outbreaks of covid-19 were successfully controlled, and had no peak time. there would be only more than 40 people that were infection and finally recovered at london, wuhan, uk and hubei. the overall period of covid outbreak was less than 100 days. this finding was as similar as the proof in [15] . notably, the simulated situation of wuhan, london and hubei were same, it was mainly because we initialised the same value of confirmed cases as 3, and m = 15 in all cases. when taking highly effective surveillance and isolation, the transmission of covid-19 was limited and controlled within a small group of population. the population difference would not affect the total infectious ones. but in the uk case with m = 12, low population density limited the effectiveness of surveillance and isolation, as a result of more infectious population. it implied another fact that to these countries with low population density, it was challenging to take high quality of intervention like surveillance and isolation. feasibility study of mitigation and suppression strategies for controlling covid-19 outbreaks then, we evaluated when the outbreak of covid-19 could occur by adjusting the value of parameter β 2 in the uk case. as shown in table 2 , we recorded the total recovered population, and if there would be a peak of outbreak. as the increased β 2 , the total recovered population was dramatically increased and generated a peak as β 2 = 0.075. that meant that if we cannot guarantee at least 92.5% of uk population being not contacted by infectious people, it would be indispensable to have an outbreak of covid-19. if the isolation intervention was less effective; the more population would be infectious; and the peak day was brought forwarded. in the early stage, taking high effective surveillance and isolation in any regions is necessary to avoid the outbreak of covid-19. the suppression strategy was recognized as the most effective solution to reduce the infectious population, where it was taken in wuhan on 23 rd january 2020. in the work [11] , zhong has reported that taking suppression strategy has successfully limits the overall infectious population in hubei on 22 nd february 2020 to 50k. and if the suppression strategy was taken one week earlier, this figure would reduce to 18k. thus, we would like to simulate the situation of taking suppression strategy in london. the parameter m was given as 15 to 4 in london, in comparison to wuhan from 15 to 3. the simulation results were given in fig 6. after taking intensive suppression on 23rd march in the uk, the change trend of the basic regeneration number in the uk and wuhan is consistent. a rapid decline in r has occurred in later march, from 2.81[1. 16-5.19 ] at the 24th day (1st march 2020) to 0.68[0.58-0.79] at the 51st day (28th march 2020). it implied implementing suppression in the uk performed significantly impact on reduction of infections. the results showed that taking suppression strategy, the cases in wuhan and london appeared a similar trend that daily exposed and infectious population would be greatly reduced. the outbreak of covid-19 was controlled by the 100 th days, and can be nearly ended by the 150 th days. the difference was that the daily infectious population of london was nearly double to the ones in wuhan. it was probably because we simulated the date of taking suppression strategy in wuhan (the 32 nd day) is 3 days earlier than london (the 35 th day). another possible reason was that considering the impact of culture difference, the value of m was only limited to 4 in london, but not as lower as 3 in wuhan. in fact, the suppression in wuhan was actually applied to limit mobility in community level with very high intensity, which was hard to be followed by london. we considered another two situations of taking suppression intervention 1 week earlier or 1 week later in london, as shown in fig 6. the results showed that the overall infectious population would be greatly reduced to 3.5 thousand if taking actions one week earlier; oppositely it would increase to 178 thousand infection if taking actions one week later. we used our model to estimate the impacts of suppression on controlling infections of other 6 eu countries (italy,spain, germany, france, belgium and switzerland), as shown in table 3 . most suppression in other countries began around 10 th -17 th march (the 28 th -40 th day from first confirmed case).for each country, we model the number of infections, the number of deaths, and r, the effective reproduction number over time. specific interventions are assumed to have the same relative impact on r in each country when they were introduced there and are informed by mortality data across all countries. fig 6. (a, c) wuhan and (b, d, e, f) london by taking suppression intervention. note that a,b; c,d,e and f have different scales. and the orange dotted line on the x axis represents the date of implementation of the intervention, a, c is the 32nd day, b, d, e, f is the 35th day. https://doi.org/10.1371/journal.pone.0236857.g006 as shown in table 3 , in italy from 8th february 2020, the total number of infections is about 1.9 million, the total number of deaths is about 41 thousand, the true mortality rate is 2.17%. in spain from 1st february 2020, the total number of infections is 2 million, the number of deaths is 41 thousand, the true mortality rate is 2.07%. in germany from 11th february, the total number of infections is about 0.77 million, and the number of deaths is about 11 thousand. the true mortality rate is 1.5%. in france from 15th february 2020, the total number of infections is about 1.6 million, and the number of deaths is about 33 thousand. the true mortality rate is 2.09%. in belgium from 15th february 2020, the total number of infections is about 0.62 million and the number of deaths is about 12 thousand. the true mortality rate is 1.93%, and. lastly, in switzerland 19th from february 2020, the total number of infections is 0.23 million people, the number of deaths is about 3.4 thousand people, the real mortality rate is 1.47%. the time of intervention in these six european countries is similar, but from the analysis of the infections in these six european countries can be seen that the intervention effects of germany, belgium and switzerland are better, and the mortality rate of germany and switzerland is less than four other countries. from the data we collected can be seen that germany and switzerland have adequate medical resources, while italy, spain, france and belgium have insufficient medical resources. this corresponds to the difference between the number of deaths and mortality we predicted. the above also confirms the previously mentioned point of view. when medical resources are insufficient, premature intervention may cause strain on medical resources, leading to more deaths and higher mortality. another two important issues of taking suppression strategy were intervention length and the peak time. in order to effectively control the outbreak, the intervention length of taking actions at above three timing points all required at least 100 days. it potentially led to significant side effects to economic and society, including job loss, mental health, etc.also, the peak time arrived earlier than its nature transmission if taking actions one week earlier. this might increase a shorter time to government for preparing sufficient resources, and causing more difficulties in control the outbreak of covid-19. the mitigation strategy was recently highlighted by researchers from imperial college [27, 28] , where this strategy was initially taken by uk government. the aim of mitigation was to use other strategies to help individuals so that not to interrupt transmission completely, but to reduce the health impacts of an epidemic. in this cases, population immunity built up through the epidemic, leading to an eventual rapid decline in case numbers and transmission dropping to low levels. thus, we simulated the situation of the uk by taking mitigation strategy with different level of strengths. the parameter m representing average number of contacts per person per day was given as 12 to the uk, and gradually reduced to 10 and 8 from the 32 nd day of first confirmed case. the simulation results were given in fig 7a and 7c . the simulation of basic regeneration numbers(r) compared to suppression strategy, mitigation strategy taken in the uk gave a slower decline in r in march, from 2.73[0.97-5.40] on the 24th day (1st march 2020) to 0.98[95% ci 0.88-1.09] on the 110th day (27th may 2020). it implied that before r drops below 1, there were still much growth of infections in the uk. and it can be seen from the fig 7 that the more relaxed the intervention, the longer it takes r to fall below 1. the results showed that taking mitigation strategy was effective to reduce daily infectious population, further lead to huge reduction of total infectious population. by reducing the parameter of m from 12 to 10 or 8, the peak of daily infectious population reduced from 4.5 million to 2.5 million or 1 million. on the other hand, the peak time of infectious population would be delayed as taking mitigation intervention, where the peak dates of infectious population at m = 12, 10 and 8 were roughly on the 80 th , 110 th and 170 th days. the overall period of outbreak would be extended from 180 days to 200 or 250 days. above simulated figures appeared a similar trend as findings from [25] . taking mitigation intervention in the uk was capable of reducing the impact of an epidemic by flattening the curve, reducing peak incidence and overall death. while total infectious population may increase over a longer period, the final mortality ratio may be minimized at the end. but as similar as taking suppression strategy, the mitigation interventions need to remain in place for as much of the epidemic period as possible. however, the timing of introducing this mitigation intervention was important, where too early execution may allow transmission to return once they were lifted and sufficient "herd immunity" has not been developed. in terms of above discussion, the effectiveness of taking any one intervention (either suppression or mitigation) is likely to be limited. it is highly necessary to consider the possibility of taking multiple interventions to be combined to have a substantial impact on social and economic cost reduction. we simulated one simple situation of taking multiple strategy in london from the 35 th day, by giving a hybrid of suppression and mitigation strategies every 2 weeks. the m was given as a pattern of 6-4.5-3-4.5-6 in london, where it meant mitigation and suppression strategies were taken in an every 2 weeks roll. for minimizing side effects of taking interventions on human mobility, the application of first mitigation to reduce m from 12 to 6 spends 2 days. the simulation results were given in fig 7b and 7d the results showed that the epidemic appeared a multi-modal decline trend over 500 days. the first peak of infectious population occurred on the 53 rd days with 1017 infections after taking suppression intervention to reduce m from 12 to 3. after two weeks, mitigation strategies were taken so that the second peak of infectious population raised up to 750 infections. the total infectious population was 53075 over 500 days; the deaths was limited to 520. apparently, taking multiple intervention in the uk is capable of reducing the impact of an epidemic by fluctuating the curve, reducing overall infections and death. while the total period will be extended, final mortality ratio may be minimised at the end. but the longer period of limiting human mobility might increase economic risks and reduce employment ratio. there will be plenty of choices to taking multiple interventions through adjusting the strength and length of intervention. the consequence possibility show a similar multimodal curve but with different peak incidence. as we mentioned in section 1, the question on how and when to take what level of interventions to control an epidemic is highly challenging, particularly in light of multiple natures and capabilities of countries. in many cases, it is even hard to evaluate effectiveness until the end of epidemic, and there is always controversy on taking any one intervention. however, our findings contribute to several useful suggestions on controlling covid-19 outbreak. the first point is that highly effective surveillance and isolation strategy is necessary to control an epidemic in early stage. ideally, if this strategy can be executed in excellent level, there will be no huge outbreak later on. considering the area, transportation, migration flows and population density of a region, most countries cannot achieve excellent level of isolation in contain phase, probably only in fine or good level. the outbreak of an epidemic is inavoidable. but considering its low social and economic cost, this strategy is still a cost-effective option. secondly, the cases in wuhan and london approve high effectiveness of suppression strategy to reduce the overall infection. probably in the uk or similar countries, suppression will minimally require a combination of social distancing of the entire population, home isolation of cases and household quarantine of their family members. but its practical effectiveness is not possible to achieve as same as wuhan, as the success of suppression strategy in wuhan is based on locking down human mobility to community level and sufficient resource support from other cities or provinces in china. if there are no sufficient external support, it will be risky to take intensive suppression to entire country due to huge impacts on its economics. also, taking such intensive intervention to control an epidemic will need to be maintained until vaccine released (up to 12 months or more). if intensive interventions are relaxed at any time points, the transmission will quickly rebound. this is more like a multi-modal curve when taking multi-intervention strategies. thirdly, we also find out that while covid-19 is estimated as a high production rate (r = 2-2.5) [24] , experimental evaluation results show that in either wuhan or london cases fitted with real data in the last 6 weeks, high percentage of exposed or infectious population (at least 62.9% of infectious population in wuhan) are actually self-recovered. these people may have no or mild symptoms but been not checked as confirmed cases. this is one important issue that zhong's seri model [11] has ignored. it will answer the model [8] predicts practical infectious population in wuhan that ten times over figures in [11] . similarly, it could explain the estimation of practical mortality ratio can be varied in [11] and [8] . lastly, one limitation of our model is that its prediction of infections and deaths depends on a parameter estimation of intervention intensity that presented by average-number contacts with susceptible individuals as infectious individuals in a certain region. we assume that each intervention has the same effect on the reproduction number in different regions over time. the measures of suppression intervention in different countries and regions are similar, so the culture or other issues of different countries will not change the impact of suppression intervention on the basic regeneration number. as implementing hybrid intervention, the policy needs to be specific and well-estimated at each day according to the number of confirmed cases, deaths, mortality ratio, health resources, etc. this paper conducts a feasibility study by defining a mathematical model named semcr that analyses and compares mitigation and suppression intervention strategies for controlling covid-19 outbreaks in london and wuhan cases. the model not only fits and evaluates through public data sets containing the number of daily confirmed active cases in wuhan, london, hubei province and the united kingdom, but also uses the trained model to predict and analyze six other european countries at the end. the experimental findings show that the optimal timing of interventions differs between suppression and mitigation strategies, as well as depending on the definition of optimal. in the future, we can expand our model to realize the comparative analysis of the number of severe cases and the number of medical resources by adding medical resources, and optimize the timing and intensity of interventions to reduce the demand for medical resources. conceptualization: po yang, gaoshan bi. world health organization infectious diseases citation patterns: mapping the literature 2008-2010 a 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investigation of three clusters of covid-19 in singapore: implications for surveillance and response measures feasibility of controlling covid-19 outbreaks by isolation of cases and contacts feasibility of controlling covid-19 outbreaks in the uk by rolling interventions infectious disease modeling-a hybrid system approach the switched sir model. infectious disease modeling on fast multi-shot covid-19 interventions for post lock-down mitigation alternating quarantine for sustainable mitigation of covid-19 the effect of multiple interventions to balance healthcare demand for controlling covid-19 outbreaks: a modelling study modelling the covid-19 epidemic and implementation of population-wide interventions in italy seroprevalence of immunoglobulin m and g antibodies against sars-cov-2 in china report of the who-china joint mission on coronavirus disease 2019 (covid-19). who-china jt. mission coronavirus dis comment how will country based mitigation measures influence the course of the covid-19 epidemic early estimation of the case fatality rate of covid-19 in mainland china: a data-driven analysis key: cord-288616-7i1kukmn authors: wan, kelvin h.; huang, suber s.; ko, chung-nga; lam, dennis s.c. title: the end of cordon sanitaire in wuhan: the role of non-pharmaceutical interventions date: 2020-05-14 journal: public health doi: 10.1016/j.puhe.2020.05.007 sha: doc_id: 288616 cord_uid: 7i1kukmn abstract the effectiveness of the non-pharmaceutical interventions implemented in wuhan are described and discussed. in the absence of vaccine and proven specific safe and effective treatments, the experience and results achieved by wuhan could serve as a good reference for leaders and policymakers around the world in formulating their strategies and policies in fighting against covid-19. wuhan, the initial epicenter of coronavirus disease 2019 (covid-19), has lifted its cordon sanitaire on 8 april, 2020 after being in place for 76 days. however, epidemics are getting very serious in some countries such as america and italy. soon after the start of the outbreak, when the transmission dynamics and epidemiology had become a little bit clearer, the chinese government has reacted swiftly with liberal testing, immediate case isolation, rigorous contact tracing and quarantine, social distancing, community containment, and mass masking. "desperate times call for desperate measures", said by hippocrates, the famous ancient greek physician describes vividly the decision to lockdown the wuhan city on 23 january 2020. this was a major decision that needs much political will and wisdom. the report of the who-china joint mission on covid-19 concluded that "such an approach is warranted to save lives and to gain the weeks and months needed for the testing of therapeutics and vaccine development." 1 the effectiveness of these non-pharmaceutical interventions have now become evident and can serve as an important reference in managing covid-19 pandemic. temperature checking stations were set up across transportation hub, designated fever clinics and wards were established in hospitals for suspected cases. different tiers of healthcare facilities were established in anticipation of the overwhelming number of new cases. sports stadiums and convention halls were converted into makeshift hospitals to relieve the pressure in hospital for mild covid-19 cases. huoshenshan and leishenshan, the two dedicated hospitals with 2,600 beds for treating the seriously-or critically-ill patients were completed in 2 weeks. over 42,000 medical personnel from all over china were deployed to the epicenter soon after the outbreak. for isolation to be effective in preventing transmission, patients should be detected ideally before the onset of viral shedding. transmission from asymptomatic patients has made temperature and symptom-based screening less effective. 4 in china, testing for the coronavirus is free and easily accessible; 320,000 tests have been performed in the guangdong province alone in just over 2 weeks. 1 one reason that has attributed to the reduction of new cases in south korea has been its widespread testing together with a digital crowdsourced contact tracing strategy; they have performed over 608,000 tests as of 28 april, 2020. 5 testing must be widely available and hurdles to get tested must be reduced. rapid testing protocols also ensure the optimal use of isolation room and other facilities at the hospitals. through widely available testing and contact tracing, followed by isolation and quarantining, this will be a part of the strategy of breaking the transmission chains. companies across the world are developing and manufacturing diagnostic kit to increase the abundance of testing kits. the use of facemask as part of the respiratory hygiene is ubiquitous in southeast asian countries such as china, south korea, and japan. many provinces in china made it mandatory by law to wear a facemask in public during covid-19. in contrast, citizens are advised to wear facemask only when they are ill in most non-asian countries. some opposing parties believe that the limited supply of facemask should be reserved for healthcare workers. this has led to racial stigmatism and aggravation among mask wearers in some of the countries in the current pandemic. as a public health intervention, mass masking protects the wearer but also each 5 other, and would eliminate discrimination. there is limited evidence, but not evidence of absence, on whether mask masking is effective in protection against coronavirus infection. 6 an adequate supply of medical masks to the public is likely to be a key bottleneck that determines whether such a strategy could be implemented as one of the non-pharmaceutical interventions in a country. real-time information was broadcasted by the chinese government through popular instant messaging apps such as wechat and weibo. various it platforms have increased the accessibility to information, health services, and minimized fake news. video conferencing and telemedicine platforms reduced exposure to healthcare workers. wuhan wuchang smart field hospital, one of the makeshift hospitals, was staffed with robots. robots were equipped with infrared thermometry; they delivered meals and medications and disinfected areas. smart bracelets and rings worn by patients monitored their vitals with data fed to remote medical staffs. unmanned aerial drones transported supplies to those under quarantine; they also replaced police officers in patrolling areas to enforce quarantine restriction. these innovative technologies reshape how we can protect medical personnel and care for our patients during health emergencies. china enforced unprecedented public health efforts such as surveillance, prompt isolation of patients, quarantine close contacts, social distancing, and community quarantine. a modeling 6 study showed that changes to contact patterns via workplace and school closure significantly delayed the epidemic peak and flattened the curve of wuhan. 7 another model revealed that larger travel restriction of >90% together with a strong transmissibility reduction delays the epidemic growth such that the daily incidence does not exceed 1 case per 1000 in china. 8 the series of multifaceted public health measures led to a reduction in r t to less than 1.0 on 6 february and to below 0.3 on 1 march, 2020 in wuhan. 9 these encouraging results highlight the importance of the synergistic effect of all public health measures. such measures allow the healthcare system to better prepare their capacity to respond to an overwhelming influx of patients, minimize the morbidity and mortality, while hoping for an effective vaccine or antiviral to come. who director-general commented that the "chinese government is to be congratulated for the extraordinary measures it has taken to contain the outbreak." 10 report of the who-china joint mission on coronavirus disease early dynamics of transmission and control of covid-19: a mathematical modelling study impact of non-pharmaceutical interventions (npis) to reduce covid-19 mortality and healthcare demand transmission of 2019-ncov infection from an asymptomatic contact in germany the updates on covid-19 in korea as of respiratory virus shedding in exhaled breath and efficacy of face masks the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in 8 china: a modelling study. the lancet public health the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak association of public health interventions with the epidemiology of the covid-19 outbreak inwuhan, china who director-general's statement on ihr emergency committee on novel coronavirus patient and other consents: not applicable, not required acknowledgments: none key: cord-294333-6azdm42x authors: wang, s; xie, l; xu, y; yu, s; yao, b; xiang, d title: sleep disturbances among medical workers during the outbreak of covid-2019 date: 2020-05-06 journal: occup med (lond) doi: 10.1093/occmed/kqaa074 sha: doc_id: 294333 cord_uid: 6azdm42x background: the outbreak of corona virus disease-2019 (covid-19) has posed unprecedented pressure and threats to healthcare workers in wuhan and the entire country. aims: to assess the effect of the covid-19 outbreak on the sleep quality of healthcare workers in a children’s healthcare centre in wuhan. methods: a cross-sectional, anonymized, self-reported questionnaire survey was conducted at the children’s healthcare centre of renmin hospital, wuhan university, wuhan, china. the questionnaire consisted of three parts, including socio-demographic characteristics and covid-19 epidemic-related factors, the pittsburgh sleep quality index (psqi), and zung’s self-rating anxiety scale (sas) and self-rating depression scale (sds). results: in total, 47 out of 123 (38%) participants with psqi scores > 7 were identified as having sleep disturbance. a logistic regression analysis showed that sleep disturbance was independently associated with being an only child (adjusted odds ratio (or) and 95% confidence interval (ci) 3.40 (1.21–9.57), p < 0.05), exposure to covid-19 patients (adjusted or and 95% ci 2.97 (1.08–8.18), p < 0.05) and depression (adjusted or and 95% ci 2.83 (1.10–7.27), p < 0.05). conclusions: we observed that, during the outbreak of covid-19, sleep disturbance was highly prevalent among paediatric healthcare workers, and sleep disturbance was independently associated with being an only child, exposure to covid-19 patients and depression. therefore, more mental health services are required for front-line paediatric healthcare workers in wuhan. in december 2019, an outbreak of novel coronavirus pneumonia originated in wuhan, china, and subsequently spread rapidly all over china and to many other countries and regions [1] , this outbreak has placed extraordinary demands upon healthcare systems worldwide [2] . on 11 february, the world health organization officially named the disease corona virus disease-2019 (covid19) . as of 11 february 2020, a total of 44 672 confirmed cases of covid-19 were reported, including 1716 among healthcare workers, resulting in 1023 deaths, including at least five among healthcare workers [3] . covid-19 is characterized by its efficient transmission, high risk of infection among healthcare workers and even fatal risk for healthcare workers [4] . the lack of protective materials for front-line healthcare workers further increases the risk of infection. in addition, with the rapid increase in the number of patients, healthcare workers are facing high work intensity, and most of them were not able to be reunited with their families for the spring festival, the most important traditional festival in china. there is no doubt that, in order to combat covid-19, healthcare workers have been substantially burdened. some healthcare staff may face sleep disturbance, or anxiety and depression, especially those who work in emergency, respiratory and critical care departments. according to the early epidemiological data, cases of covid-19 among children are rare [4, 5] . however, with the progress of the epidemic, it has been confirmed that the entire population is generally susceptible, and the number of paediatric patients is gradually increasing [3, 6] . paediatric healthcare workers also experience great work pressure. despite a large epidemiological literature on communicable diseases, there is little information available regarding the psychological impact on healthcare workers during the outbreak of covid-19. this study attempted to measure the psychological impact of covid-19 on the healthcare workers at a children's healthcare centre at a large teaching hospital in wuhan; in particular, this study evaluated sleep quality. a cross-sectional, anonymized, self-reported questionnaire survey was conducted at the children's healthcare centre of renmin hospital of wuhan university, wuhan, china, from 30 january to 7 february 2020. at present, the centre has 246 healthcare staff, >200 open beds and receives ~200 000 paediatric patients annually. it is one of the largest children's healthcare centres in wuhan. the questionnaire was completed by participants on their own smartphone and consisted of three parts, including socio-demographic characteristics and covid-19 epidemic-related factors, the pittsburgh sleep quality index (psqi) for evaluating sleep quality, and zung's self-rating anxiety scale (sas) and self-rating depression scale (sds) for evaluating psychological stress, which took ~10 min to complete. before the survey, the researchers explained the purpose of the study to each participant. in 1 week, 129 people completed the survey (51% of all workers). however, six questionnaires that did not provide normative key information were eliminated. in total, 123 subjects were included. the study protocol was approved by the ethics committee of renmin hospital of wuhan university. socio-demographic data were gathered on sex, age, education level, marital status, birthplace, only child status and job title. in addition, we collected some epidemic-related factors, including their current location, contact with covid-19 patients, quarantine status, current physical condition, relatives suffering from covid-19 and family reunion during the spring festival (yes/no). in our study, the psqi was employed to evaluate sleep quality [7] . the psqi is used to evaluate sleep quality in the previous month. it consists of 19 self-evaluation items and produces seven scores: sleep quality, sleep latency, sleep duration, sleep efficiency, sleep disturbance, the use of sleeping medications and daytime dysfunction. the score ranges from 0 to 3 for each dimension, and the summed score of the seven dimensions is the global score (range: 0-21) for subjective sleep quality; the higher the score, the poorer the subjective sleep quality. chinese researchers found that a psqi score > 7 cut-off point, with a high sensitivity of 98% and specificity of 90% (kappa = 0.89, p < 0.01), is suitable for chinese people [8] . in this study, a psqi score > 7 was also used to determine sleep disturbance. in terms of psychological distress, sas [9] (cronbach's α coefficient 0.897, p < 0.001) and sds [10] (cronbach's α coefficient 0.920, p < 0.001) were used to evaluate anxiety and depression. the sas and sds were compiled by william w. k. zung. the two scales have become one of the most common and convenient psychological measurement tools. the sas is a self-rating scale with 20 questions. questions 1-5 are used to evaluate the emotional symptoms of anxiety, while questions 6-20 are used to evaluate the physical symptoms of anxiety. the score for each question ranges from 1 to 4, and the total score of each item is raw scores, which is then multiplied by 1.25 to obtain the standard score; a standard score ≥50 indicates 'psychological anxiety'. the sds is what is already known about this subject: • healthcare workers in china have been substantially burdened by corona virus disease-2019. • previous studies have found that sleep disturbance is common among healthcare workers in china. • during the severe acute respiratory syndrome outbreak in 2003, studies found that healthcare staff had psychological stress, including post-traumatic stress disorder, anxiety and depression. what this study adds: • we found that 38% of paediatric healthcare workers were suffering from sleep disturbance, in addition, 7% and 25% of paediatric haealthcare workers had anxiety and depression. • seep disturbance in paediatric healthcare workers in wuhan was independently associated with depression, being an only child and contact with corona virus disease-2019 patients. what impact this may have on practice or policy: • more mental health services are required for paediatric healthcare workers in wuhan, and a larger sample survey of front-line healthcare workers is urgently needed. a self-rating scale with 20 questions, including the four dimensions of mental-emotional, physical, psychomotor disorder and psychological disorder. the score for each question ranges from 1 to 4, and the total score of each item is the raw score, which is then multiplied by 1.25 to obtain the standard score. the cut-off standard score for depression is 50, and the higher the score, the more likely one is to be depressed. statistical analysis was performed using the statistical package for social science (spss inc., version 20.0, ibm). independent t-tests for continuous variables or chi-square tests for categorical variables were used to examine the differences between healthcare workers with and without sleep disturbance. odds ratios (ors) and 95% confidence intervals (95% cis) were calculated to examine the association of sleep disturbance with socio-demographic characteristics, covid-19 epidemic-related factors and psychological stress factors using multivariate logistic regression analysis with a full entry model. initially, univariate analyses were calculated with sleep disturbance as the dependent variable and each of the potential explanatory variables as independent variables; p < 0.05 was considered statistically significant. a total of 123 healthcare workers were included in the study, including 22 (10%) male and 111 (90%) female healthcare workers, with an average age of 33.75 ± 8.41 years. table 1 compares the differences in the sociodemographic characteristics and covid-19 epidemicrelated factors between the research subjects with and without sleep disturbance. the results suggest that sleep values are n (%). percentages may not add up to 100 due to rounding. *p < 0.05; **p < 0.01; ***p < 0.001. disturbance was statistically related to job title, being an only child and contact with covid-19 patients (p < 0.05) but not to sex, age, education level, marital status, quarantine status, current health status, family reunion during the spring festival or having relatives who suffer from covid-19. the average psqi score of all research subjects was 7.22 ± 2.62; 47 (38%) participants had scores >7 and were identified as sleep disturbance. the total score of the psqi and its component scores of sleep quality, sleep latency, sleep duration, sleep efficiency and sleep disturbance in the research subjects with sleep disturbance were significantly higher than those among the subjects without sleep disturbance (p < 0.05), but there was no significant difference in the component scores of sleep disturbance or the use of sleeping medication (p > 0.05). in terms of psychological stress, the average sas score of all research subjects was 34.44 ± 7.21, and nine subjects (7%) had sas scores ≥50, while the average sds score was 45.67 ± 8.67, and 31 subjects (25%) had sds scores ≥50. these results suggest that sleep disturbance was associated with anxiety and depression (p < 0.05) ( table 2) . the factors related to sleep quality, including job title, being an only child, contact with covid-19 patients, anxiety and depression, shown in tables 1 and 2, were included in the logistic regression analysis. the results showed that being an only child (adjusted or and 95% ci 3.40 (1.21-9.57), p < 0.05), contact with covid-19 patients (adjusted or and 95% ci 2.97 (1.08-8.18), p < 0.05) and depression (adjusted or and 95% ci 2.83 (1.10-7.27), p < 0.05) were independently associated with sleep disturbance in healthcare workers (table 3 ). we observed that during the outbreak of covid-19, 38% of paediatric healthcare workers were suffering from sleep disturbance, in addition, 7% and 25% of paediatric healthcare workers had anxiety and depression. in addition, we found that the sleep disturbance in healthcare workers was independently associated with depression, being an only child and contact with covid-19 patients. to the best of our knowledge, this is the first study concerning the sleep quality of paediatric healthcare workers in wuhan, which is at the centre of the covid-19 epidemic. our results showed that 38% of the paediatric healthcare workers participating in this study suffered from sleep disturbance, which was significantly higher than in the general population or in other professional occupations, consistent with the previous research [11] [12] [13] [14] . a study in tehran found that 43% of healthcare workers had sleep disturbance [13] . a large sample (n = 5012) study found that, in china, the proportion of healthcare workers with sleep disturbance was as high as 64% [12] . the results of the above two studies are significantly higher than those of this study. we speculate that the reason for the difference may be that psqi > 7 was selected as the cut-off point in our study. in addition, our study found that some healthcare workers had obvious anxiety and depression, which is also consistent with previous studies. during the severe acute respiratory syndrome (sars) outbreak in 2003, studies in beijing [15] , taiwan [16] , hong kong [17] , singapore [18] and canada [19] found that healthcare staff had obvious psychological stress, including post-traumatic stress disorder, anxiety, depression, etc. in 2014, during the ebola epidemic in africa, researchers found that chinese healthcare workers who assisted the healthcare workers in africa also faced psychological pressure [20] . in fact, the psychological pressure on healthcare staff caused by public health emergencies is substantial, so the results are not unexpected. the results of the logistic regression analysis demonstrated that being an only child, contact with the covid-19 patients and depression were independently associated with sleep disturbance. although there was more anxiety reported among the healthcare workers with sleep disturbance than among those without sleep disturbance, the logistic regression analysis results showed that anxiety was not significantly associated with sleep disturbance in healthcare workers. however, although the difference was not statistically significant, doctors were more likely to have sleep disturbance than nurses. in china, due to the one-child policy, only children are a group with special characteristics [21] . at present, the research shows that only children have more psychological problems than non-only children. only children are more stubborn, more self-centred, lonelier, more dependent on the family and parents, less able to adapt to the social environment, and more likely to be pessimistic and have badly behaved [16, 22, 23] . not surprisingly, the only child group has suffered greater psychological distress and is more likely to develop sleep disturbance. covid-19 is highly infectious; it is mainly transmitted by respiratory droplets and close person-to-person contact and may be transmitted in the form of aerosols in a specific environment. at present, thousands of healthcare workers have been infected and some have died [3] . therefore, healthcare workers who are in contact with covid-19 patients have greater psychological distress, including depression, anxiety, sleep disturbance, etc. in addition, in the treatment and care of covid-19 patients, to avoid infection, healthcare workers need to adhere to very strict protective measures. to reduce the consumption of protective materials, they often cannot eat, drink or defecate while they are in their protective clothing, with high temperatures and negative pressure during long working hours, and the workers are physically and mentally tired, which will undoubtedly increase the risk of psychological distress in these healthcare workers. depression is prone to persistent sleep disorders, which are manifested as insomnia, difficulty falling asleep, early waking, sleep rhythm disorder and other forms. sleep time and quality are difficult to guarantee [22] . a study in taiwan found that depression, but not anxiety, was associated with sleep disturbance in local health workers, which is consistent with the results of this study [16] . these findings provide valuable information for policymakers and mental health professionals worldwide regarding the psychological impact of an infectious disease outbreak. according to a study of healthcare workers in beijing who participated in the sars epidemic in 2003 [15] , this effect still exists for a long time after the end of the epidemic. therefore, it is necessary to provide mental health services to these healthcare workers who are on the front line providing anti-epidemic therapy. there are some limitations to this study. firstly, with a cross-sectional study design and self-reported measures, our findings cannot be used to draw conclusions regarding causal relationships. the research subjects in this study were limited to a children's healthcare centre at one hospital, which may not reflect the sleep quality of all healthcare workers in wuhan, so further evidence through multicentre and large sample size research is required. in addition, the use of the sas and sds to measure anxiety and depression symptoms cannot diagnose depression and anxiety disorders. in conclusion, we observed that, during the outbreak of covid-19, sleep disturbance was highly prevalent among paediatric healthcare workers, and sleep disturbance was independently associated with being an only child, exposure to covid-19 patients and depression. therefore, it is necessary to provide more mental health services to front-line paediatric healthcare workers in wuhan, and a larger sample survey of all front-line healthcare workers is urgently needed. a novel coronavirus emerging in chinakey questions for impact assessment a novel coronavirus outbreak of global health concern clinical characteristics of 138 hospitalized patients with 2019 novel coronavirusinfected pneumonia in wuhan epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study diagnosis and treatment of 2019 novel coronavirus infection in children: a pressing issue the pittsburgh sleep quality index: a new instrument for psychiatric practice and research reliability and validity of the pittsburgh sleep quality index a rating instrument for anxiety disorders a self-rating depression scale epidemiologic study of sleep disturbances and psychiatric disorders. an opportunity for prevention? sleep disturbances among chinese clinical nurses in general hospitals and its influencing factors sleep quality among health care workers gender differences in insomnia-a study in the hong kong chinese population depression after exposure to stressful events: lessons learned from the severe acute respiratory syndrome epidemic psychological distress of nurses in taiwan who worked during the outbreak of sars severe acute respiratory syndrome (sars) in hong kong in 2003: stress and psychological impact among frontline healthcare workers psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in singapore factors associated with the psychological impact of severe acute respiratory syndrome on nurses and other hospital workers in toronto mental distress among liberian medical staff working at the china ebola treatment unit: a cross sectional study china's infamous one-child policy sleep, insomnia, and depression childhood memory and self-description in young chinese adults: the impact of growing up an only child we thank all of the participants of this study. the authors declared no conflict and interest related to this article. none declared. key: cord-304165-4f84pc83 authors: zhuang, zian; cao, peihua; zhao, shi; lou, yijun; wang, weiming; yang, shu; yang, lin; he, daihai title: estimation of local novel coronavirus (covid-19) cases in wuhan, china from off-site reported cases and population flow data from different sources date: 2020-03-02 journal: nan doi: 10.1101/2020.03.02.20030080 sha: doc_id: 304165 cord_uid: 4f84pc83 backgrounds: in december 2019, a novel coronavirus (covid-19) pneumonia hit wuhan, hubei province, china and spread to the rest of china and overseas. the emergence of this virus coincided with the spring festival travel rush in china. it is possible to estimate total number of cases of covid-19 in wuhan, by 23 january 2020, given the cases reported in other cities and population flow data between cities. methods: we built a model to estimate the total number of cases in wuhan by 23 january 2020, based on the number of cases detected outside wuhan city in china, with the assumption that if the same screening effort used in other cities applied in wuhan. we employed population flow data from different sources between wuhan and other cities/regions by 23 january 2020. the number of total cases was determined by the maximum log likelihood estimation. findings: from overall cities/regions data, we predicted 1326 (95% ci: 1177, 1484), 1151 (95% ci: 1018, 1292) and 5277 (95% ci: 4732, 5859) as total cases in wuhan by 23 january 2020, based on different source of data from changjiang daily newspaper, tencent, and baidu. from separate cities/regions data, we estimated 1059 (95% ci: 918, 1209), 5214 (95% ci: 4659, 5808) as total cases in wuhan in wuhan by 23 january 2020, based on different sources of population flow data from tencent and baidu. conclusion: sources of population follow data and methods impact the estimates of local cases in wuhan before city lock down. keyword: covid-19; mobility; pneumonia; transportation; outbreaks . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. in december 2019, a cluster of patients with pneumonia of unknown causes were reported in wuhan, hubei province, china [1] . on 7 january 2020, a novel coronavirus, named covid-19, was identified as the cause of this outbreak [2] . this covid-19 virus shares the common characteristics of coronavirus and is expected to become more virulent when establishing efficient human-to-human transmission [3] . the emergence of this virus coincided with the spring festival travel rush in china. it was estimated that there would be around 3 billion trips made in china during the period of 10 january to 18 february 2020 [4] . some researchers have pointed out the risk of regional and global disease spreading during the spring festival travel rush [5] . however, due to the small number of severe patients reported by mid-january and most cases were linked to the huanan . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . seafood market of wuhan city, neither international nor regional travelling restrictions were implemented to wuhan at the early stage of this outbreak. on 13 january 2020, the first exported case from wuhan was reported in thailand and the case numbers dramatically increased after the diagnostic kits became available in mid-january. as of 23 february 2020, there were 77042 laboratory confirmed cases and 2445 deaths (46.93% and 75.91% in wuhan) [6] . in recognition of a wide-spreading outbreak, the government has suspended all public transportations inside wuhan city since 23 january 2020, and some regional travelling restrictions were also implemented by other cities [3] . at early stage of this outbreak, the cases might have been seriously underreported due to the lack of diagnostic kits and insufficient screening for all suspected cases. several efforts have been made to estimate the case numbers using different modelling approaches, and the estimates range from 1732 to 4000 during the period of 17-20 january [7, 8, 9] . in this study, we aimed to estimate the number of covid-19 cases in wuhan, utilizing the cases exported to other large cities of mainland china and different sources of the population flow data between wuhan and these cities. the estimates were made by 23 january 2020 (before the suspension of public transportations in wuhan). we assumed that the exported cases were less likely underreported, as stringent temperature screening was implemented at airports and railway stations. we compare these estimates to daily numbers of confirmed cases exported from wuhan in surveillance data to evaluate the extent of underreporting. we obtained daily number of inbound and outbound domestic passengers travelling by air, train or road to/from wuhan from three data sources: . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.02.20030080 doi: medrxiv preprint 2) baidu map database (see: https://qianxi.baidu.com/). according to location data of baidu's mobile software users, population flow number from 1 to 20 january 2020 was generated, between wuhan and twenty-seven cities/regions (anhui, beijing, chongqing, fujian, gansu, guangdong, guangxi, guizhou, hainan, hebei, heilongjiang, henan, hunan, hubei(outside wuhan), jiangsu, jiangxi, jilin, liaoning, ningxia, shandong, shanghai, shanxi, shannxi, sichuan, tianjin, yunnan, zhejiang). 3) the news platform. it has reported that there were 4.1 million outbound passengers from wuhan in the first ten days of the spring festival travel rush (10-19 january 2020) via railways, highways and airways [10] . we equally divided the data to get an average daily population flow. as shown in fig 1, we also collected daily numbers of exported cases from wuhan to other cities in china, and all secondary cases of family or hospital clusters were excluded from analysis [11] . eight cases from guangdong were excluded due to the lack of traveling history to hubei prior to illness onset. as for rest 371 cases that not specified as secondary case, we assume that the probability of a single case being an imported case is θ , and each case is independent from each other. then all of these unspecified cases follow a binomial distribution (n, θ ), where θ represents the probability that a case is exported from wuhan. since the most cases detected outside wuhan are imported cases, by 23 january 2020 [12] , we estimated daily numbers of imported covid-19 cases from wuhan based on different level of probability θ (1,0.9,0.8), see table s1 in appendix. binomial distribution [7], as in eqn (1), where n is total number of cases and p is probability of finding any cases overseas. the probability p can be derived from dividing daily outbound international passengers of wuhan by the population size that the wuhan airport serves and multiplying by the average time of case discovery, see eqn (2). similarly, we used exported cases from wuhan to predict numbers of local imported covid-19 cases. we assumed a population of 19 million (catchment population) travelling through the airport, railway stations and highways in wuhan, and a 10-day delay on average, which accounted for the . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint apart from predict number of covid-19 cases through overall data, we also tried to forecast number of covid-19 cases base on separate city/region's data since more details may convey more information. a parameter λ was set as total covid-19 cases. based on the data obtained from each city/region, we estimated the λ , which is the most likely to make these results appear by calculating maximum of log-likelihood. in equation (3), is the total log-likelihood. the k represents the total number of cities/regions calculated. the n, p represents the number of cases reported overseas and probability of finding any cases overseas respectively. after obtaining λ , since residuals of log maximum likelihood estimation follows chi-square distribution [13] , 95% confidence intervals (95% ci) of log-likelihood, l, can be calculated. then we can extrapolate a 95% ci about covid-19 cases. in addition, we analyze the correlation between the two data sources. we found that pearson as for separate cities/regions data, based on different data sources, we summed the total population flow from wuhan to other cities/regions and the total number of cases in those cities. then we estimate total number and 95% confidence interval (95% ci) about covid-19 cases. we predicted 1326 (95% ci: 1177, 1484), 1151 (95% ci: 1018, 1292) and 5277 (95% ci: 4732, 5859) as total cases in wuhan by 23 january, based on different source of data, see table 1 . as for separate cities/regions data, we estimated total number of cases, λ , by using the maximum log-likelihood estimation (mle) approach based on the population flow data from tencent and baidu, see fig 2 (a,b) . then we estimated 95% confidence interval (95% ci) about covid-19 cases. we predicted 1059 (95% ci: 918, 1209), 5214 (95% ci: 4659, 5808) as total cases in wuhan by 23 january 2020, based on different sources of population flow data, see table 2 . . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint [7, 9] . this is partly because the screening effort targeting population from wuhan in other cities is much more effective than the local screening effort in wuhan due to the worsen situation. based on three different sources of population flow data, we generated the total covid-19 cases prediction closest to the official report through tencent data. baidu data provided closest result to the forecast by imai et al. [8] . meanwhile, in sensitivity analysis, table 1 and table 2 show that slight fluctuations of probability that a case is exported from wuhan will have little impact on the forecast. estimates of the population outflow provided by news, baidu and tencent show substantial fluctuation, resulting in wide predictions. we found that baidu and tencent data show significant linear relation, which verified each other that the general pattern of data is reasonable. after simple linear transformation, two sets of data become similar (see fig 3) . further expanding the scope of epidemic monitoring, the gap between the estimated number and official reported cases will be further narrowed. according to our results, statistics of population flow also play significant roles in prediction. at present, many researches use data from baidu and . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.02.20030080 doi: medrxiv preprint tencent platforms [9, 15, 16] . it is not clear which data source can be used to make the most accurate prediction yet, while it is possible for forecasts based on a single data source to be inaccurate. to sum up, it is necessary to make a comprehensive analysis based on different statistics before reaching any conclusions. population flow data were used in estimating the size of the epidemic of covid-19 in wuhan, china before the lock down. we found that population flow data from different sources may lead to significantly different estimates, although all estimates suggested much larger sizes than officially reported. using cases reported off-site to estimate the size (course) of the epidemic in the epicenter is a common technique and will be used in future epidemics, especially when the epicenter lacks medical resources thus cases are under-reported. we argue that reliability of estimates of population flow data should be taken into consideration. the ethical approval or individual consent was not applicable. all data and materials used in this work were publicly available. not applicable. disclaimer . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.02.20030080 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.02.20030080 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.02.20030080 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. a novel coronavirus from patients with pneumonia in china a novel coronavirus outbreak of global health concern. the lancet in 2020, the national passenger volume of spring festival transportation will reach about 3 billion person times pneumonia of unknown etiology in wuhan, china: potential for international spread via commercial air travel real time epidemic data', released on 23 february 2020 by estimation of epidemiological parameters and epidemic predictions nowcasting and forecasting the wuhan 2019-ncov outbreak preprint published by the school of public health of the university of hong kong wuhan has sent more than 4 million passengers by railways, highways and airlines and 80 million passengers by public transport situation report of the pneumonia cases caused by the novel coronavirus by the national health commission of each province of people's republic of china risk for transportation of 2019 novel coronavirus (covid-19) from wuhan to cities in china the large-sample distribution of the likelihood ratio for testing composite hypotheses. the annals of mathematical statistics report of hubei provincial health committee on pneumonia caused by new coronavirus' released on 24 january 2020 by health commission of hubei province population movement, city closure and spatial transmission of the 2019-ncov infection in china the impact of traffic isolation in wuhan on the spread of 2019-ncov author/funder, who has granted medrxiv a license to display the preprint in perpetuity . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. key: cord-266963-belin2jq authors: cowling, benjamin j; leung, gabriel m title: epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-ncov) outbreak date: 2020-02-13 journal: euro surveill doi: 10.2807/1560-7917.es.2020.25.6.2000110 sha: doc_id: 266963 cord_uid: belin2jq nan it is now 6 weeks since chinese health authorities announced the discovery of a novel coronavirus (2019-ncov) [1] causing a cluster of pneumonia cases in wuhan, the major transport hub of central china. the earliest human infections had occurred by early december 2019, and a large wet market in central wuhan was linked to most, but not all, of the initial cases [2] . while evidence from the initial outbreak investigations seemed to suggest that 2019-ncov could not easily spread between humans [3] , it is now very clear that infections have been spreading from person to person [2] . we recently estimated that more than 75,000 infections may have occurred in wuhan as at 25 january 2020 [4] , and increasing numbers of infections continue to be detected in other cities in mainland china and around the world. a number of important characteristics of 2019-ncov infection have already been identified, but in order to calibrate public health responses we need improved information on transmission dynamics, severity of the disease, immunity, and the impact of control and mitigation measures that have been applied to date. infections with 2019-ncov can spread from person to person, and in the earliest phase of the outbreak the basic reproductive number was estimated to be around 2.2, assuming a mean serial interval of 7.5 days [2] . the serial interval was not precisely estimated, and a potentially shorter mean serial interval would have corresponded to a slightly lower basic reproductive number. control measures and changes in population behaviour later in january should have reduced the effective reproductive number. however, it is too early to estimate whether the effective reproductive number has been reduced to below the critical threshold of 1 because cases currently being detected and reported would have mostly been infected in mid-to late-january. average delays between infection and illness onset have been estimated at around 5-6 days, with an upper limit of around 11-14 days [2, 5] , and delays from illness onset to laboratory confirmation added a further 10 days on average [2] . chains of transmission have now been reported in a number of locations outside of mainland china. within the coming days or weeks it will become clear whether sustained local transmission has been occurring in other cities outside of hubei province in china, or in other countries. if sustained transmission does occur in other locations, it would be valuable to determine whether there is variation in transmissibility by location, for example because of different behaviours or control measures, or because of different environmental conditions. to address the latter, virus survival studies can be done in the laboratory to confirm whether there are preferred ranges of temperature or humidity for 2019-ncov transmission to occur. in an analysis of the first 425 confirmed cases of infection, 73% of cases with illness onset between 12 and 22 january reported no exposure to either a wet market or another person with symptoms of a respiratory illness [2] . the lack of reported exposure to another ill person could be attributed to lack of awareness or recall bias, but china's health minister publicly warned that pre-symptomatic transmission could be occurring [6] . determining the extent to which asymptomatic or pre-symptomatic transmission might be occurring is an urgent priority, because it has direct implications for public health and hospital infection control. data on viral shedding dynamics could help in assessing duration of infectiousness. for severe acute respiratory syndrome-related coronavirus (sars-cov), infectivity peaked at around 10 days after illness onset [7] , consistent with the peak in viral load at around that time [8] . this allowed control of the sars epidemic through prompt detection of cases and strict isolation. for influenza virus infections, virus shedding is highest on the day of illness onset and relatively higher from shortly before symptom onset until a few days after onset [9] . to date, transmission patterns of 2019-ncov appear more similar to influenza, with contagiousness occurring around the time of symptom onset, rather than sars. transmission of respiratory viruses generally happens through large respiratory droplets, but some respiratory viruses can spread through fine particle aerosols [10] , and indirect transmission via fomites can also play a role. coronaviruses can also infect the human gastrointestinal tract [11, 12] , and faecal-oral transmission might also play a role in this instance. the sars-cov superspreading event at amoy gardens where more than 300 cases were infected was attributed to faecal-oral, then airborne, spread through pressure differentials between contaminated effluent pipes, bathroom floor drains and flushing toilets [13] . the first large identifiable superspreading event during the present 2019-ncov outbreak has apparently taken place on the diamond princess cruise liner quarantined off the coast of yokohama, japan, with at least 130 passengers tested positive for 2019-ncov as at 10 february 2020 [14] . identifying which modes are important for 2019-ncov transmission would inform the importance of personal protective measures such as face masks (and specifically which types) and hand hygiene. the first human infections were identified through a surveillance system for pneumonia of unknown aetiology, and all of the earliest infections therefore had modelling studies incorporating healthcare capacity and processes pneumonia. it is well established that some infections can be severe, particularly in older adults with underlying medical conditions [15, 16] , but based on the generally mild clinical presentation of 2019-ncov cases detected outside china, it appears that there could be many more mild infections than severe infections. determining the spectrum of clinical manifestations of 2019-ncov infections is perhaps the most urgent research priority, because it determines the strength of public health response required. if the seriousness of infection is similar to the 1918/19 spanish influenza, and therefore at the upper end of severity scales in influenza pandemic plans, the same responses would be warranted for 2019-ncov as for the most severe influenza pandemics. if, however, the seriousness of infection is similar to seasonal influenza, especially during milder seasons, mitigation measures could be tuned accordingly. beyond a robust assessment of overall severity, it is also important to determine high risk groups. infections would likely be more severe in older adults, obese individuals or those with underlying medical conditions, but there have not yet been reports of severity of infections in pregnant women, and very few cases have been reported in children [2] . those under 18 years are a critical group to study in order to tease out the relative roles of susceptibility vs severity as possible underlying causes for the very rare recorded instances of infection in this age group. are children protected from infection or do they not fall ill after infection? if they are naturally immune, which is unlikely, we should understand why; otherwise, even if they do not show symptoms, it is important to know if they shed the virus. obviously, the question about virus shedding of those being infected but asymptomatic leads to the crucial question of infectivity. answers to these questions are especially pertinent as basis for decisions on school closure as a social distancing intervention, which can be hugely disruptive not only for students but also because of its knock-on effect for child care and parental duties. very few children have been confirmed 2019-ncov cases so far but that does not necessarily mean that they are less susceptible or that they could not be latent carriers. serosurveys in affected locations could inform this, in addition to truly assessing the clinical severity spectrum. another question on susceptibility is regarding whether 2019-ncov infection confers neutralising immunity, usually but not always, indicated by the presence of neutralising antibodies in convalescent sera. some experts already questioned whether the 2019-ncov may behave similarly to mers-cov in cases exhibiting mild symptoms without eliciting neutralising antibodies [17] . a separate question pertains to the possibility of antibody-dependent enhancement of infection or of disease [18, 19] . if either of these were to be relevant, the transmission dynamics could become more complex. a wide range of control measures can be considered to contain or mitigate an emerging infection such as 2019-ncov. internationally, the past week has seen an increasing number of countries issue travel advisories or outright entry bans on persons from hubei province or china as a whole, as well as substantial cuts in flights to and from affected areas out of commercial considerations. evaluation of these mobility restrictions can confirm their potential effectiveness in delaying local epidemics [20] , and can also inform when as well as how to lift these restrictions. if and when local transmission begins in a particular location, a variety of community mitigation measures can be implemented by health authorities to reduce transmission and thus reduce the growth rate of an epidemic, reduce the height of the epidemic peak and the peak demand on healthcare services, as well as reduce the total number of infected persons [21] . a number of social distancing measures have already been implemented in chinese cities in the past few weeks including school and workplace closures. it should now be an urgent priority to quantify the effects of these measures and specifically whether they can reduce the effective reproductive number below 1, because this will guide the response strategies in other locations. during the 1918/19 influenza pandemic, cities in the united states, which implemented the most aggressive and sustained community measures were the most successful ones in mitigating the impact of that pandemic [22] . similarly to international travel interventions, local social distancing measures should be assessed for their impact and when they could be safely discontinued, albeit in a coordinated and deliberate manner across china such that recrudescence in the epidemic curve is minimised. mobile telephony global positioning system (gps) data and location services data from social media providers such as baidu and tencent in china could become the first occasion when these data inform outbreak control in real time. at the individual level, surgical face masks have often been a particularly visible image from affected cities in china. face masks are essential components of personal protective equipment in healthcare settings, and should be recommended for ill persons in the community or for those who care for ill persons. however, there is now a shortage of supply of masks in china and elsewhere, and debates are ongoing about their protective value for uninfected persons in the general community. the table summarises research gaps to guide the public health response identified. in conclusion, there are a number of urgent research priorities to inform the public health response to the global spread of 2019-ncov infections. establishing robust estimates of the clinical severity of infections is probably the most pressing, because flattening out the surge in hospital admissions would be essential if there is a danger of hospitals becoming overwhelmed with patients who require inpatient care, not only for those infected with 2019-ncov but also for urgent acute care of patients with other conditions including those scheduled for procedures and operations. in addressing the research gaps identified here, there is a need for strong collaboration of a competent corps of epidemiological scientists and public health workers who have the flexibility to cope with the surge capacity required, as well as support from laboratories that can deliver on the ever rising demand for diagnostic tests for 2019-ncov and related sequelae. the readiness survey by reusken et al. in this issue of eurosurveillance testifies to the rapid response and capabilities of laboratories across europe should the outbreak originating in wuhan reach this continent [23] . in the medium term, we look towards the identification of efficacious pharmaceutical agents to prevent and treat what may likely become an endemic infection globally. beyond the first year, one interesting possibility in the longer term, perhaps borne of wishful hope, is that after the first few epidemic waves, the subsequent endemic re-infections could be of milder severity. particularly if children are being infected and are developing immunity hereafter, 2019-ncov could optimistically become the fifth human coronavirus causing the common cold. none declared. a pneumonia outbreak associated with a new coronavirus of probable bat origin early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in wuhan, china, as 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pandemic in u.s. cities laboratory readiness and response for novel coronavirus (2019-ncov) in expert laboratories in 30 european union/european economic area countries wrote first draft: bjc. critically revised draft and approved final version: bjc and gml. this is an open-access article distributed under the terms of the creative commons attribution (cc by 4.0) licence. you may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made.any supplementary material referenced in the article can be found in the online version. key: cord-292144-jprbp1ua authors: song, haitao; li, feng; jia, zhongwei; jin, zhen; liu, shengqiang title: using traveller-derived cases in henan province to quantify the spread of covid-19 in wuhan, china date: 2020-08-04 journal: nonlinear dyn doi: 10.1007/s11071-020-05859-1 sha: doc_id: 292144 cord_uid: jprbp1ua wuhan shutdown was implemented on january 23 and the first level response to public health emergencies (flrphe) was launched over the country, and then china got the outbreak of covid-19 under control. a mathematical model is established to study the transmission of covid-19 in wuhan. this research investigates the spread of covid-19 in wuhan and assesses the effectiveness of control measures including the wuhan city travel ban and flrphe. based on the dynamical analysis and data fitting, the transmission of covid-19 in wuhan is estimated and the effects of control measures including wuhan city travel ban and flrphe are investigated. according to the assumptions, the basic reproduction number for covid-19 estimated that for wuhan equal to 7.53 and there are [formula: see text] infectious people in wuhan as of january 23. the interventions including the wuhan city travel ban and flrphe reduce the size of peak and the cumulative number of confirmed cases of covid-19 in wuhan by 99%. the extraordinary efforts implemented by china effectively contain the transmission of covid-19 and protect public health in china. in december 2019, the novel coronavirus pneumonia case was reported in wuhan, a metropolis with a population of 14.1865 million. on 20 january 2020, humanto-human transmission of the novel corona virus disease 2019 (covid-19) was confirmed [1, 2] . by january 23, 2020, 495 confirmed cases and 23 deaths were reported. however, no vaccine and special medicine are used to treat the patients of covid-19. then, a series of control measures were implemented to prevent and control the transmission of covid-19. to stop the further dispersal of covid-19 from wuhan to other cities, wuhan shutdown was implemented to limit movement of people in and out of wuhan on jan-uary 23, 2020 [3] , which is the most stringent quarantine measures for a metropolis with a population of over 10 million in human history. on the same day, the first-level response to public health emergencies (flrphe) [4] was launched in hubei province. after the wuhan shutdown, confirmed and suspected cases are quarantined, crowds are stopped, close contracts are tracked and isolated at home, public transport, schools and entertainment places are closed, floating population are managed and information and hygienic knowledge are released. the control measures implemented provide lessons for other countries or regions to prevent and control the transmission of covid-19. mathematical modelling could be used particularly to investigate the transmission of diseases such as covid-19, and can also dynamically forecast the development trend of diseases based on the previous information [5] [6] [7] . using the number of cases detected outside mainland china, imai et al. [8] estimated the number of cases in wuhan city by 18th january. wu et al. [9] posed a transmission dynamics model of covid-19 in wuhan and estimated the overall symptomatic case fatality risk. song et al. [10] developed a mathematical model base on the epidemiology of covid-19, computed the basic reproduction number, predicted the final size of covid-19 in china, and investigated the effects of isolation of healthy people, confirmed cases and close contacts on the transmission of covid-19 in china. tang et al. [11] assessed the transmission risk of covid-19 in china and showed the effect of interventions on the transmission of covid-19. although the spread of covid-19 in wuhan has been largely studied [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] , the transmission patterns of covid-19 and the effectiveness of interventions are unclear [2] . thus, a quantitative analysis is implemented to study the spread of covid-19 before wuhan shutdown and assess the effectiveness of control measures including the wuhan city travel ban and flr-phe in wuhan. reports provide the evidence that public health systems in wuhan were unable to bear a heavy burden, which led to many unconfirmed cases of covid-19 [12] . therefore, the spread of covid-19 in wuhan is estimated using traveller data from wuhan to henan province. this method is used to estimate the cumulative number of cases based on two assumptions which are that 100% detection in travellers after arrival over the destination and the same infection rate between travellers and residents in wuhan. to estimate the spread of covid-19 by january 23 and assess the effectiveness of control measures including the wuhan city travel ban and flrphe, a mathematical model with immigration from wuhan to henan province is built. using the mathematical model, the size of the epidemic on january 23 is estimated, the peak time and value, and the cumulative number of cases without interventions including wuhan city travel ban and flrphe are simulated, and the effectiveness of interventions is assessed. the paper is organized as follows. the mathematical model and dynamics analysis are shown in sect. 2. section 3 gives the estimation of the parameters. the effects of control measures including the wuhan city travel ban and flrphe are investigated in sect. 4 . section 5 provides the discussion and conclusion. the mathematical model is used to estimate the epidemic of covid-19 in wuhan. the 6th edition treatment of novel coronavirus pneumonia [23] and report of the who-china joint mission on covid-19 [24] imply that most people are susceptible and the infected people in the incubation period has infectiv-ity. susceptible people are infected by infectious people and become infected people. the patients go to the hospital and are diagnosed. finally, the patients removed from the hospital. the imported cases in henan province are used to estimate the spread of covid-19 in wuhan. then, the population of wuhan (n ) is divided into susceptible people (s 1 ), unfound infectious people (i 1 ), found infectious people (h 1 ) and removed people (r 1 ), respectively. the population of imported cases in henan province from wuhan is divided into unfound infectious people (i 2 ), found infectious people (h 2 ) and removed people (r 2 ), respectively. in the model, the following assumptions are given. the natural birth and death rates are not incorporated into the model due to that the short period span is considered. the unfound infectious people has the same infectivity. the transmission of covid-19 in henan province is not considered. the susceptible people and unfound infectious people can travel from wuhan to other places, and found infectious people and removed people cannot travel from wuhan to other places by january 23. in this study, the effects of control measures including the wuhan city travel ban and flrphe since january 23 are investigated. the imported cases from wuhan to henan province were detected from january 4 to february 14. therefore, the initial time is chosen as january 4 and the twentieth day corresponds to january 23. based on the epidemiological pattern of covid-19 and previous work [12, 13] , the transmission dynamics of covid-19 is established by the following equations (the flow diagram is shown in fig. 1 ): where β is the transmission rate, γ 1 and γ 2 denote the discovery rates of infectious people, and δ 1 and δ 2 are the removed rates. according to the real data [21], the imported cases per day from wuhan to henan province satisfy the normal distribution function ω(t), where u is the expectation and σ is the standard deviation, and b is the proposition of outflow of infectious people from wuhan to henan province per day. θ is an emigration coefficient ratio of infectious people from wuhan based on the imported cases from wuhan to henan province. μ (μ 1 ) is the emigration rate of susceptible people from wuhan to other places. μ (b) is μ 1 (b 1 ) before january 23 and 0 after january 23 because that wuhan city travel was banned on january 23. this model is supplemented by the initial values theorem 2.1 for system (1) with initial values (2), the solutions system (1) are nonnegative and ultimately bounded. proof using the theorem 5.2.1 in [25] , the nonnegativeness of s 1 (t), from the first equation of system (1), define a lyapunov function obviously, f(t) ≥ 0(∀t ≥ 0). then, differentiating f(t) along the solutions of system (1) leads to then, and r 2 (t) are ultimately bounded. the proof is completed. since that ω(t) varies as time goes on, then ω(t) is reduced the mean value ω in the theoretical analysis. using the next-generation matrix theory [26, 27] , the basic reproduction number in wuhan is computed as in the following, the stability of the disease-free equilibrium point e 0 would be analyzed. proof since the stability of r 1 (t), i 2 (t), h 2 (t) and r 2 (t) are determined by s 1 (t), i 1 (t) and h 1 (t), it is sufficient to analyze the dynamics of the system with s 1 (t), i 1 (t) and h 1 (t), then system (1) reduces the following differential equations now the jacobian matrix of system (3) at the diseasefree equilibrium point e 0 is then, the characteristic equation (4) have negative real parts. therefore, the diseasefree equilibrium point e 0 is locally asymptotically stable. now the global stability of the disease-free equilibrium point e 0 is proved. define a lyapunov function obviously, l(t) ≥ 0(∀t ≥ 0). then, differentiating l(t) along the solutions of system (3) leads to if r 0 < 1, then l (t) ≤ 0. based on the above discussions, the largest compact invariant set in {l (t) = 0} is the singleton {e 0 }. using the lasalle invariance principle [28] and the local stability of e 0 , the diseasefig. 2 . in this case, the susceptible people will vanish as time goes on. removed people r 1 and r 2 approach to r * 1 and r * 2 , respectively. case 2: μ = 0. setting the parameter β = 0.1, γ 1 = 0.09, θ = 16.7, ω = 0.009, γ 2 = 0.1, δ 1 = 0.05, δ 2 = 0.1 and initial value (s 1 (0), 100, 10, 0, 0, 0, 0, 0) . the time series of variables in system (1) are shown in fig. 3 . in this case, the variable s 1 (t) converges to s * 1 , removed people r 1 and r 2 approach to r * 1 and r * 2 , and other variables tend to zero. as of january 19, 2020, the epidemiological investigation of 198 confirmed cases by the chinese center for disease control and prevention (cdc) [22] showed that 22% of patients (43 cases) had direct exposure to the huanan seafood wholesale market which was closed on january 1, 2020. since it was difficult to trace all infections of covid-19 in wuhan, 82 cases of covid-19 in wuhan (twice of 41 cases in our baseline scenario) by a constant zoonotic force of infection are assumed. for sensitivity analysis, 123 and 164 cases (twice and triple higher than the baseline scenario value) are assumed. the imported cases are people who have travel history from wuhan to henan province. the active track of imported cases from wuhan to henan province was traced in detail. these data provide the date of arrival at henan province, date of symptoms onset, date of confirmation, the time between arrival and symptoms onset, the time between symptoms onset and confirmation, and time of treatment. during the spring festival from january 21 to february 2, 2019, there was an average outflow of 5.2 million people from wuhan before the chinese lunar new year. in 2020, about 5 million people travelled out of wuhan before january 23 (a) the second scenario: the initial infectious people are twice higher than our baseline scenario value; (b) the third scenario: the initial infectious people are triple higher than our baseline scenario value which is the time of wuhan city travel ban. the average number of travellers from wuhan between january 4 and january 23 was obtained from the baidu migration data [31] , where the first imported cases from wuhan to henan province arrived at henan province on january 4, 2020. then, estimation of the average proposition of daily travel volume from wuhan was given and about 0.3 million people travelled from wuhan to henan province between january 4 and january 23, 2020. the average proposition of daily exported cases from wuhan to other places was computed based on the imported cases and the number of travellers from wuhan to henan province and the number of travellers out of wuhan between january 4 and january 23, 2020. these data used are from publicly available data sources. wuhan is a metropolis with a population of 14.1865 million including 9.0935 million permanent population and 5.103 million floating population. the cumulative number of cases in wuhan before january 23, 2020 is estimated based on the confirmed cases exported to henan province from january 4 (the arrival time of the first imported case from wuhan to henan province) to january 23. according to the data of imported cases from wuhan to henan province [21], the time between arrival and symptoms onset is defined as the mean incubation period which is 7.9 days, the time between arrival and confirmation is 10.6 days (γ 2 = 1 10.6 ), and time of treatment in henan province is 10 days (δ 2 = 1 10 ), respectively. since about 5 million people travelled out of wuhan before january 23 and about 0.3 million people travelled from wuhan to henan province between january 4 and january 23, then the proposition of emigration of susceptible people from wuhan to other places per day is 0.0018 (μ 1 = 0.0018), and the emigration coefficient ratio of infectious people from wuhan to other places is 50 3 (θ = 50 3 ). the initial values on january 4 are s 1 (0) = 14.1865 * 10 6 , h 1 (0) = 41, r 1 (0) = i 2 (0) = h 2 (0) = r 2 (0) = 0, and i 1 (0) is defined in table 1 . based on the mathematical model and the cumulative number of confirmed cases, using markov chain monte carlo (mcmc) method employing the adaptive metropolis-hasting algorithm with 20,000 iterations and a 10,000 iteration burn-in period [32] , parameter values β, b 1 , γ 1 , δ 1 , u and σ are estimated for three different scenarios. furthermore, the mean value, standard deviation (std) and 95% confidence interval (95% ci) are given in table 1 for three different scenarios. therefore, the basic reproduction number of three different scenarios are 7.53, 6.27 and 6.35, respectively. regarding the uncertainty of estimated parameter values, the mcmc method is used to assess the performance of our model using the estimated parameter values in table 1 . in the baseline scenario, fig. 4 displays the estimated cumulative number of imported people and real data from wuhan to henan province, and shows the 95% confidence interval of simulation results. it is obvious that our simulations are consistent with the real data, which verifies the exactitude of our model. simulation results for the cumulative number of confirmed cases by january 23 for three different scenarios are given in figs. 5, 6 and 7. in the baseline scenario, fig. 5 shows that the cumulative number of cases of covid-19 in wuhan arrives at 4.718 × 10 4 as of january 23, 2020. if the initial infectious cases by zoonotic force of infection were twice higher than our baseline scenario value, fig. 6 reveals that the cumulative number of cases of covid-19 in wuhan is 3.828 × 10 4 as of january 23, 2020, which means that the cumulative number of cases of covid-19 would be 19% lower than the baseline scenario. if the initial infectious cases by zoonotic force of infection were triple higher than our baseline scenario value, fig. 7 indicates that the cumulative number of cases of covid-19 in wuhan was 4.595 × 10 4 as of january 23, 2020, which means that the cumulative number of cases of covid-19 would be 2.6% lower than the baseline scenario. fig. 8 in the baseline scenario, simulation results of the spread of covid-19 in wuhan without interventions (february 9), 2020, and the cumulative number of cases of covid-19 in wuhan would arrive 8.83×10 6 (8.46× 10 6 and 8.49 × 10 6 ) in the baseline scenario (twice and triple higher than the baseline scenario value), which means that the peak time is consistent with the real data, but interventions including wuhan city travel ban and flrphe reduce peak value and the cumulative number of cases of covid-19 by about 99%. since the first case of covid-19 was reported in wuhan in december 2019, covid-19 has spread rapidly over all provinces in china and caused 50,008 reported cases and 2574 deaths in wuhan by april 13. in our study, a mathematical model of the covid-19 transmission was established. based on the dynamical analysis and data fitting, the estimated basic reproduction number is 7.53 and the estimated cumulative number of cases of covid-19 reaches 4.718 × 10 4 in wuhan as of january 23, 2020 which is greater than the cases reported due to the difficulties of tracing all infections and lack of sufficient medical resources. the basic reproduction number estimated is consistent with the value in [33] , where a median value r 0 of 5.7 (95% ci: 3.8-8.9) is calculated, which means that the epidemic was very serious in wuhan. the cumulative number of cases estimated in our study is greatly less than the epidemic size estimated in [12] which overestimated the epidemic size of covid-19 in wuhan by january 23, 2020. therefore, our results truly reflect the spread of covid-19 in wuhan as of january 23, 2020 since the imported cases in henan province from wuhan were traced in detail. furthermore, the interventions including wuhan city travel ban and flrphe reduce the peak value and the cumulative number of cases of covid-19 in wuhan by over 99%. the interventions effectively contained the spread of covid-19 and protected public health all over the world [3, 34] . the interventions implemented by china have provided lessons for other countries to prevent and control the transmission of covid-19. in our study, there are two assumptions on the estimation of the epidemic size of covid-19 in wuhan. the first assumption is that the detection rate of imported cases in henan province is 100% sensitive. when our model is correct, the epidemic size of covid-19 in wuhan as of january 23, 2020 is estimated using the lower bound of detection rate since that the imported infectious people including asymptomatic patients or low severity cases were not detected. the second assumption is the same infection rate between travellers and residents in wuhan. according to the discussions in [13] , the true prevalence between travellers and residents might be different due to that the people visiting few individuals produced fewer infections and some visitors have less exposure to the infection than residents for a short time. however, the transmission of covid-19 in henan province was not considered in our model which incorporated the transmission of covid-19 in wuhan and imported cases in henan province from wuhan. the mathematical modelling used in our study is similar with the work to model the epidemic dynamics of covid-19 [8, 9, [14] [15] [16] [17] [18] . the mathematical model with emigration from wuhan to henan province provides support for our estimation of the epidemic size of covid-19 in wuhan and the assessment of interventions using the imported cases and baidu migration data. nevertheless, our study has some limitations. first, the epidemic size of covid-19 in wuhan was estimated using the imported cases in henan province which might not completely reflect all exported cases from wuhan. second, the other interventions were not considered and incorporated into our model, which might overestimate the epidemic size in wuhan as of january 23, 2020. third, whether the transmission of covid-19 was influenced by temperature and precipitation or not, the related study could not be found out. although covid-19 has been under control in china, the normal production and life return to the previous status. but the epidemic of covid-19 in the world is very serious and the imported cases from overseas continue to appear, which leads to an increase in the transmission risk of covid-19 in china. therefore, people must maintain vigilance against the potential second epidemic of covid-19 in china [10, 35] . a novel coronavirus from patients with pneumonia in china a novel coronavirus outbreak of global health concern covid-19 control in china during mass population movements at new year tibet activates 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covid-19 monotone dynamical systems: an introduction to the theory of competitive and cooperative systems: an introduction to the theory of competitive and cooperative systems on the definition and the computation of the basic reproduction ratio r 0 in models for infectious diseases in heterogeneous populations reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission philadephia (1976) 29. national health commission of the people's republic of china world health organization (who): coronavirus disease (covid-2019) situation reports baidu migration data dram: efficient adaptive mcmc high contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2 the effect of human mobility and control measures on the covid-19 epidemic in china modelling covid-19 transmission: from data to intervention conflict of interest the authors declare that they have no conflict of interest. key: cord-297552-n4uvsi3v authors: zou, li; dai, lijun; zhang, yangyang; fu, wenning; gao, yan; zhang, zhaohui; zhang, zhentao title: clinical characteristics and risk factors for disease severity and death in patients with coronavirus disease 2019 in wuhan, china date: 2020-08-13 journal: front med (lausanne) doi: 10.3389/fmed.2020.00532 sha: doc_id: 297552 cord_uid: n4uvsi3v objective: to describe the clinical manifestations and outcomes of covid-19, and explore the risk factors of deterioration and death of the disease. methods: in this retrospective study, we collected data from 121 covid-19 cases confirmed by rt-pcr and next-generation sequencing in renmin hospital of wuhan university from january 30, 2019, to march 23, 2020, and conducted statistical analysis. results: a total of 121 patients were included in our study, the median age was 65 years (iqr, 55.0–71.5 years), and 54.5% cases were men. among those cases, 52 (43.0%) cases progressed to severe, and 14 (11.6%) died. overall, the most common manifestations were fever (78.5%) and respiratory symptoms (77.7%), while neurological symptoms were found in only 9.9% of the patients. 70.2% of all the cases had comorbidities, including hypertension (40.5%) and diabetes (20.7%). on admission, cases usually show elevated levels of neutrophils (27.3%), d-dimer (72.6%), interleukin-6 (35.2%), interleukin-10 (64.4%), high-sensitivity c-reactive protein (82.6%), and lactate dehydrogenase (62.0%), and decreased levels of lymphocytes (66.9%), cd3 cells (67.2%), and cd4 cells (63.0%). the proportional hazard cox models showed that the risk factors for severity progression and death included comorbidities (hr: 4.53, 95% ci: 1.78–11.55 and hr: 7.81, 95% ci: 1.02–59.86), leukocytosis (hr: 1.13; 95% ci: 1.05–1.22 and hr: 1.25, 95% ci: 1.10–1.42), neutrophilia (hr: 1.15, 95% ci: 1.07–1.13 and hr: 1.28, 95% ci: 1.13–1.46, and elevated ldh (hr: 1.14, 95% ci: 1.12–1.15 and hr: 1.11, 95% ci: 1.10–1.12). elevated d-dimer (hr: 1.02, 95% ci: 1.01–1.03), il-6 (hr: 1.01, 95% ci: 1.00–1.02) and il-10 levels (hr: 1.04, 95% ci: 1.01–1.07) were also risk factors for the progression of disease severity. meanwhile, lymphopenia and wake immune responses [e.g., lower cd3, cd4, or cd19 counts (all hr < 1)] were associated with disease deterioration and death. conclusions: severe cases and death of covid-19 are associated with older age, comorbidities, organ dysfunction, lymphopenia, high cytokines, and weak immune responses. coronavirus disease 2019 (covid19) was first reported in wuhan, china, and is now spreading in more than 37 countries, including the united states, japan, south korea, australia, and france (1) . the pathogen of covid-19 was identified to be severe acute respiratory syndrome coronavirus 2 (sars-cov-2), which is closely related to sars-like coronavirus (2) . in the phylogenetic tree, sars-cov-2 was identified as an βcoronavirus 2b lineage. by examining the full-length genome of sars-cov-2, it was found that this novel virus shares 87.99% homologous sequences with sars-like coronavirus (3) . early research has shown that sars-cov-2, like sars-cov, can infect humans cells expressing angiotensin-converting enzyme 2 (ace2) (4) . based on the information up to date, sars-cov-2 is believed to be the third zoonotic human coronavirus in this century (4) . early reports from wuhan found that the covid-19 was sars-like atypical pneumonia, and can be transmitted from person to person, mainly through respiratory droplets, but also through contact with eye mucosa. although the virus has been detected in feces, the transmission through the digestive tract remains to be further confirmed. the incubation period is generally 2-14 days. mild cases are characterized by fever, muscle pain, fatigue, and dry cough. a few patients had neurological and digestive symptoms. in severe cases, dyspnea can occur after a week. ultimately, the severe patients develop acute respiratory distress syndrome, septic shock, and metabolic acidosis that are difficult to manage (5) (6) (7) . according to the early epidemiological studies, the basic reproduction number (r0) of sars-cov-2 was estimated to be about 2.2 and even more (ranging from 1.4 to 6.5). the low fatality and high morbidity of covid-19 make it difficult to prevent the spread of the virus (8) (9) (10) . description of clinical features, laboratory indicators, and radiological characteristics of the disease is crucial for early diagnosis of the disease, quarantine of patients, and identification of close contacts. our goal is to describe the epidemiological, clinical, and laboratory characteristics of patients diagnosed with covid-19, to compare the clinical characteristics of severe and non-severe cases, and to describe the potential risk factors for disease deterioration and death. our study included 121 inpatients diagnosed as covid-19 who was hospitalized in renmin hospital of wuhan university in china. the diagnosis was based on clinical symptoms, computed tomography (ct), real-time rt-pcr and nextgeneration sequencing. the admission date was from january 16 to march 3, 2020. all the patients involved in this study lived in wuhan during the covid-19 outbreak. we collected data including demographic information (age, gender, and address of usual residence), clinical characteristics (including medical history, comorbidities, symptoms, and signs), initial laboratory findings (hematologic, blood biochemicals, coagulation function, infection-related, and immune-related indices), and clinical outcomes (survival and death). this study was approved by the hospital ethics committee of the renmin hospital of wuhan university [wdry2020-k136]. according to the diagnostic and treatment guideline for sars-cov-2 issued by the chinese national health committee (version 3-7), the severity of covid-19 patients was defined. severe cases were designated when the patients had one of the following criteria: (1) respiratory distress with rr ≥30/min; (2) oxygen saturation ≤93% at rest; (3) arterial partial oxygen pressure (pao 2 )/oxygen absorption concentration (fio 2 ) ≤300 mmhg; (4) respiratory failure that needs mechanical ventilation; (5) shock or with organ failure requiring icu care. epidemiological, clinical and outcome data from electronic medical records were reviewed and collected by professionals. throat swabs samples were collected from all patients and texted by real-time rt-pcr and next-generation sequencing. laboratory tests on admission included routine blood test [including leucocytes, lymphocytes, eosinophils, hs-crp, procalcitonin (pct), serum amyloid a (saa), and others], coagulation function, serum biochemical tests (including renal and liver function, creatine kinase and ldh), and immunological indicators (including lymphocyte differential counts, inflammatory factors, and sars-cov-2-specific antibodies igm and igg). these findings are the initial laboratory results of the patient during hospitalization. thus, these results have not been affected by the treatment. continuous variables were described as medians and interquartile range (iqr), and categorical variables were described as frequency rates and percentages. we used the chisquare (χ 2 ) test or the fisher's exact test to compare categorical data. mann-whitney-wilcoxon test was applied to compare non-normally continuous variables. the proportional hazard cox models were used to determine hr and 95% cis between individual factors on progression to severe or death. the sample size varied due to missing data, and missing data were not imputed. the analyses regarding different factors were based on non-missing data. all statistical analyses were performed using spss software (v.23.0). two-tailed p values were considered statistically significant at <0.05. the demographic and clinical characteristics are shown in table 1 . a total of 121 patients were included in this study. the median age was 65 years (iqr, 55.0-71.5 years) (figure 1a) , of which 54.5% were male. on admission, 69 and 52 patients met the diagnostic criteria for non-severe and severe disease, respectively. the age distribution of these two groups was different ( figure 1c) . of the 121 patients, most (107, 88.4%) survived to discharge, and 14 patients (11.6%) dead ( figure 1b) . the most common self-reported symptoms at the time of onset were fever (78.5%) and respiratory symptoms (77.7%), whereas chest distress, fatigue, gastrointestinal symptoms, and neurological symptoms were found in 28.1, 36.4, 23.1, and 9.9% of the patients, respectively. among the 121 patients, 70.2% had at least one comorbidity, including hypertension, diabetes, cardiovascular and cerebrovascular diseases (excluding hypertension), cancers, and chronic pulmonary diseases. the median age of the severe group was higher than that of the non-severe group (69.5 vs. 60.0, p < 0.001). additionally, the proportion of subjects with at least one comorbidity is more common in the severe group as compared with the non-severe group (88.5 vs. 56.5%, p < 0.001). especially, the incidence of hypertension, cardiovascular and cerebrovascular diseases, and chronic pulmonary diseases in severe cases were significantly higher than that in non-severe cases (all p < 0.05). there was no significant difference in demographics and initial clinical characteristics between the survivors and non-survivors. the differences in laboratory findings between non-severe cases and severe cases, as well as survivors and non-survivors table 3 . compared with the non-severe group, the severe group showed higher white blood cell (median, 4.83 vs. 7.11, p < 0.001) and neutrophil counts (2.90 vs. 5.63, p < 0.001) (figure 2a) , as well as higher scr (59.0 vs. 73.0, p < 0.001) and ldh (395.0 vs. 238.0, p < 0.001). as for coagulation function, the severe group showed longer pt and aptt, and higher levels of d-dimer and fdp, as well as lower platelet count (all p < 0.01) as compared with non-severe group. when compared to the non-severe cases, the severe cases showed abnormal immune function, including fewer cd3, cd4, cd8, cd19, cd16+cd56 t-cells (figure 2b) , and complement c3 levels, as well as higher levels of il-6 and il-10 (all p < 0.01). moreover, lower median values of lymphocyte (0.68 vs. 1.05, p < 0.001), albumin (34.40 vs. 37.70, p < 0.001), and egfr (86.99 vs. 98.4, p < 0.001) were found in severe cases compared to non-severe cases. the differences of laboratory indicators between the survivors and non-survivors are shown in table 3 . the non-survivors showed higher leucocyte and neutrophil counts, higher levels of ldh and fdp, longer pt, and fewer counts of lymphocytes, platelets, cd3, cd4, cd8, cd19 t-cells, and lower levels of complement c3 and c4 as compared to the survivors (all p < 0.05). table 4 shows the bivariate cox regression of factors associated with disease progression from onset to severe disease or to death. patients over 65 were at higher risk of developing severe disease than those under 65 (hr, 2.26; 95% ci, 1.23-4.05; p < 0.01). cases with comorbidities were 4.53 times more likely to progress to severe than cases without comorbidities (hr, 4.53; 95% ci, 1.78-11.55, p < 0.01). in addition, cox regression models illustrated that comorbidities (hr, 7.81; 95% ci, 1.02-59.86; p < 0.05), leukocytosis (hr, 1.25; 95% ci, 1.10-1.42; p < 0.01), and neutrophilia (hr, 1.28; 95% ci 1.13-1.46; p < 0.001) were risks factors for mortality. elevated ldh was also a risk factor for the severity deterioration and the development of death (hr, 1.14; 95% ci 1.12-1.15; p < 0.001 and hr, 1.11; 95% ci 1.10-1.12; p < 0.001). fewer platelets, cd3 or cd4 counts, lower complement c3 level, lymphopenia, and elevated aptt, il-6 or il-10 also were related to the progression from oneset to death (all p < 0.05). this retrospective descriptive study included 121 confirmed cases of covid-19 with a median age of 65. the median age of the severe group was 9.5 years older than that of the non-severe group. the proportion of males in the severe with influenza. this result is consistent with other reports (11, 12) . in addition, there is no obvious difference in the initial clinical manifestations between non-severe and severe cases, or survivors and non-survivors, suggesting that the progression of the disease cannot be predicted only based on the symptoms on admission. this conclusion was also confirmed by the proportional hazard cox models (data not shown). in our study, 70.2% of all cases had at least one comorbidity, including hypertension, diabetes, cardiovascular and cerebrovascular diseases, cancers, or chronic pulmonary diseases. likewise, the adopted cox models showed that cardiovascular and cerebrovascular diseases were the vital risk factors to predict the severity of the disease. analysis of the laboratory indicators shows that the increase of leukocytes, neutrophils, d-dimer, ldh, il-6, il-10, tnf, and ifn-γ, and the decrease of lymphocytes, cd3, cd4, and platelets counts were related to disease progression and adverse clinical outcomes. interestingly, we found eosinophilia in 18.2% of the patients, which seems to be indicator of better outcomes. this observation is different from an early study (13) . the eosinophil counts in non-severe cases are significantly higher than that in severe cases. when compare the survivors and nonsurvivors, the former also show higher eosinophil counts. all cases did not have history of allergic diseases such as asthma. it is conceivable that inflammatory factors released by the eosinophils can trigger cough, sputum discharge, and sneezing, which are beneficial for the patients to expel the virus and fight against viral toxicity. the exact role of eosinophils in covid-19 remains to be further illustrated. in our study, leukocytosis was often accompanied by neutropenia and lymphopenia, and this phenomenon was more common in severe cases. consistently, the median value of neutrophils was higher in the severe group than in the non-severe group, which could be a sign of excessive inflammatory response. according to the bivariate cox regression analysis, neutropenia was a risk factor for severe cases and adverse clinical outcomes. lymphocytosis has been reported by many clinical investigators and is also common in severe cases. we also found that cd3, cd4, cd19, and cd16 + cd56 t-cell counts decreased to varying degrees and were more pronounced in severe cases and deaths. significantly reduced lymphocyte counts in the severe cases indicate impaired immune function in these patients. the pathological and anatomical examination of patients with covid-19 also showed that the number of cd4 and cd8 t-cells was greatly reduced (14) . therefore, we speculate that impaired immune function is one of the risk factors for elderly patients with poor clinical outcomes. although recent studies have emphasized that sars-cov-2 can infect immune cells through cd147, thereby affecting the immune function, the cause of immune function impairment in patients with covid-19 needs to be further studied (15) . another notable finding was that il-6, il-10, tnf, and ifnγ were generally elevated in severe cases. studies showed the that inflammatory factor storm was one of the crucial causes of disease progression and adverse clinical outcomes (16) (17) (18) . therefore, the prevention of inflammatory factor storm should be considered for patients with severe covid-19 (19, 20) . many subjects show increased serum ck-mb and ldh, indicating the sars-cov-2 can cause myocardial damage. this coincides with the latest covid-19 research findings of the department of cardiology and cardiac ultrasound (21, 22) . furthermore, the bivariate cox regression analysis emphasized higher ldh as a risk factor for the development of severity disease and the progression of death. it is worth noting that myocardial damage should be treated properly to reduce mortality. coagulation dysfunction was another risk factor for death. there are also reports of vascular embolism in patients with covid-19 (23, 24) . in this study, 72.6% and 46.4% of the cases showed high d-dimer and fdp, respectively. compared with non-severe cases (median, 3.93), the d-dimer of severe cases (median, 0.85) is significantly increased, suggesting that the increase of d-dimer may be one of the risk factors for the deterioration of the disease, and attention should be paid to monitor coagulation function. longer pt and aptt, with higher d-dimer and fdp in the initial laboratory findings of dead cases may suggest the possibility of disseminated intravascular coagulation (dic). the strengths of the present study as follows: the inpatients of this research came from wuhan, where is the hit-hardest region of china in this epidemic. understanding the clinical manifestations and prognosis of cases, and analyzing the risk factors of disease progression and death can provide a theoretical basis for clinical diagnosis and intervention. clinicians, especially critical care physicians, have a deep understanding of the condition of covid patients upon admission, which is more helpful in controlling the progression of the disease and improving the prognosis. limitations of this study were that this study conducted in a single hospital with limited sample size. information and selection bias may influence the result. a larger-scale multicenter study of covid-19 patients will help to further determine the clinical features and risk factors of this disease. this study included 121 confirmed covid-19 cases with a median age of 65. fever and respiratory symptoms were the most common manifestations. age and comorbidity were the risk factors for death and disease progression. myocardial injury markers and renal function also suggest the possibility of deterioration. abnormal coagulation function suggests the risk of dic in severe cases. the immune-related laboratory results indicate the presence of inflammatory factor storm and impaired immune function, which are closely related to the adverse clinical outcomes. thus, these indicators deserved special attention. early intervention should be considered to treat impaired immune functions to reduce mortality. most factors that are related to the development of disease deterioration were associated with death, indicating the same pathophysiological mechanisms mediate the progression from hospital admission to severity worsening and from onset to death. all datasets presented in this study are included in the article/supplementary material. this study was approved by the hospital ethics committee of the renmin hospital of wuhan university [wdry2020-k136]. written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements. covid-19): situation report−39. world health organization (2020) genomic characterisation and epidemiology of 2019 novel coronavirus: 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characteristics, and treatment strategy clinical characteristics of 140 patients infected with sars-cov-2 in wuhan pathological findings of covid-19 associated with acute respiratory distress syndrome meplazumab treats covid-19 pneumonia: an open-labelled, concurrent controlled add-on clinical trial. medrxiv il-6 as a keystone cytokine in health and disease the cytokine storm of severe influenza and development of immunomodulatory therapy pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in wuhan, china the pathogenesis and treatment of the 'cytokine storm' in covid-19 suspected myocardial injury in patients with covid-19: evidence from front-line clinical observation in wuhan, china association of cardiac injury with mortality in hospitalized patients with covid-19 in wuhan, china acute pulmonary embolism in covid-19 patients on ct angiography and relationship to d-dimer levels autopsy findings and venous thromboembolism in patients with covid-19 lz had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. wf were helped statistical analysis and gave technical support. ld and lz draft the manuscript. lz and yz designed the study. yz and yg helped in the acquisition of data. zhez and zhaz were responsible for data interpretation and the critical revision of the manuscript. all authors contributed to the article and approved the submitted version. we thank members of the medical team from qinghai province and shanghai city for their efforts in recruiting patients. the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.the reviewer xw declared a shared affiliation with one of the reviewers wf to the handling editor at time of review.copyright © 2020 zou, dai, zhang, fu, gao, zhang and zhang. this is an openaccess article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord-297470-lx3xwg92 authors: pan, yunbao; li, xinran; yang, gui; fan, junli; tang, yueting; hong, xiaoyue; guo, shuang; li, jin; yao, dongai; cheng, zhenshun; yuan, yufeng; li, yirong; wang, xinghuan title: seroprevalence of sars-cov-2 immunoglobulin antibodies in wuhan, china: part of the city-wide massive testing campaign date: 2020-10-07 journal: clin microbiol infect doi: 10.1016/j.cmi.2020.09.044 sha: doc_id: 297470 cord_uid: lx3xwg92 objectives: the outbreak of 2019 coronavirus disease (covid-19) pandemic in wuhan, china, has subsided after a hard hit by the disease and subsequent city lockdown. information on the number of people involved in wuhan is still inadequate. this study aimed to describe the screening results of 61,437 community members in wuchang district, wuhan. methods: in mid-may 2020, wuhan launched a population-scale city-wide sars-cov-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in wuhan. here we show the screening results of cluster sampled 61,437 residents in wuchang district, wuhan, china. results: a total of 1470 (2.39%, 95% ci: 2.27-2.52) individuals were detected positive for at least one antiviral antibody. among the positive individuals, 324 (0.53%, 95% ci: 0.47-0.59) and 1200 (1.95%, 95% ci: 1.85-2.07) were positive for immunoglobulin igm and igg, respectively, and 54 (0.08%, 95% ci: 0.07-0.12) were positive for both antibodies. the positive rate of female carriers of antibodies were higher than those of male counterparts (male-to-female ratio of 0.75), especially in elderly citizens (ratio of 0.18 in 90+ age subgroup), indicating a sexual discrepancy in seroprevalence. in addition, viral nucleic acid detection using real-time pcr had showed 8 (0.013%, 95% ci: 0.006-0.026) asymptomatic virus carriers. conclusions: the seroprevalence of sars-cov-2 in wuhan was low. most of wuhan residents are still susceptible to this virus. precautions, such as wearing mask, frequent hand hygiene, and proper social distance, are necessary before an effective vaccine or antiviral treatments are available. severe acute respiratory syndrome coronavirus 2 (sars-cov-2) related coronavirus disease (covid-19) is a respiratory transmissible disease that may cause critical illness to death (1, 2) . various control measures against sars-cov-2 were implemented in wuhan, the first city hit by the coronavirus. after months of endeavor, the viral transmission was largely contained (3). however, sporadically infected cases and asymptomatic carriers were still detected. hence, wuhan launched a population-scale, massive sars-cov-2 testing campaign for detecting viral nucleic acid and antibodies in residents to further prevent viral transmission, screen out infected patients who were in the incubation period or were asymptomatic virus carriers, and map the epidemiological sero-distribution of this infectious disease in the epicenter. wuchang district, one of the 13th administrative divisions in wuhan, is located in the central urban area and is adjacent to the yangtze river. according to the wuhan statistical yearbook 2018, the total population of wuchang district is 1.28 million, accounting for 11.7% of the wuhan population. the present study described the screening results of 61,437 community members in wuchang district, wuhan. j o u r n a l p r e -p r o o f individual blood samples were collected at community sampling stations. the the graphs of age and sex distribution were depicted for the entire tested population. for the seropositive populations, the positive rates in each age and sex group were calculated by dividing the corresponding entire tested population. the 95% confidence interval (ci) was presented. the male-to-female ratio (mfr) was calculated as the male positivity rate divided by the female positivity rate. among 61,437 community members included in the study, 30,032 (48.88%) were male. the age range is from several months to 101 years old and the median age was 48 (interquartile range (iqr): 32-64) years. the sex and age distribution is depicted in figure 1 . as shown in table 1 table 1 ). furthermore, the participants were voluntarily recruited, and hence it was reasonable to speculate that a small proportion of mobility-impaired individuals were reluctant to participate, although they performed fewer activities during the outbreak and had fewer chances to be infected. the present study was conducted in wuchang district, while data in different districts in wuhan hit by covid-19 might vary. however, the observed rate was comparable with that reported in other similar studies. a recent study detected 17,368 individuals from different geographic regions in china, including 1993 residents from different wuhan sub-cohorts. it suggested a seropositivity rate of 3.8%, 3.2%, and 3.8% in healthcare workers, their family members, and their staff members, respectively, from hotels designated for the accommodation of healthcare workers during city lockdown in wuhan between march 30 and april 10, 2020 (5) . as the exposure of healthcare workers and their close contacts to sars-cov-2 was relatively higher than that of most of the other citizens, it was reasonable that the seropositivity from these j o u r n a l p r e -p r o o f subgroups was higher than that from populations with massive testing. another study testing 452 asymptomatic hong kong residents evacuated from hubei province in early march 2020 indicated a 3.76% (17/452) seropositivity rate (6) . all these seropositivity rates indicated that the prevalence of the population carrying the antibody in wuhan was low. eight (0.013%), 324 (0.53%), and 1200 (1.95%) individuals were detected positive for nucleic acid, igm and igg, respectively. as igm is regarded as the first class of immunoglobulins in response to initial exposure, the presence of igm antibody represents an early exposure to the antigen (7). the anti-sars-cov-2 igm antibody could be detected in patients after 4 days of onset, peaking at 2-3 weeks after the onset of symptoms before its level started to decline (8, 9) . however, igm positivity alone may not be a good diagnostic indicator because not all of the people develop a detectable igm antibody (8) . in addition, the igm antibody may still be detectable after several months, although it is considered as an "early infection". most of the recent studies showed detectable sars-cov-2 anti-igm antibodies after one to two months (10, 11) . igg represents the most robust and long-duration antibody against the virus (12) . remarkably, the present study detected more female carriers of asymptomatic antibodies compared with male carriers in most age subgroups and a reverse correlation trend of mfr with the increase in age. another study in wuhan also reported similar findings (13) . indeed, it was suggested that sars-cov-2 affected women less compared with men, due to different innate immunity, steroid hormones, and factors related to sex chromosomes (14) . however, this female over male trend in asymptomatic carriers was not captured in other areas and countries, such as south korea, thailand, iran, spain, and california of usa (15) (16) (17) (18) . whether this trend is observed only in wuhan or can be observed in other parts of china or other countries too needs further investigation. this study had several limitations. first, several groups of people were not included in the study, which might have had different impacts on detecting real seropositivity. second, the rates were affected by the quality of the kit. as (19) . these intrinsic shortcomings of the rapid immunochromatographic kit might inevitably cause false-positive and false-negative results. third, massive tests were conducted within 12 days, and hence the possibility of a more false-positive or false-negative rate due to the labor-intensive work was unavoidable. fourth, a rapid and ready-to-use method, the immune colloidal gold technique, was adopted for the screening test because a large number of samples were needed for handling and the technicians had some limitations. the test provided only a qualitative positive or negative result. a more quantitative result may be obtained using the chemiluminescence enzyme immunoassay. in summary, the majority of the residents in wuhan are still immunologically naive to sars-cov-2, far from herd immunity. although wuhan re-opened since april 8, 2020, proper control measures, such as frequent hand hygiene, wearing face masks, and keeping proper social distance, are necessary before effective vaccines or antiviral drugs are available. clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study the effect of human mobility and control measures on the covid-19 epidemic in china strengthening the reporting of molecular epidemiology for infectious diseases (strome-id): an extension of the strobe statement seroprevalence of immunoglobulin m and g antibodies against sars-cov-2 in china seroprevalence of sars-cov-2 in hong kong and in residents evacuated from hubei province, china: a multicohort study. the lancet microbe role of natural and immune igm antibodies in immune responses serological immunochromatographic approach in diagnosis with sars-cov-2 infected covid-19 patients patterns of igg and igm antibody response in covid-19 patients profile of igg and igm antibodies against severe acute respiratory syndrome coronavirus 2 (sars-cov-2) analytical performances of a chemiluminescence immunoassay for sars chronological evolution of igm, iga, igg and neutralisation antibodies after infection with sars-associated coronavirus seroprevalence and epidemiological characteristics of immunoglobulin m and g antibodies against sars-cov-2 in asymptomatic people in wuhan, china coronavirus cov-19/sars-cov-2 affects women less than men: clinical response to viral infection igg seroprevalence of covid-19 among individuals without a history of the coronavirus disease infection in daegu antibody in thai community hospitals seroprevalence of covid-19 virus infection in guilan province covid-19 antibody seroprevalence in sars-cov-2-induced humoral immunity through b cell epitope analysis and neutralizing activity in covid-19 infected individuals in japan key: cord-289451-yjrh5l4u authors: xiao, huidi; shu, wen; li, menglong; li, ziang; tao, fangbiao; wu, xiaoyan; yu, yizhen; meng, heng; vermund, sten h.; hu, yifei title: social distancing among medical students during the 2019 coronavirus disease pandemic in china: disease awareness, anxiety disorder, depression, and behavioral activities date: 2020-07-14 journal: int j environ res public health doi: 10.3390/ijerph17145047 sha: doc_id: 289451 cord_uid: yjrh5l4u background: during the coronavirus disease (covid-19) pandemic, harsh social distancing measures were taken in china to contain viral spread. we examined their impact on the lives of medical students. methods: a nation-wide cross-sectional survey of college students was conducted from 4–12 february 2020. we enrolled medical students studying public health in beijing and wuhan to assess their covid-19 awareness and to evaluate their mental health status/behaviors using a self-administered questionnaire. we used the patient generalized anxiety disorder-7 and health questionnaire-9 to measure anxiety disorders and depression. we used multivariable logistic regression and path analysis to assess the associations between covariates and anxiety disorder/depression. results: of 933 students, 898 (96.2%) reported wearing masks frequently when going out, 723 (77.5%) reported daily handwashing with soap, 676 (72.5%) washed hands immediately after arriving home, and 914 (98.0%) reported staying home as much as possible. prevalence of anxiety disorder was 17.1% and depression was 25.3%. multivariable logistic regression showed anxiety to be associated with graduate student status (odds ratio (aor) = 2.0; 95% confidence interval (ci): 1.2–3.5), negative thoughts or actions (aor = 1.6; 95% ci: 1.4–1.7), and feeling depressed (aor = 6.8; 95% ci: 4.0–11.7). beijing students were significantly less likely to have anxiety than those in the wuhan epicenter (aor = 0.9; 95% ci: 0.8–1.0), but depression did not differ. depression was associated with female students (aor = 2.0; 95% ci: 1.2–3.3), negative thoughts or actions (aor = 1.7; 95% ci: 1.5–1.9), and anxiety disorder (aor = 5.8; 95% ci: 3.4–9.9). path analysis validated these same predictors. conclusions: despite medical students’ knowledge of disease control and prevention, their lives were greatly affected by social distancing, especially in the wuhan epicenter. even well-informed students needed psychological support during these extraordinarily stressful times. coronavirus disease (covid-19) is a public health emergency of worldwide concern [1] . up through june 2020, covid-19 had affected 213 countries, territories or areas, and two international conveyances (cruise ships) [2] since its initial december 2019 report as an "unknown pneumonia" in wuhan, hubei province, china [3] . infections and deaths increased rapidly with global travel fueling transmission spread worldwide, first to other parts of china, south korea, and iran, and soon thereafter to europe and the united states. other nations such as russia and brazil then experienced expanding case numbers while infections in africa have also been mounting. to interrupt further transmission, many chinese provinces and cities suspended public transportation [4] and even locked down cities altogether. these were unprecedented and harsh social distancing measures and they affected every aspect of daily life in china, as elsewhere. "social distancing" is done to reduce close physical interactions (<2 m) between people to avoid viral transmission. chinese measures included closure of schools, office buildings, and public markets; events were cancelled, and gatherings discouraged [5] . the united nations educational, scientific and cultural organization (unesco) estimates that nationwide closures in more than 160 countries have affected over 87% of students in the world, with wider closures affecting even more [6] . a 2009 influenza a (h1n1) pandemic survey in hong kong demonstrated marked anxiety associated with distancing [7] . a 2020 covid-19 survey in china found that many respondents (including students) reported symptoms of moderate to severe anxiety and depression [8] . medical students are a reservoir for the future health labor force. in the early response in the epicenter in china, as well as other countries, the sudden outbreak overwhelmed health professional's preparedness in terms of personal protective equipment (ppe) shortages and psychological readiness [9, 10] . it is critical to understand how much the pandemic affects this future health labor force. we sought to understand the psychological effects of distancing measures and possible effects on medical student wellness. even without pandemic stresses, medical students may have some anxiety and depression due to their high study-related or job-seeking burdens [11] [12] [13] . we studied the associations between covid-19 distancing and the lives of public health students on anxiety [14] , depression, and other behaviors. we also examined the differences among public health students in two universities, capital medical university (ccmu) in beijing, and huazhong university of science and technology (hust) in wuhan, the early epicenter of the covid-19 outbreak in china. we conducted a cross-sectional survey among the medical students in two schools of public health at two universities: ccmu in beijing and hust in wuhan. the present study is part of a nation-wide cross-sectional survey of college students conducted from 4-12 february 2020. we developed a self-administrated, 84-item questionnaire focused on: (1) covid-19 awareness; (2) personal protective measures; (3) mental health status; and (4) behavioral changes in the past 14 days. our instrument was based on social-cognitive theory and the theory of planned behavior and we measured knowledge, attitude, belief, and practice (kabp) [15] , enhanced with psychological assessments. we used the validated generalized anxiety disorder-7 (gad-7) and patient health questionnaire-9 (phq-9) to assess anxiety disorder and depression, respectively [16, 17] . most questions were one-choice, brief, and easy to answer, such that it took only 10 min on average to complete the survey. we used wenjuanxing ® (changsha haoxing information technology co., ltd., changsha, china) software for the informed consent process and the online survey questionnaire. participants obtained and completed the self-administrated questionnaire on the mobile phone by scanning the qr code using wechat ® software. after consent was obtained, we detailed the workflow of the survey with one page of text. the investigators received the completed questionnaires via the software platform. facilitated by their teachers, we approached all medical students with public health majors in the ccmu and hust schools of public health. the study was approved by ethics review board of capital medical university (2020sy004) and anhui medical university (20200319). informed consent and a response to the questionnaire were obtained from 933 of 1061 (87.9%) students who were approached. hence, we could infer the different preventive knowledge, behaviors, and psychological status modified by distance to the epicenter amid social distancing in the pandemic. covariates included socio-demographic characteristics, knowledge of covid-19, personal protective measure, behaviors, and degree of worry about the virus. variables included sex, age, year of study, university, living quarters, knowledge about the covid-19 incubation period, mortality, susceptibility (e.g., chronic illness), drugs taken, mask wearing, face and hand hygiene, times and reasons for going out, room cleanliness and ventilation via windows, and concerns about the covid-19 epidemic and contracting the virus. we also asked about negative thoughts or actions ("always feel dirty", "feel uneasy in a crowded place", "often suspect being infected", "worse appetite than before", "feel less energic than before", "hold unhappy intentions in my heart" and "angry with others when in a bad mood"), positive thoughts or actions ("accept the truth when facing an obstacle" and "relieve pain in a positive way"), healthy lifestyles ("work and rest regularly", "arise regularly", "sleep regularly" and "have meals regularly"), video screen time per day, and the number of anger episodes or quarrels in the past week. principal outcomes were anxiety disorder and depression measured by scale scores of gad-7 and phq-9, respectively. the gad-7 scale score was divided into four categories: normal (0-4), mild (5-9), moderate (10) (11) (12) (13) (14) , and severe (15) (16) (17) (18) (19) (20) (21) . the phq-9 scale score was divided into five categories: normal (0-4), mild (5-9), moderate (10) (11) (12) (13) (14) , moderate to severe (15) (16) (17) (18) (19) , and severe (20) (21) (22) (23) (24) (25) (26) (27) . if a participant's score was ≥5 points (i.e., mild or above), we considered the student to have evidence of anxiety disorder. we used descriptive statistics including the chi-squared test for the associations of covid-19 knowledge with sociodemographic characteristics and use of personal protective measures. we used multivariable logistic regression to examine the association between independent variables and covariates with anxiety disorder and/or depression. we deployed the hosmer-lemeshow test to determine the goodness-of-fit of the logistic regression model. only variables with two-sided p ≤ 0.05 were deemed significant in the final model. we used path analysis to determine the interplay of covariates with anxiety disorder and depression via a structural equation model. we used maximum likelihood estimation and assessed the goodness-of-fit by absolute fit indices that determine how well the a priori model predicts the actual data, including the root mean square error of approximation (rmsea), goodness of fit index (gfi), and adjusted goodness of fit index (agfi). we also used incremental or relative fit indices, specifically the incremental fit indices (ifi), comparative fit indices (cfi), normed fit index (nfi), and the non-normed fit tucker-lewis index (tli). rmsea < 0.10 and gfi and agfi > 0.90 indicate the model fits well. the incremental fit measures-cfi, nfi, ifi, and tli-are >0.90 when the model fits well. we used spss statistic ® 21.0 and spss amos ® 26.0 graphics software (ibm spss statistics, new york, ny, usa). of 933 participated students, 558 students attended ccmu (94.4% agreed to participate) in beijing, and 375 students attended hust (79.6% agreed) in wuhan. graduate students doing masters of public health degrees did better than undergraduates in the knowledge questions that were answered correctly (p = 0.037). it is important to note that the chinese system has undergraduate medical students and before graduation, medical students can pursue specialties such as public health, pediatrics, etc.; then at the graduate level they may choose to major in epidemiology and statistics, environmental health, etc., if they chose the public health specialty. the prevalence of anxiety disorder (p = 0.015) and depression (p < 0.001) in women was significantly higher than in men. anxiety disorder was higher in wuhan students than ccmu students (p = 0.001; table 1 ). the correct answers to the four knowledge questions were given by 97.2%, 67.1%, 69.3%, and 89.4% of respondents (table s1 ). the awareness of mortality risk was higher in hust students than ccmu students (p = 0.04). as to preventive measures and behaviors during social distancing, 898 (96.2%) reported wearing masks frequently when going out, 869 (93.1%) washed their hands with water regularly, 723 (77.5%) washed their hands with soap every day, 676 (72.5%) washed their hands immediately after arriving home, 239 (25.6%) considered it difficult to wash their hands for at least 20 s, 295 (31.6%) washed their hands for more than 20 s frequently, 914 (98.0%) avoided unnecessary outings (i.e., they tried to stay at home as much as possible), and 878 (94.1%) kept clean, well-ventilated rooms. beijing-based ccmu students were significantly more likely to report wearing masks (p = 0.037), avoiding touching their mouths, noses, and eyes with their hands (p < 0.001), washing their hands immediately after arriving home (p < 0.001), and handwashing for at least 20 s (p < 0.001). wuhan-based students at hust were more likely to report washing their hands with soap (p < 0.001), staying at home (p = 0.028), and keeping their rooms clean and well-ventilated (p = 0.044; table 2 ). assessing anxiety disorder, 773 (82.9%) were classified as normal, 117 (12.5%) had mild anxiety, 30 (3.2%) had moderate anxiety, and 13 (1.4%) had severe anxiety disorder. assessing depression, 697 (74.7%) students were classified as normal, 165 (17.7%) had mild depression, 43 (4.6%) had moderate depression, 18 (1.9%) had moderate to severe depression, and 10 (1.1%) had severe depression. the prevalence of anxiety disorder differed between the two universities, and was significantly higher in wuhan (p = 0.001) which was far more severely affected by covid-19. the prevalence of depression between the two universities was also higher in wuhan, but this may have been due to chance (p = 0.12; table 1 and figure 1 ). bar charts present the distribution of different degrees of anxiety disorder and depression, comparing students at capital medical university (ccmu) in beijing with students at huazhong university of science and technology (hust) in wuhan. the x-axis represents the different degrees of anxiety disorder and depression, and the y-axis represents the proportion of students. bar charts present the distribution of different degrees of anxiety disorder and depression, comparing students at capital medical university (ccmu) in beijing with students at huazhong university of science and technology (hust) in wuhan. the x-axis represents the different degrees of anxiety disorder and depression, and the y-axis represents the proportion of students. multivariable logistic regression shows that being a graduate student (adjusted odds ratio (aor) = 2.03; 95% confidence interval (ci): 1.18-3.49; p = 0.011), having negative thoughts or actions (aor = 1.55; 95% ci: 1.38-1.73; p < 0.001), and feeling depressed (aor = 6.84; 95% ci: 4.00-11.71; p < 0.001) were associated with a higher likelihood of anxiety. students at ccmu, far from the wuhan epicenter, were less likely to experience anxiety (aor = 0.90; 95% ci: 0.82-1.00; p = 0.049; table 3 ). women students (aor = 1.98; 95% ci: 1.19-3.29; p = 0.009), persons having negative thoughts or actions (aor 1.68; 95% ci: 1.50-1.88; p < 0.001), and persons with anxiety (aor = 5.81; 95% ci: 3.43-9.86; p < 0.001) had higher odds of having some depression. having a healthy lifestyle was associated with less depression (aor = 0.88; 95% ci: 0.79-0.97; p = 0.013). a includes: "always feel dirty", "feel uneasy in a crowded place", "often suspect being infected", "worse appetite than before", "feel less energic than before", "hold unhappy intentions in my heart", and "angry with others when in a bad mood". b includes: "accept the truth when facing obstacles", and "relieve pain in a positive way". c includes: "work and rest regularly", "arise regularly", "sleep regularly", and "have meals regularly". across the two sites, 426 (48.7%) students reported using computers or other electronic devices over 4 h daily, 484 (51.9%) used their cellphones over 4 h daily, 635 (68.1%) woke up later than usual, 234 (24.0%) went to bed later than usual, 234 (35.1%) worked and rested irregularly, 157 (16.8%) had meals irregularly, and 221 (23.7%) ate different volumes of food from usual (either more or less). within one week before the survey, 306 (32.8%) reported having gotten angry at others, 201 (21.5%) reported one or more quarrels, 585 (62.7%) felt terrible because of the epidemic, and 112 (12.0%) quarreled with others online. figure 2 shows the factors relevant to anxiety disorder and depression, and table s2 presents standardized estimation of coefficient values. students in their senior grade year (β = 0.074) suffered more from anxiety disorders. negative thoughts or actions were associated with depression (β = 0.86) while healthy lifestyles (β = −0.077) were negatively associated with depression. longer video screen time (β = −0.24) negatively affected a healthy lifestyle. concerns about the covid-19 epidemic were associated with more negative thoughts or actions (β = 0.23) and anger and quarreling behaviors (β = 0.20); negativity and anger/quarrels were correlated (β = 0.34). overall, negative thoughts or actions predicted a higher impact of both anxiety disorders (β = 0.87) and depression (β = 0.86). goodness-of-fit indices for the model were good and key parameters were rmsea = 0.051, gfi = 0.93, agfi = 0.91, cfi = 0.93, nfi = 0.91, ifi = 0.93, and tli = 0.92. standardized estimation of coefficient values. students in their senior grade year (β = 0.074) suffered more from anxiety disorders. negative thoughts or actions were associated with depression (β = 0.86) while healthy lifestyles (β = −0.077) were negatively associated with depression. longer video screen time (β = −0.24) negatively affected a healthy lifestyle. concerns about the covid-19 epidemic were associated with more negative thoughts or actions (β = 0.23) and anger and quarreling behaviors (β = 0.20); negativity and anger/quarrels were correlated (β = 0.34). overall, negative thoughts or actions predicted a higher impact of both anxiety disorders (β = 0.87) and depression (β = 0.86). goodnessof-fit indices for the model were good and key parameters were rmsea = 0.051, gfi = 0.93, agfi = 0.91, cfi = 0.93, nfi = 0.91, ifi = 0.93, and tli = 0.92. our survey findings suggest that the awareness of medical students of covid-19 fundamentals was very high, as might be expected given the profile in chinese society by february 2020. anxiety and depression were common among medical students in whom social distancing was reported with longer video screen time and less healthy lifestyles. concern about the epidemic was associated with negative actions and thoughts, which were, in turn, associated with an increased likelihood of anxiety disorders. the hust medical students in wuhan, the epicenter, presented with higher anxiety than our survey findings suggest that the awareness of medical students of covid-19 fundamentals was very high, as might be expected given the profile in chinese society by february 2020. anxiety and depression were common among medical students in whom social distancing was reported with longer video screen time and less healthy lifestyles. concern about the epidemic was associated with negative actions and thoughts, which were, in turn, associated with an increased likelihood of anxiety disorders. the hust medical students in wuhan, the epicenter, presented with higher anxiety than did ccmu medical students in beijing. the findings underscore our study's significance that the health reservoir suffer from psychological stress and need attention. less than half (43.7%) of the medical students had fully correct (four out of four questions) knowledge of the covid-19 epidemic situation. students, all of whom were studying public health, were less knowledgeable about mortality and susceptible groups, compared to incubation period and available drugs (table s1 ). over 90% of students complied with social distancing and effective preventive measures, like wearing masks frequently when going out, washing hands with water regularly, avoiding unnecessary outings (i.e., staying at home), and keeping their rooms clean and ventilated [18] . according to our findings, students preferred washing their hands with only water to also using soap; about half (54%) of students tried to avoid touching their mouth, nose, and eyes with their hands, though both behaviors can reduce the risk of exposure [19] . a quarter (25.6%) of the students considered it hard to wash their hands for at least 20 s and less than a third (31.6%) washed their hands over 20 s frequently. given that good hand hygiene can effectively prevent virus transmission [20] and washing hands for at least 20 s is a basic component of hand hygiene as per the world health organization (who, geneva, switzerland), it was disappointing to learn from medical students that they found this challenging [21] . it is likely that, comparing the two participating universities, notable differences were fueled by the differing epidemiologic context of the two urban venues. among the 44.0% of students from hust who lived in the epicenter of hubei province or adjacent provinces, they were more likely to obey harsher social distancing rules, like staying at home and deploying hand hygiene. while most students (88.2%) from ccmu lived far away from hubei province, they reported being more fastidious in wearing masks. during social distancing, our study showed 17.1% of students had anxiety disorder symptoms (mainly mild), and 25.3% of students had depression symptoms (mainly mild). an interesting survey in 190 chinese cities surveyed the general population twice: during the initial outbreak and during the epidemic's peak four weeks later [22] . they surveyed demographics, symptoms, knowledge, concerns, and precautionary measures against covid-19. among the 333 persons who took both surveys, post-traumatic stress disorder (ptsd by the mean impact of event scale-revised (ies-r) scale scores) declined with time, but at both surveys, the mean ies-r scores of the first-and second-survey respondents were above the cut-off scores (>24) for ptsd symptoms, suggesting that the reduction in scores was not of clinical significance [22] . previous studies report that student populations can be more vulnerable towards stress-related anxiety and depression [22, 23] . our findings underscore the importance of providing essential psychological support to students, even when they are as well-informed as are medical students in a public health track. both multivariable logistic regression and path analysis reinforced the findings of principal factors related to anxiety disorder and depression. compared to undergraduates, graduate students had a higher risk of anxiety [13, 24] . we think that this may be due to increased pressure for job-seeking or completion of thesis required for graduation. females were more likely to be depressed compared to men, consistent with prior studies [24, 25] . healthy lifestyles were negatively associated with depression, compatible with other findings that healthy lifestyles can improve mental health [26] . some students adopted an unhealthy lifestyle during social distancing, reflecting difficulties in adjusting to domestic life for a prolonged time; as expected, many students reported bad moods and/or behaviors [27] . nearly a quarter of students (23.7%) changed their diets by eating more or less than usual. either excessive or poor appetites can be symptoms of depression [28] . longer video screen time had an indirect impact on depression, as other studies reported [29, 30] . half of our participants spent over four hours on electronic devices; aside from increasing risk for depression, this can negatively affect vision, or spawn weight gain and cardiovascular risk from adoption of a sedentary life [31] . we found that the prevalence of anxiety disorder was higher in wuhan than in beijing (p = 0.001), while depression was also somewhat higher (p = 0.12). research on college students from changzhi medical college (shanxi province, about midway between wuhan and beijing) in the same time period reported that 24.9% of students had anxiety disorder using screening criteria similar to ours [32] . it is unclear whether differences in reported prevalence are related to school location, though it is plausible that proximity to the pandemic's epicenter would be more anxiety-provoking [33] . that negative thoughts or actions, anger and quarreling behaviors, and concerns about covid-19 were all positively related to either depression or anxiety disorder has been seen in other studies [32, 34, 35] . many of our participants reported that they had been angry and quarreling within one week before the survey; 46.7% of them felt terrible because of covid-19. it is plausible that irritable behaviors suggest that mental status or moods may have been affected by social distancing due to lack of normal social activities during the pandemic [36] . as expected, we found a strong positive interaction effect between anxiety disorder and depression. reduced physical activity may increase anxiety or depression, but we did not find a clear association in our survey. strengths of the study include its uniqueness, a survey in two sites (including wuhan) conducted just two months after the report of the pulmonary syndrome and one month after recognition of sars-cov-2 circulation in china. limitations include the cross-sectional survey design. while we could compare sites and assess predictors of anxiety and depression, we could not assess mental health circumstances before the emergence of the virus and therefore cannot infer temporality, the vital element to assess causality. the participants are medical students studying public health from two universities; therefore, results and conclusions cannot be generalized to other populations. moreover, because we used self-rating scales, the frequency of anxiety disorder and depression symptoms self-reported by the students is less reliable than thorough clinical diagnoses. as an emerging disease, our understanding of covid-19 keeps evolving and we selected "knowledge questions" based on what was known in late january 2020, based on several rounds of expert consultations and consistent with who and us centers for disease control and prevention updates. the covid-19 pandemic has posed an unprecedented impact on the lives of medical students. necessary psychological support was not available to them during the time of social distancing beyond an awareness campaign regarding preventive measures. it is likely that more economically vulnerable persons would have stress levels exceeding that of medical students, but we learned that this well-informed population was nonetheless in substantial distress in the context of epidemic concerns. mental health pressures in medical students are likely compounded among practicing clinicians; these professionals need psychosocial assistance at the time of pandemic mental stress. we recommend incorporating pandemic preparedness education within health education, including mental health elements, especially within the healthcare labor force. supplementary materials: the following are available online at http://www.mdpi.com/1660-4601/17/14/5047/s1, table s1 : preventive knowledge of covid-19, comparing correct answer frequencies between the two universities (n = 933), table s2 the sponsors had no role in the study design; in the collection, analyses, and interpretation of data; in the writing of the report; and in the decision to submit the paper for publication. china coronavirus: who declares international emergency as death toll exceeds 200 who. coronavirus disease (covid-19) situation report the continuing 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students in china factors associated to depression and anxiety in medical students: a multicenter study associations between negative life events and anxiety, depressive, and stress symptoms: a cross-sectional study among chinese male senior college students relationship between intrinsic motivation and undergraduate students' depression and stress: the moderating effect of interpersonal conflict social integration, perceived stress, locus of control, and psychological wellbeing among chinese emerging adult migrants: a conditional process analysis acknowledgments: we thank qi fu and niu piye and dean rui chen for survey facilitation and all the students participating in the survey for their time. the authors declare no conflicts of interest. key: cord-305213-bt0qsbyf authors: zhou, jian; sun, jingjing; cao, ziqin; wang, wanchun; huang, kang; zheng, fang; xie, yuanlin; jiang, dixuan; zhou, zhiguo title: epidemiological and clinical features of 201 covid-19 patients in changsha city, hunan, china date: 2020-08-21 journal: medicine (baltimore) doi: 10.1097/md.0000000000021824 sha: doc_id: 305213 cord_uid: bt0qsbyf in december 2019, a cluster of coronavirus disease 2019 (covid-19) occurred in wuhan, hubei province, china. the present study was conducted to report the clinical characteristics of 201 covid-19 patients in changsha, china, a city outside of wuhan. all of the patients with confirmed covid-19 were admitted to the first hospital of changsha city, the designated hospital for covid-19 assigned by the changsha city government. the clinical and epidemiological characteristics, data of laboratory, radiological picture, treatment, and outcomes records of 201 covid-19 patients were collected using electronic medical records. this study population consisted of 201 hospitalized patients with laboratory-confirmed covid-19 in changsha by april 28, 2020. the median age of the patients was 45 years (iqr 34–59). about half (50.7%) of the patients were male, and most of the infected patients were staff (96 [47.8%]). concerning the epidemiologic history, the number of patients linked to wuhan was 92 (45.8%). the most common symptoms were fever (125 [62.2%]), dry cough (118 [58.7%]), fatigue (65 [32.3%]), and pharyngalgia (31 [15.4%]). one hundred and forty-four (71.6%) enrolled patients showed bilateral pneumonia. fifty-four (26.9%) patients showed unilateral involvement, and three (1.5%) patients showed no abnormal signs or symptoms. the laboratory findings differed significantly between the intensive care unit (icu) and non-icu groups. compared with non-icu patients, icu patients had depressed white blood cell (wbc), neutrocytes, lymphocytes, and prolonged prothrombin time (pt). moreover, higher plasma levels of erythrocyte sedimentation rate (esr), c-reactive protein (crp), procalcitonin (pct), alanine aminotransferase (ala), aspartate aminotransferase (ast), creatine kinase (ck), creatine kinase-mb (ck-mb), creatinine (crea), and lactate dehydrogenase (ldh) were detected in the icu group. in this single-center study of 201 covid-19 patients in changsha, china, 22.4% of patients were admitted to icu. based on our findings, we propose that the risk of cellular immune deficiency, hepatic injury, and kidney injury should be monitored. previous reports focused on the clinical features of patients from wuhan, china. with the global epidemic of covid-19, we should pay more attention to the clinical and epidemiological characteristics of patients outside of wuhan. in december 2019, a series of covid-19 occurred in wuhan, hubei province, china, [1] [2] [3] [4] which was caused by sars-cov-2 infection. most of the covid-19 patients were concentrated in wuhan, and their exposure history related them to the huanan seafood wholesale market at the beginning. [5] however, the infection rapidly spread from wuhan to all over the country because of the population movement during the spring festival. [6, 7] acute respiratory infection symptoms, including high temperature, dry cough, fatigue, and breathing difficulty, are the main early symptoms of the disease. [8] along with disease progression, some patients rapidly develop acute respiratory distress syndrome (ards), acute respiratory failure, and other several complications, especially for older patients or those with immunodeficiency. in the past month, several studies [9] [10] [11] [12] [13] reported the epidemiological, demographic, clinical, laboratory, and radiological characteristics of covid-19 patients in wuhan city. in the present study, we performed a comprehensive analysis to describe the clinical features, epidemiologic characteristics, treatment, and outcomes of 201 covid-19 patients in changsha, china, a city outside of wuhan, and the differences of clinical features between icu and non-icu patients were analyzed. our study findings provide information about covid-19 patients outside of wuhan. related data were collected from the first hospital of changsha city, the designated hospital for covid-19 assigned by the changsha city government. all of the patients enrolled in this report were admitted from january 1, 2020 to april 28, 2020. during the entire outbreak, a total of 242 patients received treatment in the first hospital of changsha city. forty-one patients were excluded because of plenty of data missing and 201 covid-19 patients were involved in the present study. criteria for patients admitted into icu: according to previous study, [14] the basic reproductive number (r 0 ) was 2.43 (95% ci = 2.42-2.44) and that 92.9% (95% ci = 92.5-93.1%) of total cases were not reported, so many patients might not be reported in changsha, china. the first hospital of changsha city is located in changsha, hunan province, a neighboring province of hubei province. the ethics commissions approved this study of the first hospital of changsha city, and written consents were obtained from the enrolled patients. all of the patients involved in the present study were diagnosed according to world health organization interim guidance. [15] the clinical outcomes, including discharge and death, were recorded up to april 28, 2020. the research team from the second xiangya hospital of central south university and the first hospital of changsha city conducted a comprehensive analysis of the medical information of covid-19 patients. in this report, we obtained the clinical and epidemiological characteristics, data of laboratory, radiological picture, treatment, and outcomes records using electronic medical records. the medical information, including demographic data (age, gender, and occupation), exposure history, medical history, comorbidities, signs, symptoms, chest computed tomographic (ct) scans, laboratory results, and treatment, such as antibacterial therapy, glucocorticoid therapy, and antiviral therapy, was collected. the durations from exposure to wuhan to the onset of disease and the course of disease were recorded. the laboratory test assays of 2019-ncov were conducted according to the who recommendation. [16] laboratory identification of 2019-ncov was performed in three different institutions: the first hospital of changsha city, hunan center for disease control, and prevention (hunan cdc) and chinese cdc (ccdc). upper and lower respiratory tract specimens were collected for extracting sars-cov-2 rna. rna was obtained and further tested by rt-pcr through the same method previously described. [17] other respiratory viruses (influenza a virus, influenza b virus, respiratory syncytial virus) and parainfluenza virus were also tested in this study. continuous variables were described as median and iqr. categorical variables were expressed using the number and percentages. mann-whitney u test was performed for continuous variables, and the x 2 test or fisher's exact test was conducted for categorical variables. a two-sided a < .05 was considered to be statistically significant. additionally, normality test was also conducted to test whether the data conforms to the normal distribution. all of the statistical analyses were performed using statistical package for the social sciences (spss) version 17.0 software. the study funders/sponsors had no role in the design and conduction of the study, including the collection, management, analysis, and interpretation of the data, preparation, review, or approval of the manuscript, and the decision to submit the manuscript for publication. the datasets used and/or analyzed during the present study are available from the corresponding author on reasonable request. this study population consisted of 201 hospitalized patients aged (fig. 1) . fifty-four (26.9%) patients showed bilateral pneumonia, and three (1.5%) patients showed no abnormal signs or symptoms. resting heart rate and mean arterial blood pressure did not differ between the two groups (p > .05). compared with patients who did not receive icu care, patients who received icu care had a higher respiratory rate (p = .0457). forty-five (100%) patients, 44 (97.8%) patients, and 44 (97.8%) patients in the icu group received treatments of antibiotic, glucocorticoid, and immunoglobulin, respectively; the frequency of patients who received no icu care receiving these treatments was lower ( table 2) . the laboratory findings differed significantly between the icu and non-icu groups. concerning the blood counts of patients on admission, the white blood cell count of 75 patients (37.3%) was <4 â 10 9 /l, and the lymphocyte count of 46 patients (22.9%) was <0.8 â ) and a higher level of d-dimer (median 0.25 [iqr 0.14-0.52]) on admission were found in the icu patients. levels of ala, ast, ck, and ldh were significantly increased in the icu group. these laboratory results were recorded on the first day after admission for all of the patients, and then on those who later received icu care or not (table 3) . the number of covid-19 patients is increasing, and so is the death toll. [11, 18] several studies [9] [10] [11] [12] [13] reported the epidemiological and clinical characteristics of covid-19 patients, providing information for sars-cov-2 evolution, infectivity, transmissibility, and pathogenicity. in this study, we reported a total of 201 patients with sars-cov-2 infection outside of wuhan, china. among them, 45 (22.4%) patients required icu care, and 156 (77.6%) were admitted to the isolation ward of the first hospital of changsha city. patients in the icu group were older, while no significant difference in sex ratio was found between the two groups, which suggests that age may be a risk factor for a poor outcome. the occupational composition of the icu group differed from the non-icu group, and the number of patients exposed to wuhan city in the icu group was significantly higher than that of the non-icu group, which indicates that the exposure history to wuhan city may affect the outcome of covid-19 patients. no significant differences in the duration and incubation were found between the icu group and the non-icu group. as of april 28, 2020, 199 (99%) of 201 patients had been discharged. two (1%) patient of the icu group in this study died. more patients had a poor prognosis in icu group compared to non-icu group (p < .05) and this overall mortality was lower than that reported for wuhan (4.3%). [11] in terms of clinical features, patients with cardiovascular or respiratory diseases were more likely to require icu care. in addition, the maximum temperature of patients in the icu group was significantly higher than that in the non-icu group, and more patients in the icu group presented fatigue and anhelation. moreover, the respiratory rate of cases in the icu group was higher than those of the non-icu group, which may be attributed to inflammation of the lungs. patients in the icu group must breathe more frequently to provide the oxygen required compared to patients in the non-icu group. the most common laboratory abnormalities observed in the present report included depressed wbc, neutrocytes, lymphocytes, prolonged prothrombin time, and elevated esr, crp, pct, and ldh. previous studies indicated the role of neutrophil biology and related signaling in covid-19. yu et al reported that elevated levels of neutrophil activation in covid-19 patients were related to higher risk of morbid thrombotic complications. [19] liu et al indicated that neutrophil-to-lymphocyte ratio was an independent risk factor of the in-hospital patients. [20] the rising trend in neutrophil-to-lymphocyte ratio may indicate a risk of death for participants with covid-19. [21] the interplay between stat3 and stat5 signaling pathways from normal and diseasespecific g-csfr may lead to abnormal neutrophil productions. [22] compared with the non-icu group, numerous laboratory abnormalities were detected in the icu group. a previous study [10] indicated that sars-cov-2 might mainly act on lymphocytes, including t lymphocytes. sars-cov-2 could induce a cytokine storm in the body, thereby generating a series of immune responses and causing changes in peripheral white blood cells and lymphocytes. additionally, several reports confirmed that the decrease of lymphocytes indicates that coronavirus consumed many immune cells and inhibited cellular immune function, which might lead to exacerbations of covid-19 patients. [23] in this report, lower levels of neutrocytes and lymphocytes were detected in the icu group, which may be caused by the cellular immune deficiency of the icu group. in addition, higher levels of esr, crp, and pct were detected in the icu group, which indicated higher levels of inflammation in the icu group. a longer prothrombin time was found in the icu group, which might represent coagulation activation in the icu group. compared with non-icu patients, higher levels of ala, ast, ck, ck-mb crea, and ldh were detected in patients of the icu group, which was similar to previous reports. [11] these abnormalities suggest that the sars-cov-2 infection may be associated with myocardial injury, hepatic injury, and kidney injury. it may also be that people with these organ dysfunctions are more likely to be infected by sars-cov-2. according to the suggestion of the diagnosis and treatment of pneumonitis with 2019-ncov infection (dtpi) published by the national health commission of the prc, all of the patients in this study were given lopinavir, and ritonavir tablets (2 pills bid peros), which were used for hiv infection in the past, combined with interferon alfa-2b injection (5 million iu add into 2 ml of sterile water, inhalation bid), and 51.7% received antibacterial agents. during the severe acute respiratory syndrome (sars) period in 2003, usage of high doses of glucocorticoids caused a series of sequelae in survivors such as osteonecrosis of the femoral head and glucose metabolism disorders. because of this lesson, we gave a small dose (40-80 mg/day) of glucocorticoid therapy in a short period (5 days) and adjusted the dose and time of medication according to the dynamic changes of the patient's chest ct imaging to control the immune response in the lungs. the patients avoided the occurrence of cytokine storms, thereby reducing the risk of complications, such as acute ards, in patients. glucocorticoid therapy was given to 32.8% of patients. there are several limitations to this study. first, covid-19 was diagnosed by rt-pcr using throat swab samples, while no in this single-center study of 201 covid-19 patients in changsha, china, 22.4% of patients were admitted to icu. we found that the risk of cellular immune deficiency, hepatic injury, and kidney injury was higher in icu group, which should be monitored. because sars-ncov-2 has pandemic potential, the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia report of novel coronavirusinfected pneumonia in china clinical features of patients infected with 2019 novel coronavirus in wuhan, china novel coronavirus (2019-ncov) situation reports. situation report -21 wuhan coronavirus (2019-ncov) global cases a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical and high-resolution ct features of the covid-19 infection: comparison of the initial and follow-up changes clinical and ct features in pediatric patients with covid-19 infection: different points from adults estimation of unreported novel coronavirus (sars-cov-2) infections from reported deaths: a susceptibleexposed-infectious-recovered-dead model available at: https:// www.who.int/publications-detail/clinical-managementof-severe-acute-re spiratory-infection-when-novelcoronavirus-(ncov)-infection-is-sus pected laboratory diagnostics for novel coronavirus a novel coronavirus from patients with pneumonia in china epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan, china neutrophil extracellular traps and thrombosis in covid-19 neutrophil-to-lymphocyte ratio as an independent risk factor for mortality in hospitalized patients with covid-19 2020 dynamic changes of d-dimer and neutrophillymphocyte count ratio as prognostic biomarkers in covid granulocyte colony-stimulating factor receptor signaling in severe congenital neutropenia, chronic neutrophilic leukemia, and related malignancies t-cell immunity of sars-cov: implications for vaccine development against mers-cov medicine (2020) 99:34 www.md-journal the authors would like to thank all of the co-investigators and colleagues who made this study possible. the authors would like to thank changsha cdc, hunan cdc, and ccdc for their assistance with laboratory testing. we thank letpub (www. letpub.com) for its linguistic assistance during the preparation of this revised manuscript. conceptualization: jian zhou and zhiguo zhou. key: cord-291583-1nxfh9yt authors: zhou, hongmei; zhang, gangcheng; deng, xiaoxian; jin, bowen; qiu, qiu; yan, menghuan; wang, xi; zheng, xuan title: understanding the current status of patients with pulmonary hypertension during covid-19 outbreak: a small-scale national survey from china date: 2020-05-18 journal: pulm circ doi: 10.1177/2045894020924566 sha: doc_id: 291583 cord_uid: 1nxfh9yt pulmonary hypertension is a chronic disease developing progressively with high mortality. pulmonary hypertension patients need persistent medical care; however, limited reports focused on them when there was an outbreak of coronavirus disease 2019 in china. this national survey was aimed to evaluate the overall condition of pulmonary hypertension patients during this period. a questionnaire regarding the living condition of pulmonary hypertension patients during coronavirus disease 2019 was designed by pulmonary hypertension diagnostic experts in wuhan asia heart hospital. pulmonary hypertension patients and their family members were invited to participate in this survey online. one-hundred twenty pulmonary hypertension patients and 23 family members participated in the survey; 64.8% (n = 87) participants came from hubei, and others were from 15 other provinces; 98.6% (n = 141) participants were in home quarantine; 65.8% (n = 79) were pulmonary arterial hypertension associated with congenital heart disease; and 76.7% (n = 92) patients proclaimed their heart function was well maintained at class i or ii. one (0.8%) patient was confirmed severe acute respiratory syndrome coronavirus 2 infection. two (1.7%) patients were hospitalized due to heart function worsening. nearly 70% (n = 100) participants implied shortage in medications during coronavirus disease 2019 outbreak. a total of 24.2% (n = 29) patients indicated that medications were discontinued due to the insufficient supply. most of the participants stayed optimistic on either coronavirus disease 2019 outbreak or their pulmonary hypertension disease, and 61.7% (n = 74) patients would go to the hospital for follow-up immediately after outbreak. these preliminary data show pulmonary hypertension patients are able to avoid severe disease when they are in home quarantine. medication supplement is important for pulmonary hypertension patients when their heart function is well maintained. in addition, there might be increasing requirements of medical care for pulmonary hypertension patients after the outbreak. pulmonary hypertension (ph) is a chronic and progressive lung disease caused by multiple differing etiologies. increasing pulmonary vascular resistance led to overloading of the right ventricle and eventually death. 1 ph is characterized by a mean pulmonary artery pressure (mpap) ! 25 mmhg at rest. in addition to the treatment of relieving symptoms, targeted therapy aiming to improve heart function extended three-year survival of pulmonary arterial hypertension (pah) from 39% to 75%. 2, 3 coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was first reported in wuhan, china, in last december. 4 studies observed severe damage in the lung, which raised the hypothesis that ph patients might be more vulnerable than others. 5 subsequently, the whole country was placed in lockdown to prevent the spread of the disease, which potentially could compromise ph patient care. all these factors made ph patients a potentially vulnerable group. hereby, we designed a questionnaire for ph patients to understand their disease condition, mental condition, medication supplement, and requirements in medical care during covid-19 outbreak. the survey would provide general information for future medical care and support to ph patients in such conditions. the study was conducted by experts from congenital heart disease center at wuhan asia heart hospital in wuhan in collaboration with other ph centers and unofficial patients groups. patients diagnosed with ph and their families were considered for the survey. ph was defined as mpap ! 25 mmhg at rest. all diagnosis was made according to right heart catheter examination. a small-scale national online survey was performed. ph patients and one of their family members were invited to participate in the survey via quick response (qr) code. all answers were listed in non-medical descriptions and reviewed by unprofessional individuals for better understanding. no personal information was included. the study protocol and questionnaire were reviewed and approved by the ethics committee of wuhan asia heart hospital (2020-s-002). participants were given informed consent during the survey. the questionnaire was designed by experts on ph in wuhan asia heart hospital, wuhan, china. to understand the status of ph patients during covid-19 outbreak in china, the questions were designed to cover the following issues: (1) basic clinical information of the patients, including age, gender, medical history of ph, and current heart function; (2) physical and mental conditions associated with covid-19; and (3) details of the medications they were using and requirements for medical care if any. questions were designed in single choice and multiple choices. ''yes'' or ''no'' were offered for most questions, and answers other than choices were required to fill. the questionnaire is still open for recruitment (questionnaire in supplement). here, we present the preliminary data from the first respondents. baseline characteristics are presented as number for categorical data, and mean ae standard deviation or median with interquartile range as appropriate for continuous data. percentage is applied for illustrating constitution. comparison was made between variables using student's t-test or wilcoxon signed-rank test for continuous variables regarding their distributions and with the v 2 test for categorical variables. a p-value of < 0.05 was considered as statistically significant. all statistical analyses were performed with spss 23.0 (ibm corp, armonk, ny). over 300 individuals were invited to participate in this survey. a total of 120 ph patients and 23 family members from 16 provinces responded from 1 march 2020 to 11 march 2020. all questionnaires were included in final analysis. a total of 64.8% (n ¼ 87) participants were from hubei, among which 29.9% (n ¼ 26) were from wuhan; 13.3% (n ¼ 19) were from henan, 7.0% (n ¼ 10) from anhui, and 18.9% (n ¼ 27) came from other 13 provinces (as shown in fig. 1 ). both patients and their family members completed the survey in 13 families; however, we failed to identify them due to the design. table 1 shows general information of the participants. overall participants were aged 32.3 ae 11.5 years. a total of 61 patients suffered ph more than seven years. three family participants did not know ph history of their relatives. possibly due to the different etiology, 6 chd-pah contributed most in ph groups (79, 65.8% in patients; 13, 56.5% in family participants; p < 0.001). a total of 98.6% (n ¼ 141) participants were in home quarantine during covid-19 outbreak. table 1 shows the majority of participants (121, 84.6%) felt not much change on disease progress. surprisingly, most patients were with less severe symptoms as 46.9% (n ¼ 67) participants proclaimed new york heart association heart functional class i and 44 (30.8%) were class ii. a total of 83.3% (n ¼ 100) patients and 91.3% (n ¼ 21) family participants reported the disease progression was the same as before. fatigue and less active was more reported in patients (20% vs 0, p ¼ 0.026); however, cough was common in both patients and family participants (5.8% vs 13.0%, p ¼ 0.203) (as shown in fig. 2 ). symptoms in ''others'' included not sleeping well, chest pain, aching pain in limbs, and catching a cold but recovered. there were three (2.5%) patients hospitalized during covid-19 outbreak, two of them were because of heart failure and one was due to pneumonia. none of the family participants reported death of patients. actually, three patients passed away by 11 march 2020. one of the patients died due to an unexpected fall and unable to go to hospital during outbreak. two died from worsening of pah. all deaths were reported by family privately, and not included in the survey. fever is an important symptom indicating covid-19. in our survey, 5.0% (n ¼ 6) patients had fever with highest temperature of 39.8 c. one patient was confirmed sars-cov-2 infection, and two patients reported covid-19 related symptoms (cough) in their families. all family participants denied covid-19 related symptoms in either themselves or patients. bosentan, ambrisentan, tadalafil, and sildenafil were most commonly used medications for target therapy (as shown in fig. 3 ). specifically, ambrisentan was preferred in 57.5% (n ¼ 69) patients and 60.9% (n ¼ 14) family participants. a total of 21.6% (n ¼ 26) patients and 26.1% (n ¼ 6) family participants chose chinese generic ambrisentan because of the lower price in chinese generic medication. there were 17 patients enrolling in clinical trial and using macitentan for free. patients were more sensitive to the shortage of medications than family participants (62, 51.7% vs 4, 17.4%, p ¼ 0.003). there were 26.6% participants (29 in patients; 9 in family participants) who thought they had enough medications by the time of survey, when it was at least 40 days after national lockdown (as shown in fig. 4a) . a total of 40.0% (n ¼ 48) patients were able to buy more medications with great effort; however, 24.2% (n ¼ 29) discontinued one or more medications. there were 10 (7.0%) patients changing their medications without consulting their doctors (as shown in fig. 4a) , two of which previously took macitentan. a total of 100 participants (69.9%) thought they had medications shortage during covid-19 outbreak (as shown in fig. 4b ). psychological conditions over 20.0% patients (n ¼ 29) and family participants (n ¼ 6) had panic, but most of them (89, 62.2%) thought protection was important (as shown in fig. 5a ). though 48.3% (n ¼ 58) patients and 39.1% (n ¼ 9) family participants felt bad due to the disease, more than 70% (85 in patients; 18 in family participants) participants still kept optimistic at the same time (as shown in fig. 5b ). both ph patients and their families requested further medical care despite of a lack of clear clinical worsening according to our survey. a total of 11.7% (n ¼ 14) patients and 26.1% (n ¼ 6) family participants would like to contact their doctors during covid-19 outbreak; 61.7% (n ¼ 74) patients would go to the hospital for follow-up immediately after public transportation was available, eight of whom preferred hospitalization; and 60.9% (n ¼ 14) family participants would ask their relatives with ph go to the hospital as soon as possible, which was similar to patients. additionally, 73.9% (n ¼ 17) family participants would also encourage patients to be more positive. the outbreak of covid-19 changed most people's life in last winter. specifically, patients with chronic diseases might suffer from the high risk of covid-19 and uncontrolled existing diseases at the same time. ph patients require sustained medical care similar to other chronic diseases. any interruption in medications may result in clinical worsening and death. however, their living condition during covid-19 was unknown. our small-scale national survey brought an insight to this group. the results of the questionnaire indicated that the incidence of covid-19 was not higher in ph patients according to our survey. regardless of incidental cough and fever in our patients, only one patient was confirmed sars-cov-2 infection. medication insufficiency was the most common problem in our patients as nearly 70% participants implied their medications shortage during covid-19 outbreak. a total of 24.2% patients discontinued medications, and 7.0% patients changed their medications without consulting their doctor. a total of 98.6% participants stayed at home during outbreak, and most of them were not depressed by either ph or covid-19 according to our survey. however, further requirements in medical care might significantly increase due to the high desire of follow-up, even hospitalization, from both patients and their families when covid-19 outbreak is over. in early studies, covid-19 patients often stayed in wuhan for a while or had a history of exposure to confirmed cases. family cluster was also observed in several cases. 7 there were 18.2% (n ¼ 26) participants from wuhan in our study, which might be the result of hospital location, and one of the patients groups were from hubei. none of them reported covid-19, neither in patients nor in family participants. person-to-person transmission is confirmed in covid-19, 8 and lockdown in wuhan began in 24 january 2020 to prevent further spread of this infectious disease. a total of 98.6% of our patients and their families were in home quarantine during covid-19 outbreak, which might be a key factor that prevented our patients being infected. previous studies showed 32-51% patients with covid-19 had existing diseases, such as diabetes, hypertension, and other cardiovascular diseases. males were more vulnerable. mean age of the patients were 49-55 years from different study cohort. [9] [10] [11] our participants were 33 years old at mean age, which was much younger than previous covid-19 patients. our study cohort consisted of 80% females, which was quite different from the proportion of covid-19. in addition, most of our patients were chd-pah and maintained a fairly well heart function. therefore, the younger age, more females, different etiology, and better cardiac function in our ph patients might result in a lower incidence of covid-19. similar to any other chronic diseases, ph patients have to take life-time medications, and most of them had higher medication adherence. 12 bosentan was first used in pah in 2002, 13 and it significantly improved six-minute walk distance and heart function. since then, targeted treatment has extended more than half of patients' life to three or even five years. 14 combination therapy recommended in recent years has further reduced adverse events and slowed down the ph progression. 3, [15] [16] [17] in our study, patients took ambrisentan more than bosentan partly due to the lower price in chinese generic medication. a total of 17 patients were taking macitentan for free. treprostinil was used in very few patients because of the high price and inconvenience of chd-pah: pulmonary arterial hypertension associated with congenital heart disease; cteph: chronic thrombotic embolism pulmonary hypertension; ctd-pah: pulmonary arterial hypertension associated with connective tissue disease; ipah: idiopathic pulmonary arterial hypertension; na: not applicable; nyha: new york heart association; ph: pulmonary hypertension. intravenous application. 18 luckily, 40.0% of patients were able to continue their medications with great effort during the national lockdown. different from other cardiovascular diseases, ph target medications are expensive and unavailable in small cities, which might result in the shortage of medications in our ph patients. the lockdown in cities additionally prevented patients from getting supplement. nearly 30% of patients either discontinued their medications or changed without consultation. we have tried to help some of our patients to buy medications; however, shutdown of most public transportations made the process very difficult. we could hardly predict the prognosis of those who changed their treatment for less than 40 days. an interruption of treatment around three days might be tolerated, 19 but clinical worsening might happen due to the discontinuation of medications. 20 patients preferred clinic visiting to consult doctors for any modification. our patients showed higher desire to contact their doctors even though we had provided online consultation before the survey. mental condition of ph patients has aroused attentions in recent years. their concerns about the invasive examination, disease progression, and social interactions may directly impact their tolerance to treatment. 21 the outbreak of covid-19 brought an unexpected crisis first in wuhan, then spread to other cities. surprisingly, our ph patients and their families were mostly not panicking during the outbreak. they were overall positive and optimistic even though there were shortages on their medications. the reasons for such response might be as follows: first, most ph patients stayed at home which was familiar and comfort for them. second, there were not many clinical worsening in our patients. their disease condition was mostly constant during the outbreak, which maintained their optimism. third, we, the doctors, were active in patients groups, including being available for consultation online, and offering assistance for medication supplement. all these might be helpful to reduce their anxiety. our results provided preliminary view in living condition of ph patients during covid-19 in china; however, several limitations in our study need to be addressed: first of all, there were only 120 ph patients participating in the survey. the small-scale survey might give us some general information, which also might bring bias in some aspects. the results might highlight chd-pah, due to that chd-pah contributed most in the study population. further study should try to include more patients to get more details. the questionnaire was designed to generate the information from both patients and their family members; however, we failed to match patients with their family members from the beginning. studies could avoid such mistakes and focus on patients more. second, the survey was started 35 days after wuhan lockdown and lasted 10 days. most ph patients might be still stable in such a short time. studies conducted later or longer might observe more clinical worsening and anxiety in patients and their families. although no death was reported in our survey, three patients passed away based on our knowledge. neither patients nor their families would participate in the survey if they were in critical condition. therefore, our results might be more optimistic than real world. follow-up to the real mortality has been initialed. third, there were many uncertainties in online survey. we involved a question to estimate whether participants were seriously taking the survey. the result showed 86.7% patients and 91.0% family participants went through the survey carefully, which indicated there might be misunderstanding and incorrect answers. our small-scale national survey first investigated the living condition of ph patients during covid-19. as the disease is spreading all over the world, doctors should be aware that ph patients could be invulnerable to covid-19 if they are in good protection. sustaining medical care, including medication supplement, is important for ph patients at this time. covid-19 might impact ph patients psychologically other than physically. higher hospitalization even death might been seen when the outbreak is over. elevated pulmonary arterial elastance and right ventricular uncoupling are associated with greater mortality in advanced heart failure survival of chinese patients with pulmonary arterial hypertension in the modern treatment era combination therapy improves exercise capacity and reduces risk of clinical worsening in patients with pulmonary arterial hypertension: a meta-analysis a novel coronavirus from patients with pneumonia in china clinical characteristics of coronavirus disease 2019 in china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiological characteristics of 2019-ncov infections in shaanxi epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with 2019 novel coronavirus in wuhan, china the clinical dynamics of 18 cases of covid-19 outside of wuhan, china treatment patterns, healthcare resource utilization, and healthcare costs among patients with pulmonary arterial hypertension in a real-world us database bosentan therapy for pulmonary arterial hypertension survival of patients with schistosomiasis-associated pulmonary arterial hypertension in the modern management era initial dual oral combination therapy in pulmonary arterial hypertension clinical and hemodynamic improvements after adding ambrisentan to background pde5i therapy in patients with pulmonary arterial hypertension exhibiting a suboptimal therapeutic response (athena-1) combination therapy in pulmonary arterial hypertension: recent accomplishments and future challenges cost effectiveness of bosentan for pulmonary arterial hypertension: a systematic review temporary treatment interruptions with oral selexipag in pulmonary arterial hypertension: insights from the prostacyclin (pgi2) receptor agonist in pulmonary arterial hypertension (griphon) study treatment discontinuation or interruption in pulmonary arterial hypertension the importance of patient perspectives in pulmonary hypertension we would like to thank all patients and their families participating in the survey. we also would like to thank all colleagues who helped in designing and performing the survey. the study was reviewed and approved by the ethics committee of wuhan asia heart hospital (2020-s-002). xuan zheng https://orcid.org/0000-0002-8433-6198 supplemental material for this article is available online. h.z. and x.z. designed the study. g.z., b.j., x.d., q.q., m.y., and x.w. collected data. x.z. and m.y. performed the statistical analysis. x.z. and x.d. wrote the manuscript. h.z. and g.z. reviewed and edited the manuscript. all authors read and approved the final manuscript. the author(s) declare that there is no conflict of interest. key: cord-309569-b9jcgx4s authors: lin, qiu-shi; hu, tao-jun; zhou, xiao-hua title: further explanations for the eq. (3) in “estimating the daily trend in the size of the covid-19 infected population in wuhan” date: 2020-09-15 journal: infect dis poverty doi: 10.1186/s40249-020-00749-5 sha: doc_id: 309569 cord_uid: b9jcgx4s to avoid possible confusions to the readers, we provide further explanations for the eq. (3) in the research article “estimating the daily trend in the size of the covid-19 infected population in wuhan” published in the infectious diseases of poverty. in our study [1] , we proposed a new model to estimate the daily trend in the size of the covid-19 infected population in wuhan. when discussing this article with our colleagues, we found that a little more explanations for eq. (3) are needed to avoid possible confusions to the readers. in the methods section, we let x t be the number of imported cases outside hubei province on day t, and derive a binomial model to make our model clearer, here x t is in fact the number of infected individuals that travelled from wuhan to places outside hubei province on day t − d. however, among the 10 940 confirmed cases in our data, 8546 (78.1%) do not have information on the date of departure from wuhan, so the number of cases leaving wuhan every day is unknown and hard to impute. but the date of confirmation is available for each of the 10 940 cases, so we use the cumulative number of imported cases outside hubei province as of day t as apx k . since the window from infection to detection is assumed as d days in our model, the infected cases that left wuhan before day t − d should be confirmed outside hubei province before day t, thus this approximation is reasonable and would not affect the conclusion in the paper. estimating the daily trend in the size of the covid-19 infected population in wuhan none.authors' contributions ql, th, and xz interpreted the results and wrote the manuscript. all authors read and approved the final manuscript. not applicable. the authors declare that they have no competing interests. received: 3 august 2020 accepted: 1 september 2020 key: cord-301633-t8s4s0wo authors: gralinski, lisa e.; menachery, vineet d. title: return of the coronavirus: 2019-ncov date: 2020-01-24 journal: viruses doi: 10.3390/v12020135 sha: doc_id: 301633 cord_uid: t8s4s0wo the emergence of a novel coronavirus (2019-ncov) has awakened the echoes of sars-cov from nearly two decades ago. yet, with technological advances and important lessons gained from previous outbreaks, perhaps the world is better equipped to deal with the most recent emergent group 2b coronavirus. the third zoonotic human coronavirus (cov) of the century emerged in december 2019, with a cluster of patients with connections to huanan south china seafood market in wuhan, hubei province, china. similar to severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) infections, patients exhibited symptoms of viral pneumonia including fever, difficulty breathing, and bilateral lung infiltration in the most severe cases [1] . news reports of patients with an unknown pneumonia were first identified on 31st december with the wuhan municipal health commission saying they were monitoring the situation closely ( figure 1 ). on 1st january 2020, the seafood market was closed and decontaminated while countries with travel links to wuhan went on high alert for potential travelers with unexplained respiratory disease. after extensive speculation about a causative agent, the chinese center for disease control and prevention (cdc) confirmed a report by the wall street journal and announced identification of a novel cov on 9th january [2] . the novel cov (2019-ncov) was isolated from a single patient and subsequently verified in 16 additional patients [3] . while not yet confirmed to induce the viral pneumonia, 2019-ncov was quickly predicted as the likely causative agent. the first sequence of 2019-ncov was posted online one day after its confirmation on behalf of dr. yong-zhen zhang and scientists at fudan university, shanghai [4] . subsequently, five additional 2019-ncov sequences were deposited on the gsaid database on 11th january from institutes across china (chinese cdc, wuhan institute of virology and chinese academy of medical sciences & peking union medical college) and allowed researchers around the world to begin analyzing the new cov [5] . by 17th january, there were 62 confirmed cases in china and importantly, three exported cases of infected travelers who were diagnosed in thailand (2) and japan (1) [6] . the sequences of these exported cases and several additional 2019-ncov isolated in china have also been deposited on the gsaid database [5] . diagnostic tests have subsequently been developed and some are being used on suspect cases identified in other locations including vietnam, singapore, and hong kong [7] . to date there have been twenty-six fatalities associated with 2019-ncov infection, many of these cases had significant co-morbidities and were older in age (>50). a range of disease has been observed highlighted by fever, dry cough, shortness of breath, and leukopenia; patients have included mild cases needing supportive care to severe cases requiring extracorporeal membrane oxygenation; however, compared to sars-cov (10% mortality) and mers-cov (35% mortality), the 2019-ncov appears to be less virulent at this point with the exception of the elderly and those with underlying health conditions. initial monitoring of case close contacts had not revealed any further 2019-ncov cases. however, modeling analysis based on official case numbers and international spread suggested that there may be cases going undetected [8] . on 19th january, these fears were seemingly confirmed as an additional 136 cases were added from further surveys raising the total in wuhan to 198 infected patients [9] . among the 198 total cases in wuhan, 170 remained in hospitals, 126 mostly with mild symptoms, 35 in serious condition, and 9 in critical condition. the expanded numbers and extended range of onset dates (12 december 2019-18 january 2020) suggested likely human to human transmission or ongoing transmission from a market or other primary sources. on 20th january, the outbreak was further expanded to other parts of china (beijing, shanghai, & shenzhen) as well as another exported cases to south korea. as of january 24, the total case number has expanded to at least 870 total cases with 26 deaths across 25 provinces in china and 19 exported cases in 10 countries [10] . public health authorities have quarantined travel from wuhan to limit the spread of the virus and reports indicate other chinese cities have also been isolated [11] . with the heavy travel season for lunar new year underway in asia, major concerns exist for the 2019-ncov outbreak to continue and spread. the source of the 2019-ncov is still unknown, although the initial cases have been associated with the huanan south china seafood market. while many of the early patients worked in or visited the market, none of the exported cases had contact with the market, suggesting either human to human transmission or a more widespread animal source [6] . in addition to seafood, it is reported on social media that snakes, birds and other small mammals including marmots and bats were sold at the huanan south china seafood market. the who reported that environmental samples taken from the marketplace have come back positive for the novel coronavirus, but no specific animal association has been identified [6] . an initial report suggested that snakes might be the possible source based on codon usage [12] , but the assertion has been disputed by others [13] . researchers are currently working to identify the source of 2019-ncov including possible intermediate animal vectors. a zoonotic reservoir harkens back to the emergence of both sars-and mers-cov. sars-cov, the first highly pathogenic human cov, emerged in 2002 with transmission from animals to humans occurring in wet markets. surveillance efforts found sars-cov viral rna in both palm civets and raccoon dogs sold in these wet markets [14] ; however, sars-cov was not found in the wild, suggesting that those species served as intermediary reservoir as the virus adapted to more efficiently infect humans. further surveillance efforts identified highly related covs in bat species [15] . more recent work has demonstrated that several bat covs are capable of infecting human cells without a need for intermediate adaptation [16, 17] . additionally, human serology data shows recognition of bat cov proteins and indicates that low-level zoonotic transmission of sars-like bat coronaviruses occurs outside of recognized outbreaks [18] . mers-cov is also a zoonotic virus with possible origins in bats [19, 20] , although camels are endemically infected and camel contact is frequently reported during primary mers-cov cases [21] . for sars-cov, strict quarantine and the culling of live markets in se asia played a major role in ending the outbreak. with the cultural importance of camels, a similar approach for mers-cov was not an option and periodic outbreaks continue in the middle east. these lessons from sars and mers highlight the importance of rapidly finding the source for 2019-ncov in order to stem the ongoing outbreak. with limited patient data, it is difficult to make robust declarations about populations that may be most susceptible to 2019-ncov. however, disease severity following sars-and mers-cov corresponded strongly to underlying host conditions including age, biological sex, and overall health [22] . early patient reports from 2019-ncov find similar trends. severe illness with 2019-ncov has been associated with elderly patients (>60 years old), including twenty-six lethal cases. these findings correspond to increased severity and death in people over the age of 50 following both sars and mers-cov infection [23, 24] . similarly, the underlying health of the patient likely plays a critical role in overall susceptibility. for the 2019-ncov, limited comorbidity data is available; however, the twenty-six patients that have succumbed to the novel cov had significant health conditions including hypertension, diabetes, heart and/or kidney function issues that may have made them more susceptible. for the mers-cov outbreak, smoking, hypertension, diabetes, cardiovascular disease, and/or other chronic illnesses have been present in the majority of deaths and correspond to findings in animal models [25] . the results indicate vigilance is necessary for these vulnerable patients following 2019-ncov infection. the rapid sequencing of the nearly 30,000 nucleotide 2019-ncov genome by dr. zhang's group at fudan university and several other groups in china illustrate the dedication and increased capacity of the scientific infrastructure in china [4, 5] . for sars-cov, the causative agent was unknown for months and subsequently took over four weeks until a full genome was released [26] . similarly, mers-cov was only identified after several months of testing and a full-length genome available about a month later [27] . in contrast, time from the first date of patient onset (12 december 2019) to the report of several 2019-ncov full-length genomes took less than one month. combined with the immense pressure of an ongoing outbreak with an unknown agent, the effort of these scientists should be considered nothing less than remarkable. building from the sequence, the nucleotide alignment quickly distinguished the novel virus as a group 2b cov, distinct from the sars-cov strains [4, 5] . examining the whole genome, 2019-ncov maintains~80% nucleotide identity to the original sars epidemic viruses. its closest whole genome relatives are two bat sars-like covs (zc45 and zxc21) that shared~89% sequence identity with 2019-ncov; these cov sequences were deposited in early 2018 from zhejiang province in r. sinicus bats in china. comparing across the deposited 2019-ncov strains finds > 99.5% conservation; the lack of diversity suggests a common lineage and source with emergence not likely having occurred that long ago [28, 29] . a recent report has subsequently identified a bat cov sequence, ratg3, with 92% sequence identity with the novel virus which argues for bat origins for the 2019-ncov [30] . we next shifted analysis to the nucleocapsid (n) protein, the most abundant protein produced in covs. generally, the n protein is well conserved across cov families including group 2b [31] . the n protein for 2019-ncov is no exception with~90% amino acid identity to the sars-cov n protein. while less conserved than other group 2b covs like hku3-cov and shc014-cov, 2019-ncov antibodies against the n protein would likely recognize and bind the sars-cov n protein as well. n antibodies do not provide immunity to 2019-ncov infection, but the cross reactivity with sars-cov n protein would allow a serum based assay to determine exposure to the novel cov in asymptomatic cases. while previous studies have found serum reactivity to group 2b virus n proteins in chinese populations [18] , exposure to 2019-ncov should increase the dilution factor substantially if exposure/infection had occurred. importantly, this information may provide insights about susceptibly and potential routes of spread through asymptomatic carriers. examining further, we next compared the spike proteins, the critical glycoprotein responsible for virus binding and entry. overall, the 2019-ncov spike protein has roughly 75% amino acid identity with sars-cov, which is less conserved than other group 2b covs including hku3-cov [31] . however, narrowing analysis to the spike receptor binding domain (rbd) of sars-cov (amino acids 318-518), the 2019-ncov rbd is 73% conserved relative to the epidemic rbd. this conservation level places the 2019-ncov rbd between hku3-4 (62.7% conservation), a bat virus that cannot use human ace2, and rshc014 (80.8%), the most divergent bat cov spike known to use human ace2 for entry [16, 32] . importantly, the key binding residues for sars-cov have been identified [33] ; among these fourteen residues predicted to interact directly with human ace2, the receptor for sars-cov, eight amino acids are conserved in 2019-ncov. notably, several of these residues are also conserved relative to wiv1-and wiv16-cov, two bat strains closely related to sars-cov and known to use human ace2 [17, 34] . initial structural modeling suggest that the 2019-ncov may be able to use human ace2 as a receptor, although its affinity m be reduced relative to the epidemic sars-cov strains [35] . a subsequent report demonstrated that the receptor binding domain of 2019-ncov was capable of binding ace2 in the context of the sars-cov spike protein [36] . in addition, another rapid report links demonstrates 2019-ncov uses ace2 receptors from human, bat, civets, and swine [30] . together, the modeling, pseudotyping, and infection data provide strong evidence for human ace2 being the receptor for 2019-ncov. traditional identification of a microbe as the causative agent of disease requires fulfillment of koch's postulates, modified by rivers for viral diseases [37] . at the present time, the 2019-ncov has been isolated from patients, detected by specific assays in patients, and cultured in host cells (one available sequence is identified as a passage isolate), starting to fulfill these criteria. given the recentness of the 2019-ncov outbreak, at this point there is no animal model available to fulfill the remaining criteria: 1) testing the capability of 2019-ncov to cause respiratory disease in a related species, 2) re-isolating the virus from the experimentally infected animal and 3) detection of a specific immune response. these efforts will surely be an area of intense research in the coming months both in china and in cov research laboratories around the world. notably, generating small animal models of coronavirus disease can be difficult. while sars-cov readily infected laboratory mice, it does not cause significant disease unless the virus is passaged to adapt to the mouse host [38] . infection of primates produces a more mild disease than that observed in humans, although fever and pulmonary inflammation were noted [39, 40] . mers-cov is incapable of infecting rodent cells without engineering changes in critical residues of the receptor protein, dpp4 [41, 42] . however, mers-cov does infect non-human primates [43] . as such, mers mouse models of disease required a great deal of time to develop and are limited in the types of manipulations that can be performed [41] . at this point, the infectious capability of the 2019-ncov for different species and different cell types is unknown. early reports suggest that the virus can utilize human, bat, swine, and civet ace2 [30] ; notably, the group found mouse ace2 was not permissive for 2019-ncov infection dissemination of virus stocks and/or de novo generation of the virus through reverse genetics systems will enable this research allowing for animal testing and subsequent completion of koch's postulates for the new virus. while the huanan seafood market in wuhan has been associated with the majority of cases, many of the recent cases do not have a direct connection [9] . this fact suggests a secondary source of infection, either human to human transmission or possibly infected animals in another market in wuhan. both possibilities represent major concerns and indicate the outbreak has the potential to expand rapidly. for human to human transmission, there was limited data in the initial set of cases; one family cluster is of three men who all work in the market. similarly, a husband and wife are among the patients, with the wife claiming no contact with the market. in these cases, direct human to human infection may have been possible; alternatively, a contaminated fomite from the market may also be responsible as surfaces all around the market were found to test positive 2019-ncov. however, the major increase in the number of cases, the lack of direct connection to the wuhan market for many cases, and the infection of health care works all suggest human to human spread is likely [9, 44] . importantly, until the source of the virus is found, it will be difficult to distinguish zoonotic versus human to human spread. in the early part of the outbreak, the absence of infection in health care workers argued for inefficient human to human spread and distinguished 2019-ncov from both sars-cov and mers-cov. in the two prior cov epidemics, health care settings served as a major transmission point fueling both outbreaks. based on who data, 1 in 10 mers-cov cases have been found to be health care workers; these patients generally have reduced disease and death likely due to younger age and absence of existing health conditions. the recent reports of numerous infected health care workers in wuhan indicate human to human infection can occur with 2019-ncov and may be the product of a super spreading patient [44] . however, while large swaths of healthcare workers are not getting sick as seen with sars and mers-cov, it may be too early to rule out their potential exposure to the novel cov as their disease may be asymptomatic. while not described during the sars-cov outbreak, asymptomatic cases ranged from 12.5% to 25% in some mers-cov studies [45] . a similar phenomenon may be occurring with 2019-ncov and would make stopping the outbreak even more difficult to contain. another parameter to consider is the possibility of super spreading in the context of 2019-ncov. super spreading is the amplified transmission of a virus by individuals in a population and has been suggested by at least one news report [44] . both sars-and mers-cov outbreaks had documented evidence of super spreading patients [46] . in general, both epidemic covs maintain a low r 0 , the rate spread from an individual infected patient. however, roughly 10% of sars-and mers-cov patients have been associated with super spreading and an r 0 > 10. these cases seeded a significant portion of the epidemic around the world. notably, neither mutations in the viruses nor severity of disease were found to be associated with super spreading, implying that host factors contribute to the phenotype [47] . for 2019-ncov, contact tracing to date suggest limited human to human spread and a low r 0 . however, the recent increase in cases, both in and outside wuhan could signal the existence of super-spreading individuals fueling the outbreak. alternatively, super spreading could occur from the zoonotic source which has been seen in other disease outbreaks [10] . in any event, the possibility of super spreading may continue to play a role in this ongoing 2019-ncov outbreak. news of the 2019-ncov came to widespread attention through the internet. over the years, websites like flutrackers.com, promed (promedmail.org), and others have permitted the collection of disease information from around the world and facilitated dissemination to interested parties. in 2012, mers-cov first drew attention as a "novel coronavirus" entioned on promed mail and subsequently through conversation on twitter between science journalists, virologists, and public health experts. eight years later, a more connected network quickly dissected statements from the wuhan municipal health commission and speculated about possible causes. early during an outbreak, it can be difficult to distinguish between rumors with elements of truth versus baseless fear mongering. this fact can be exacerbated by language barriers and off the record sources. however, in this case, speculation of a novel coronavirus was fed by carefully worded statements that specifically excluding some virus families (influenza, adenovirus), but only excluded sars-cov and mers-cov for coronaviruses. coupled with memories of the sars outbreak, many worried that the truth may be held back. when the agent was finally confirmed as a cov, the world acted with both worry and relief: the outbreak would not be hidden. while far from perfect, the government response to 2019-ncov provides a stark contrast to the sars outbreak at the beginning of the century. the rapid release of 2019-ncov sequences permitted the research community to quickly become engaged, providing analysis and developing diagnostic tests. both the chinese cdc and the wuhan municipal health commission have posted regular updates of confirmed case numbers and patient statuses enabling public health authorities to monitor the situation in real time. researchers from around the world have connected on social media to compare updated sequence information and highlight key unknowns about the outbreak. while not always provided in a timely manner, the ability to share news updates and data in real time with researchers and public health officials around the world signals a major change in the response to outbreaks. this connectivity has facilitated awareness as well as new collaborations and a rapid response by the global research community. while there are many unknowns with 2019-ncov, the world is engaged and prepared to battle the newest emergent virus strain. perhaps this means the lessons from the sars outbreak have truly been learned. wuhan municipal health commision. wuhan municipal health and health commission's briefing on the current pneumonia epidemic situation in our city world health organization. who statement regarding cluster of pneumonia cases in wuhan gsaid database. 2020 coronavirus. available online world health organization. novel 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replication of sars coronavirus administered into the respiratory tract of african green, rhesus and cynomolgus monkeys newly discovered coronavirus as the primary cause of severe acute respiratory syndrome host species restriction of middle east respiratory syndrome coronavirus through its receptor, dipeptidyl peptidase 4 mouse dipeptidyl peptidase 4 is not a functional receptor for middle east respiratory syndrome coronavirus infection middle east respiratory syndrome coronavirus (mers-cov) causes transient lower respiratory tract infection in rhesus macaques 15 medical staff in wuhan confirmed new coronavirus pneumonia, and another suspected asymptomatic middle east respiratory syndrome coronavirus (mers-cov) infection: extent and implications for infection control: a systematic review the role of super-spreaders in infectious disease analysis of intrapatient heterogeneity uncovers the microevolution of middle east respiratory syndrome coronavirus key: cord-259229-e8m8m4ut authors: samidurai, arun; das, anindita title: cardiovascular complications associated with covid-19 and potential therapeutic strategies date: 2020-09-16 journal: int j mol sci doi: 10.3390/ijms21186790 sha: doc_id: 259229 cord_uid: e8m8m4ut the outbreak of coronavirus disease 2019 (covid-19), an infectious disease with severe acute respiratory syndrome, has now become a worldwide pandemic. despite the respiratory complication, covid-19 is also associated with significant multiple organ dysfunction, including severe cardiac impairment. emerging evidence reveals a direct interplay between covid-19 and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. the proposed pathophysiological mechanisms of myocardial impairment include invasion of sars-cov-2 virus via angiotensin-converting enzyme 2 to cardiovascular cells/tissue, which leads to endothelial inflammation and dysfunction, de-stabilization of vulnerable atherosclerotic plaques, stent thrombosis, cardiac stress due to diminish oxygen supply and cardiac muscle damage, and myocardial infarction. several promising therapeutics are under investigation to the overall prognosis of covid-19 patients with high risk of cardiovascular impairment, nevertheless to date, none have shown proven clinical efficacy. in this comprehensive review, we aimed to highlight the current integrated therapeutic approaches for covid-19 and we summarized the potential therapeutic options, currently under clinical trials, with their mechanisms of action and associated adverse cardiac events in highly infectious covid-19 patients. coronavirus-19 is an emerging infectious disease caused by the novel single-stranded rna enveloped severe acute respiratory syndrome-coronavirus-2 (sars-cov-2). the first case of covid-19 was reported on 8 december 2019 in hubei province of china [1] and within a short span of time, the disease quickly spread to other parts of the world [2] and has rapidly evolved as a global pandemic situation. the first confirmed case of covid-19 in the united states of america (usa) was reported on 20 january 2020 in the state of washington when a 35-year-old man showed symptoms of sars-cov-2 infection after returning from wuhan, china [3] . the first person-to-person transmission of a confirmed covid-19 case in usa was reported in illinois on 30 january 2020 after an initial positive diagnosis of covid-19 on the patient's wife, who returned from wuhan, china in mid-january 2020, and unfortunately, covid-19 is now widespread in all 50 states across the usa [4, 5] . according to johns hopkins coronavirus resource center, as of 9 september 2020, there are 27,699,974 confirmed covid-19 cases and 900,239 confirmed deaths worldwide [6] . usa is now the epicenter of the disease; the death toll has reached 190,763 with 6,358,983 confirmed covid-19 cases [7] . figure 1 is the graphical representation of most affected regions of confirmed cases with reported deaths across the world. countries with more than 100,000 confirmed cases with reported deaths are presented in figure 1a ,b; and countries with more than 50,000 cases (but fewer than 100,000) and corresponding reported deaths are shown in figure 1c ,d. understanding the structure and the genetic makeup of sars-cov-2 is important to appreciate the ongoing efforts to address this disease and for the discovery of drugs and vaccines. sars-cov-2 is spherical in shape and consists of multiple components which are essential for their replication and transcription: (1) several club shaped projections on the surface of the envelope, called spike glycoprotein (s), which helps in anchoring to the host cell and acts as an inducer to neutralize antibodies, (2) a small membrane envelope protein (e), (3) structural membrane protein (m), which spans the lipid bilayer, (4) hemagglutinin-esterase glycoprotein (he), which destroys the sialic acid present on the host cell and helps the virus to inject its genetic material, (5) nucleoprotein (n) and (6) the key component, the positive-sense single-stranded genomic rna [8] [9] [10] . the typical structure of covid-19 virus depicting the above-mentioned components is shown in figure 2a . the genome size of covid-19 is about 26.4-31.7 kb [11] and is the largest among all known rna viruses in this category (sars-cov and middle east respiratory syndrome, mers). sars-cov-2 encompasses several open reading frames (orf) along with its 5 utr and 3 utr regions. orf1a/b (frame shift) is the full-length gene (29.8 kb size) that encodes replicase polyprotein named pp1a protein and 16 accessary (non-structural proteins (nsps) and orf1b codes for pp1b and 10 nsps [11] [12] [13] [14] . the structural proteins including spike (s), envelope (e), membrane protein (m) and nucleoprotein (n) are coded by orfs 10 and 11 present on the 3' utr region. several other essential accessary proteins are coded by orf3, orf7a, orf7b, and orf8 [15] . the domain structure of sars-cov-2 is presented in figure 2b . the genomic sequencing data obtained from covid-19-infected patients in china revealed the distinct features of sars-cov-2 [16] . sequence comparison showed the novel sars-cov-2 was more distantly correlated with sars-cov (about 79%) and mers-cov (about 50%). some of the salient features of sars-cov-2 make it unique and virulent compared to previously known coronaviruses. reports suggest that sars-cov-2 lacks the orf8a protein present in sars-cov and has variation in the 3c and 8b proteins [12] . in addition, a single mutation at n501t in the spike protein strengthened the binding efficiency of sars-cov-2 to angiotensin-converting enzyme 2 (ace2), the primary mode of entry into host cell [17] . structural details of sars-cov binding to the host cell through spike protein give us the clue about the importance of the mutation in this region [18] . studies show that this mutation in the spike protein of sars-cov-2 increases its binding affinity to ace2 in human by 10-20 times higher than sars-cov [19] . this mutation in the spike protein may be one of the key attributes of sars-cov-2 that led to its rapid spreading around the world in a very short period. there are six different strains of sars-cov-2 identified so far, namely, (1) l strain (originated in wuhan, china and the parent orf8-l84s strain), (2) s strain (mutation of orf8, l84s), (3) v strain (variant of orf3a coding protein ns3, g251v), (4) g (mutation in spike protein, d614g), (5) gh strain (mutations in spike protein, d614g and orf3a, q57h) and (6) gr (mutation in nucleocapsid gene, rg203kr) [20, 21] . among these variants, g strain is the most widespread, has undergone several mutations since january 2020, and branched into subtypes gr and gh. the g and gr strains are prevalent in europe, including in italy, whereas the gh strain is widespread in germany and france. the most predominant variant found in north america is the gh strain, and this subtype along with the gr clades accounts for 74% of all global sequences of sars-cov-2 genome [22] . as of now, strains g, gh and gr are constantly increasing, globally, and it is yet to be determined whether the unique nature of these strains is associated with the disease intensity. covid-19 virus is predominantly transmitted from human to human through respiratory droplets or aerosols (>5-10 µm in diameter) and contact routes. inhalation of respiratory droplets and aerosols from covid-19-infected persons is the most likely potential mode of transmission of the disease [23] . once in the host system, sars-cov-2 follows the traditional steps similar to any other virus for its mode of entry into the host cells [24] . the spike protein anchors the virus to the surface of the host cell by binding to the ace2 receptor [25] . the virus undergoes conformational changes to fuse to the cell membrane of the host cells and engulfs into the cytoplasm of the cell by endosomal pathway. once inside the cell, the virus releases its genomic rna and multiplies using the host's molecular machinery. experimental evidence using hela cells demonstrate that sars-cov-2 entry into host cell is activated by cell surface proteases and lysosomal proteases such as transmembrane serine protease 2 (tmprss2) and lysosomal cathepsin [26] . ace2 is expressed in type ii alveolar cells, the predominant portal of entry in the lungs; it is also expressed in the heart, intestine and kidney as well as on the epithelial cells of oral mucosa and the tongue [27, 28] . sars-cov-2 primarily affects the respiratory tract, and infected patients suffer from pneumonia and flu-like symptoms ( figure 3 ). the patients might need intensive care and artificial ventilation after developing acute respiratory syndrome (ards) or multiple organ dysfunction syndrome (mods). the abundance of sars-cov-2 compromises the normal function and leads to complications in lungs (inflammation, hypoxia, cytokine storm, pulmonary edema, acute respiratory distress syndrome) and in heart (myocardial infarction, heart failure, myocarditis and arrhythmia). ace1, angiotensin i-converting enzyme; ace2, angiotensin-converting enzyme 2; acei, ace inhibitor; at1r, angiotensin type 1 receptor; at2r, angiotensin type 2 receptor; arbs, angiotensin ii type-i receptor blockers; ctni, cardiac troponin i; mas, mitochondrial assembly receptor; mras, mineralocorticoid receptor antagonists; tmprss2, transmembrane serine protease 2. the lungs, being a major organ targeted by sars-cov-2 infection, are severely compromised in delivering their function. one of the common clinical manifestations of covid-19 at the late stage of the disease is shortness of breath, pneumonia-like symptoms and hypoxia, which ultimately is fatal to the patients. in the pulmonary vasculature, sars-cov-2 enters through endocytosis and activates adam metallopeptidase domain 17 (adam17), which in turn cleaves ace2, which indicates the loss of protection against the renin-angiotensin-aldosterone system (raas), which is mediated by cleaved ace2 [29, 30] . the activation of adam17 also triggers acute pulmonary inflammation and infiltration of cytokines and leukocytes in the alveolar space and results in pulmonary edema [9, 31] . overactive systemic inflammation as a response to covid-19 infection results in cytokine storm and leads to respiratory difficulties and accounts for majority of the deaths during end stage of the treatment [32] . pulmonary complications associated with covid-19 infection include diseases such as acute respiratory distress syndrome (ards), vascular endothelialitis, sepsis, pulmonary edema and pulmonary embolism [33, 34] . a multicenter cohort study involving 235 hospitals from 24 countries, which includes 1128 patients and 294 cases of confirmed covid-19, suggests that up to 51.2% suffer severe pulmonary complications post-surgery and the majority of the deaths are largely due to pulmonary embolism [33] . lung autopsy reports obtained from covid-19 patients who died due to ards showed severe alveolar damage and infiltration of perivascular t-cells. histology analysis also demonstrated increased thrombus formation, intussusceptive angiogenesis and microangiopathy in covid-19 patients compared to influenza [32] . gene expression analysis using rna isolated from covid-19 patients showed several inflammatory markers and angiogenesis-related genes were differently regulated compared to healthy lungs. most importantly, there was a significantly increased positive count for ace2 in covid-19 tissues compared to control. covid-19 patients with ards were also characterized by an increased deposition of fibrin and high expression of d-dimers and fibrinogen, suggesting fibrinolysis as a determining factor of mortality [35] . although pulmonary complication is the dominant clinical manifestation of covid-19, underlying cardiovascular complication as well as developed acute cardiac injury enhances the vulnerability of the patient. acute respiratory complication/failure and cytokine storm may cause reduced oxygen supply, which could lead to acute myocardial injury in covid-19 patients [36] . patients with cardiovascular disease (cvd) have an increased risk for severity and mortality with covid-19 infection, mainly because of the abundance of ace2 receptor in the cardiovascular system, which serves as a gateway for the entry of virus in lungs and heart [37] . respiratory illness and acute cardiac injury are major clinical manifestations observed in patients infected with sars-cov-2 during the late stage complications of the disease [38] . reasonably, patients with coronary artery disease or heart failure are vulnerable to developing major cardiac injury, and once such patients are infected with sars-cov-2, they are at greatest risk of serious myocardial impairment or cardiac dysfunction, requiring hospitalization due to unexpected deterioration, and eventual mortality is greater among these patients. a brief view of cardiovascular complications associated with covid-19 is presented in figure 3 . voluminous available clinical evidence confirms that the severity of covid-19 is pronounced in patients with a prevalence of underlying cardiovascular diseases, and in many of these patients, the virus causes severe myocardial injury [39] , including myocardial dysfunction, cardiomyopathy, arrhythmias and heart failure during the course of critical illness [40] [41] [42] [43] [44] [45] [46] . according to the death data of the cdc (centers for disease control and prevention), different health conditions contribute to the deaths of covid-19 patients in united states, which are summarized in figure 4 [47] . deaths that are associated with more than one underlying condition, e.g., deaths involving both diabetes and respiratory arrest or cardiovascular complications and respiratory arrest, etc. hypertension, diabetes, cardiac arrest, ischemic heart disease, and heart failure are the major risk factors and have contributed to the fatalities in covid-19 cases. the renin-angiotensin-aldosterone system (raas) consists of an enzymatic cascade that controls blood pressure by regulating circulatory homeostasis, body fluid and systemic vascular resistance, all of which are involved in the regulation of a myriad of cardiovascular system [48] . ace1 (angiotensin i-converting enzyme) cleaves angiotensin i (ang-i) to angiotensin ii (ang-ii), which binds to and activates angiotensin type 1 receptor (at1r), which leads to vasoconstriction, inflammation, fibrosis and proliferation [28] (figure 3 ). ace2 converts ang-ii into angiotensin 1-7 (ang 1-7), which has vasodilating and anti-inflammatory effects by binding to mas receptor (mas-r). ace2 also cleaves ang-i into angiotensin-1-9, which is further converted into ang 1-7 by ace. therefore, ace2 regulates abnormal activation of the raas, which can prevent the development of hypertension, cardiac hypertrophy, and heart failure [49] . an increase in ace2/ace1 ratio protects against endothelial dysfunctions and vascular constriction, and exogenous ace2 activation attenuates thrombus formation and reduces platelet attachment to vessels [50, 51] . the etiology of ace2-dependent cardiovascular complications with covid-19 infection is rather complex. sars-cov-2 enters cardiovascular cells/tissue by binding to the membrane-bound form of ace2 (ace2 receptor). elevated levels of ace2 and its activity are the biomarkers of cardiovascular disease including patients with heart failure [52] , which indicate that these patients may be more susceptible to covid-19 infection [53] , with worsened prognosis of cardiovascular disease treatment [54] . measuring plasma angiotensin peptides and plasma ace2 levels can provide a direct evaluation on the progress of treatment and the state of the raas in covid-19 patients [55] . nevertheless, earlier clinical studies conveyed that treatment with soluble form of recombinant human ace2 (rhace2; apn01 (0.4 mg/kg, iv, bid for 7 days), gsk2586881: 0.4 mg/kg, iv, bid for 3 days) neutralized the excessive sars-cov virus in the system and preserved the protective cellular effects of ace2 in ards patients [56, 57] . consequently, scientists propose the therapeutic potential of soluble recombinant ace2, which can overwhelm sars-cov-2 to prevent its binding to cellular ace2 [58] . in addition, ace inhibitors (acei), which upregulate ace2 expression on the cell surface, have been proven to be successful, and improved the survival rate in patients undergoing covid-19 treatment [49] . abundant expression of ace2 on the cell surface following virus infection may maintain ang-ii degradation, which could reduce at1r activation and the risk of deleterious outcomes of covid-19. while the ace2 gene is located on the x-chromosome, gender has an impact among covid-19 patients, where men are at increased risk of susceptibility to covid-19 infection and cvd complications due to their hemizygous allele for ace2 compared to heterozygous allele in female [28] . interestingly, clinical data from 1485 european men and 537 women with heart failure showed elevated level of circulating plasma ace2 in men than in female [59] . this data complements with an observation of increased prevalence and susceptibility of covid-19 in males and demonstrates that abundance of ace2 receptor in cardiovascular cells can lead to severe clinical complications [60] [61] [62] . considering the importance of ace2 in the development of hypertension and diabetes mellitus, patients with covid-19 exhibit severe comorbidities including hypertension and diabetes with poor prognosis. initial evidence from 44,672 confirmed cases in china showed 4.2% with cvd and 12.8% with hypertension. however, among the death rate, 6% had hypertension, 7.3% had diabetes and 6.3% suffered from chronic respiratory disease [62, 63] . in another study involving a small population of 99 patients, 40% had underlying cvd or cerebrovascular disease [64] . interestingly, data from a small registry of 41 admitted patients showed an alarming 73% were men, with a median age of 49 [9] . however, data involving 5700 patients (admitted during 1 march to 4 april 2020) with a median age of 63 from new york city, the epicenter of covid-19 spread in the usa, showed a slightly different picture [38] . the most common underlying comorbidities were hypertension (57%), obesity (42%), and diabetes (34%). figure 4 depicts the statistics on distribution of underlying conditions among covid-19 patients based on the data from center for disease control department (cdc), usa. the data reveals that hypertension is a major comorbid factor for covid-19 fatalities. an increased risk of covid-19 death was associated with an age greater than 65 years (mortality of 10%), cvds (coronary artery disease: 10.2%; heart failure: 15.3%; cardiac arrhythmia: 11.5%), chronic obstructive pulmonary disease (14.2%), and current smoking (9.4%). another detailed observational meta-analysis (49,076 confirmed covid-19 case) of data available from public domains including databases from medline, embase and web of science showed patients with preexisting condition of cvd, diabetes and hypertension are significantly associated with a higher risk of developing severe complication with covid-19 disease. precisely, the analysis comparing the complications between severe vs non-severe (mild to moderate) covid-19 cases concluded that cvd was significantly associated with increased illness severity and adverse outcomes among covid-19 patients [65] . recently, cdc suggests that children with certain medical conditions, like neurological, genetic, and metabolic conditions, or congenital heart disease might be at increased risk of severe illness from covid-19 compared to other children. additional study comprising 191 patients from two hospitals in wuhan, china reported 48% of patients had underlying comorbidity factors: 30% with hypertension, 19% with diabetes and 8% with coronary heart disease [40] . in another cohort with 1591 confirmed covid-19 patients (during 20 february and 18 march 2020) with an average median age of 63 from lombardy, italy, 68% had at least one underlying comorbidity, hypertension (49%), cvd (21%), hypercholesterolemia (18%), or diabetes (17%) [66] . moreover, a staggering 82% of the patients were male and the mortality rate was higher in elderly patients aged ≥64 years compared to younger patients (36% vs. 15%). due to the high prevalence of hypertension in the older population, elderly male individuals may be at the highest risk of infection with worse outcomes, and an increased mortality rate with respect to younger patients. patients with hypertension are mostly treated with ace inhibitors (acei) and angiotensin ii type-i receptor blockers (arbs), which substantially increases the expression of ace2, due to negative feedback activation caused by low level of ang-i in the system [67] . considering ace2 as a preferential receptor of sars-cov-2, the patient with antihypertensive therapy with acei/arbs may be at higher risk of developing severe covid-19 with poor prognosis [67] . remarkably, clinical studies do not support this hypothesis and found no evidence to demonstrate use of acei or arb as a risk factor in covid-19 patients [49] . multiple investigators have demonstrated the beneficial therapeutic effect of acei or arb in prevention of covid-19 infection [68, 69] . independent studies conducted among hypertensive patients found no association between the use of acei or arb and increased risk of mortality in covid-19-positive cases [70, 71] . a population-based case-control study in the lombardy region of italy with a total of 6272 patients with covid-19 (21 february and 11 march 2020) reported that 22.2% patients were receiving arb and 23.9% patients were receiving acei [70] . other antihypertensive drugs were also used more in covid-19 patients than in controls and they had a more frequent history of hospitalization due to cardiovascular complications. however, this study showed no evidence of association of use of anti-hypertrophic drugs including acei or arbs and susceptibility of covid-19. another study with 12,594 patients in the new york university (nyu) langone health, in which 5894 patients were positive for covid-19 (46.8%), reported 4357 patients had a history of hypertension (34.6%) [72] . among these hypertensive patients, 2573 (59.1%) patients were positive for covid-19 (59.1%). this study also identified no substantial adverse effect with the use of antihypertensive drugs including acei or arbs in the covid-19 positive patients. therefore, prospective research is warranted to clarify the accuracy of existing contradictory hypotheses regarding the use of acei or arbs to control of blood pressure in hypertensive patients during viral infections. fundamentally, after entering into the cells via ace2 receptors and excessive binding of the sars-cov-2 result in the downregulation of ace2 by intracellular degradation and shedding, which could reduce the ang-ii degradation and activation of at1r with induction of myocardial hyper-inflammatory reaction in response to covid-19 [49, 73] . due to acei or arb treatment, more ace2 may be localized in the cell surface after virus binding, which could facilitate ang-ii degradation with reduction of at1r activation [49] . apart from hypertension and age, acute cardiac injury, chronic heart damage and heart failure have all been observed in patients treated for covid-19 infection [44, 74] . due to acute inflammation, procoagulant stimulus and endothelial cell dysfunction, various influenza rna viruses are involved in the development of human atherosclerotic plaques and progression of atherosclerosis. de-stabilization of vulnerable atherosclerotic plaques triggers acute myocardial infarction (mi) or cardiovascular death [75, 76] . myocardial infarction, commonly known as heart attack, is a clinical condition, where oxygen supply to the heart is restricted and results in the irreversible loss of cardiomyocytes due to activation of cardiac apoptosis [77] [78] [79] . a large population of patients diagnosed with covid-19 has died due to mi [80] . data obtained from a laboratory in lombardy, italy suggest that 60.7% (17 out of 28 cases) of patients with confirmed covid-19 and an existing condition of st-elevation myocardial infarction (stemi) had to undergo a repeated coronary angiogram and coronary lesion was identified as a major cause of the complication [81] . myocardial injury was also identified as a major contributor of mortality in covid-19 patients, as derived using data from hospitals in wuhan, china [39] . strikingly, the cardiac troponin i (ctni) level, a distinct marker of myocardial injury, was noticeably elevated in 52 patients out of 187 hospitalized patients with covid-19 (27.8%) and the mortality was nearly 70% in these patients with elevated ctni. progressive increased levels of c-reactive protein and n-terminal pro-b-type natriuretic peptide (nt-probnp) coexisted with elevated ctni levels in these covid-19 patients, which enhance the severity of inflammation and ventricular dysfunction. among 138 patients treated for covid-19 (admitted to zhongnan hospital of wuhan university during january 2020), 33 patients had either acute myocardial injury or cardiac arrhythmia, as suggested by their elevated ctni level of 0.011 ng/ml versus 0.0051 ng/ml for those who were treated in non-icu [82] . several other retrospective multi-center cohort studies from china have also confirmed the significant elevation of biomarkers of myocardial injury over the course of covid-19 infection that were strongly associated with rapid surge of irreversible clinical deterioration and increased mortality [40, 41, 44, 83] . although limited data are available on the incidence of heart failure in patients with covid-19, the study with 191 hospitalized patients with confirmed covid-19 (ranging in age from 18 to 87 years) in wuhan, china (until 31 january 2020) reported that heart failure was identified in 44 patients (23%), among them, 28 (52%) patients died and 16 (12%) patients recovered [40] . cardiac injury, as a common complication (19.7%), was associated with an unexpected high risk of mortality during hospitalization of elderly patients with covid-19 in wuhan, china [41] . evidence indicated in another retrospective study that apart from ards and sepsis, acute cardiac injury (77%) and heart failure (49%) were the most common critical complications of death in 113 deceased patients with covid-19 in wuhan, china [84] . several other case reports also established that acute or end-stage heart failure was the main pathophysiological manifestation of covid-19 [61, 85, 86] , which might be associated with hyperinflammation and oxidative stress [53, 87, 88] . interestingly, one recent study indicated a decline in emergency department visits for heart failure during the covid-19 pandemic, partly due to effective remote clinician-patient interactions [89] . since patients with cvd are considered to be more vulnerable to sars-cov-2 infection, with higher risk of negative consequences, these patients avoid frequent hospital visits and prefer alternative remote management. however, analyzing the clinical records during the covid-19 pandemic (between 20 february and 20 april 2020) of emergency department of san filippo neri hospital in rome, italy, a study revealed patients with acute heart failure often reported to the emergency department after significant clinical deterioration with high mortality due to failure of routine clinical assessment [90] . emerging studies indicate that severe covid-19-related death is associated with coagulopathy, venous thromboembolism ((vte) and disseminated intravascular coagulation (dic) [91] . data obtained from the covid-19 patient population in wuhan, china indicate an abnormal coagulation pattern with prolonged prothrombin time [91] . there were 183 patients registered in this study and parameters such as (dic), antithrombin activity, prothrombin time (pt) and d-dimer, a fibrin degradation product, were measured and compared between survivors and non-survivors. the results showed elevated levels of dic and d-dimers and prolonged pt in non-survivors and suggest thrombus formation may have contributed to the mortality in these patients. this notion is strongly supported by the observation that treatment of covid-19 patients with anti-coagulation drug heparin resulted in reduced mortality rate [92] . the 28-day mortality study between heparin users and nonusers indicated that only selected covid-19 patients with markedly higher sepsis-induced coagulopathy (sic) score or elevated d-dimer were benefited from the anticoagulant therapy. notably, anticoagulant treatment may endanger those patients without significant coagulopathy, because the activation of coagulation with local thrombosis/fibrin deposition could limit the survival and dissemination of microbial pathogens and reduce their invasion [93] . myocarditis is a disease marked by the inflammation of the heart muscle, most often due to viral infection. this inflammation interferes with the electrical system and compromises the pumping capacity of the heart and results in arrhythmia and cardiac arrest [94] . common diagnosis procedures include electrocardiogram (ecg), mri (magnetic resonance imaging) and a manifestation of increased cardiac troponin i (ctni) level. covid-19 patients with severe stage of illness manifest systemic hyperinflammation syndrome [95] . this data suggests an effect of adverse inflammatory reaction or cytokine storm in response to covid-19 treatment and defines a strong role for ace2 signaling in covid-19 disease [95] . several reports have shown that patients with covid-19 infection are diagnosed with myocarditis [41, 44, 61, 66] . in a case report of a 69-year-old man admitted in lombardy, italy with respiratory difficulties and required mechanical ventilator, with worsening heart condition. transthoracic echocardiography showed mild left ventricle hypertrophy (lvh) with preserved left ventricular ejection fraction and normal wall motion and elevated plasma troponin level (at 9.0 ng/ml) [83, 96] . cardiovascular mri was suggestive of myocarditis and the patient tested positive for covid-19 infection demonstrating sars-cov-2 infection was the most likely cause for the incidence of myocarditis [96] . similarly, a 53-year-old healthy woman was diagnosed with acute myopericarditis upon covid-19 infection. cardiac mri showed a severe left ventricular dysfunction (ejection fraction-35%). the patient also had myocyte necrosis with high-sensitivity cardiac troponin t (hstnt) level concentration of 0.24 ng/ml [61] . these reports suggest that patient with covid-19 infection are prone to myocarditis, and physicians would suspect such conditions along with underlying morbidity factors like hypertension and other cvd. emerging clinical and epidemiological evidence suggests that metabolic disarray, hypoxia and accentuated myocardial inflammation due to sars-cov-2 infection plays a critical role in the pathophysiology of myocardial injury and prevalence of arrhythmic complications [97] . in a clinical cohort with 138 patients with covid-19 in wuhan, china, cardiac arrhythmias were considered a major complication in 23 patients (16.7%) who were transferred to the intensive care unit (icu) [44] . specifically, cardiac arrhythmia was more common in icu patients than in non-icu patients (44.4% vs. 6.9%). a recent study from new york-presbyterian/columbia university irving medical center highlighted the spectrum of life-threatening arrhythmias observed in four patients with covid-19 infection [98] . fulminant myocarditis with cardiogenic shock could also coexist with atrial and ventricular arrhythmias, which could increase the severity of covid-19 patients, including death [99, 100] . therefore, the expected cardiac arrhythmogenic effect of covid-19 may be an important underlying risk of disease complication, which needs additional precautions and specialized management. based on the available clinical data, potential myocardial injury is a relevant challenge among hospitalized patients with covid-19 with increased risk of mortality; therefore, it is essential for multidisciplinary assessment, including blood pressure control in hypertensive patients as well as cardiovascular evaluation and therapy to reduce the morality for covid-19 infection. strikingly, a recent study in germany involving 100 patients with an average age of 49 years who recently recovered from covid-19 infection recognized the cardiovascular sequelae, irrespective of preexisting cardiac conditions [101] . cardiovascular magnetic resonance imaging (cmr) revealed that 78 patients had abnormal cardiac structural changes, 76 had detectable levels of biomarker of cardiac injury, e.g., elevated level of high-sensitivity cardiac troponin t (hstnt), lower left ventricular ejection fraction, higher left ventricle volumes, higher left ventricle mass, and raised native t1 and t2 (quantitative assessments of the myocardium composition), commonly found after a heart attack, and 60 had signs of inflammation. the exact molecular mechanism by which sars-cov-2 virus leads to cardiomyocyte injury is not completely understood. however, the abundant expression of ace-2 receptors in the heart plays an important role in the accumulation of sars-cov-2 virus in the cardiac tissue, which eventually results in hyperactivation of inflammation and cardiac tissue injury in patients. recently, autopsy results of 39 patients, who died at early stage of covid-19 infection in germany, revealed the most likely localization of sars-cov-2 not to be in the cardiomyocytes, but in interstitial cells or macrophages invading the myocardial tissue [102] . however, another emerging study using human induced pluripotent stem cell-derived cardiomyocytes (hipsc-cms) shows sars-cov-2 can directly enter and replicate in hipsc-cms and induce apoptosis, which results in cessation of cardiomyocyte beating after 72 h of infection [103] . the majority of the covid-19 patients suffering from cardiovascular complications show a significant elevation of ctni, nt-probnp and interleukin-6 (il-6) or other cytokines [il1b, il1ra, il7, il8, il9, il10, c-x-c motif chemokine 10 (cxcl10), chemokine (c-c motif) ligand 2 (ccl2), granulocyte-macrophage colony-stimulating factor (gm-csf), and tumor necrosis factor-α (tnf-α)] in their blood stream [9, 40, 104] . severe hyperinflammation or cytokine storm due to immunological dysregulation may be the primary contributor to cardiomyocyte injury [105] . epidemiological studies with other viral rnas indicated that after entering into the cytoplasm of cardiomyocytes, viral rna is further transcribed and translated into the viral structural proteins to form the complete infectious virion [106] . ultimately, infected cardiomyocytes would be lysed, which could lead to activation of the innate immune response with induction of pro-inflammatory cytokines, inflammation-induced destabilization of coronary artery plaques and development of left ventricular dysfunction [107] . collectively, uncontrolled hyperactivated t-lymphocytes with systemic inflammation appears to be the most common mechanisms of the cardiomyocyte injury in covid-19 patients with profound cardiovascular consequences. in addition to binding to ace2 of the host cell, the priming of the transmembrane spike (s) glycoprotein of sars-cov-2 by host proteases (furin, a signature protease of highly pathogenic viruses) through cleavage at the s1/s2 and the s2 sites could enhance its transmissibility and pathogenicity [108] . multiple evidences have revealed that the notch signaling plays a major role in maintaining the homeostasis of the cardiovascular system, including atherosclerosis progression and ventricular remodeling after myocardial infarction [109] [110] [111] . furin is transcriptionally induced by notch signaling, but notch is cleaved at the cell membrane by adam10/adam17 to enable final cleavage by γ-secretase to form active notch intracellular domain, which regulates the transcription of target genes in nucleus. therefore, targeting notch activation using inhibitor γ-secretase (gsi) could be a promising therapeutic strategy to block the virus entry into the cardiac cells by reducing furin and increase adam17 shedding. the notch signaling also modulates the activity of innate and adaptive immune responses by inducing macrophage polarization [112] . in microphages, it directly binds to il-6 promoter in response to interferon (ifn)-γ and promotes il-6 production, which may cause severe myocardial injury due to triggered "cytokine storm" [113] . our current understanding on the molecular mechanisms of cardiomyocyte injury for sars-cov-2 infection is limited and future in depth rigorous studies are warranted. early diagnosis of covid-19 infection in patients is crucial for the recommendation of appropriate treatment strategy and to address associated cvd complications. initial symptoms of sars-cov-2 infection include high fever or chills, cough, shortness of breath, headache, sore throat, new loss of taste or smell, diarrhea and fatigue that appears during 2-14 days after the exposure to the virus. these early indications, though similar to regular viral infection, should be taken seriously during this pandemic time and diagnosed further for the presence of covid-19 infection. currently, the established diagnostic test for the identification of sars-cov-2 infection is based on nucleic acid amplification testing (naat) or commonly called real-time reverse transcription-polymerase chain reaction (rt-pcr) assay, nucleic acid-based meta-genomic next-generation sequencing (mngs), reverse transcription loop-mediated isothermal amplification (rt-lamp) and antigen testing performed with nasopharyngeal swab specimen [114, 115] . in the absence of any pharmaceutical interventions, traditional public health measures are considered to be the mainstay of management tools to curb this worldwide covid-19 epidemic. most widely accepted practices are hygienic precautions, isolation and quarantine, social distancing and community containment [44, 116] . to minimize cardiovascular complications in highly infectious covid-19 patients, the patients with covid-19 infection require routine monitoring of cardiac parameters with echocardiography, telemetry to assess qt interval and electrocardiograph (ecg) to identify the development of cardiomyopathy, arrhythmia, ischemic heart disease and heart failure. potential therapeutic options to impede the propagation of covid-19 and its associated cardiovascular complication are desperately needed during this ongoing severe pandemic. researchers and clinicians are focusing on developing new drugs against coronavirus as well as repurposing already approved drugs for the treatment of covid-19 patients. unapproved antiviral drugs for sars-cov-1 and/or middle east respiratory syndrome coronavirus (mers-cov) diseases are also currently being reevaluated as treatment options for covid-19. however, covid-19 poses unique problems that were not encountered with the previous known viruses. the major issue was to address the cvd complications, systemic and vascular inflammation, and to deal with comorbid risk like hypertension, diabetes and heart failure. initial approaches were to emphasis on obstructing the viral replication and inflammation by using antiviral drugs, such as, remdesivir, liponovir/ritonavir, hydroxy chloroquine (hcq), corticosteroids and broad-spectrum antibiotics like azithromycin, clarithromycin to address inflammation [117, 118] . table 1 summarizes the mechanisms of action and beneficial as well as adverse effects of drug treatments used for covid-19. the antiviral drug, remdesivir (veklury, gs-5734), initially developed for ebola, inhibits rna-dependent rna polymerase and prematurely terminates the viral rna transcription and shows broad-spectrum antiviral activity against rna viruses, including sars-cov-2 in vitro, and inhibits mers-cov, sars-cov-1, and sars-cov-2 replication in animal models [119] . remdesivir is a substrate for the drug metabolizing enzymes cyp2c8, cyp2d6, and cyp3a4, as well as a substrate for organic anion transporting polypeptides 1b1 (oatp1b1) and p-glycoprotein (p-gp) transporters. remdesivir (100-200 mg/day for 10 days) either treated alone or in combination with anti-inflammatory drugs was effective in curbing the virus and shortening the recovery time of patients undergoing treatment for covid-19 [120] . a multicenter randomized, double-blind, clinical trial, involving 237 patients with severe covid-19, conducted in ten hospitals in wuhan, china, reported that seriously ill patients, receiving remdesivir (200 mg on day 1 followed by 100 mg on days 2-10 in single daily infusions) within 10 days of symptom onset, showed a numerically faster time to clinical improvement than those receiving placebo, without any antiviral effect [121] . the study also reported early termination of the treatment due to multiple adverse events (including gastrointestinal symptoms, aminotransferase or bilirubin increases, and worsened cardiopulmonary status) in the remdesivir-treated patients (66%) ( table 1) . in a small pilot study of four critically ill covid-19 patients with remdesivir, three patients tested negative for sars-cov-2 rna (swap test) after 3 days of therapy. however, these reports also indicated some adverse side effects including liver injury [122, 123] . lopinavir-ritonavir antiviral drugs such as lopinavir-ritonavir (mylan or kaletra; 400 mg and 100 mg, respectively, twice a day for 14 days), hiv protease inhibitors, used in the clinical trial provided only a moderate benefit of reducing the recovery time by 1 day [124] . although in vivo animal study shows that a combination of remdesivir with lopinavir-ritonavir yields better outcome for coronavirus infection [125] . however, the treatment with these protease inhibitors (lopinavir-ritonavir) develop cardio-metabolic complications including development of dyslipidemia with an adverse cholesterol profile, which could elicit inflammation with elevated reactive oxygen species (ros) production, altered myocardial ubiquitin proteasome and calcium-handling pathways together with decreased contractile function [126, 127] (table 1) . lopinavir-ritonavir treatment inhibits the myocardial ups (ubiquitin proteasome system) and leads to elevated calcineurin and connexin 43 expression that may contribute to cardiac contractile dysfunction [127] . without any benefit, lopinavir-ritonavir may also cause bradycardia, qt and pr interval prolongation due to the interaction with cytochrome p450 enzymes [124, 128, 129] . baricitinib (olumiant®), an inhibitor of janus kinase (jak1 and jak2) molecule and a drug for the treatment of rheumatoid arthritis was tested (2 mg or 4 mg once daily) in covid-19 patients [130] . this drug was repurposed in covid-19 treatment to curb the occurrence of inflammation process due to the use of ace inhibitors, which moderately reduced the lung inflammation and cytokine [131] . the management of hyperinflammation or cytokine storm has been challenging and accounts for the majority of the mortality associated with adverse cases of covid-19 patients. clinical practices to address this complication involves treatment with monoclonal antibody against interleukin-6 receptor (il-6r) such as tocilizumab (actrema®), siltuximab (sylvant®) and sarilumab (kevzara®) to control the infiltration of macrophages and cytokines in the respiratory system and suppression t-cell activation [132, 133] . tocilizumab specifically binds membrane-bound (mil-6r) and soluble interleukin-6 receptor (sil-6r) and inhibits signal transduction. covid-19 patients treated with tocilizumab (4 to 8 mg/kg with recommended dose of 400 mg with a maximum dose of 800 mg) in addition to routine therapy showed significant improvement of the clinical outcomes, effectively controlled body temperature with improvement of peripheral oxygen saturation and reduction of inflammatory storm [134] . considering the emergency to identify a drug that is effective in reducing the complications associated with covid-19, efforts are also underway to repurpose old drugs that are proven to be clinically safe. data from recovery trial indicates that dexamethasone, a steroid drug generally used as an anti-inflammatory agent, is effective in reducing the mortality rate by one-third in covid-19 patients subjected to mechanical ventilation or who were on ventilators compared to patients receiving standard therapy [135] . among 6400 registered covid-19 patients, 2100 of them who received 6 mg of dexamethasone for 10 days, had reduced mortality by 20% compared to 4300 patients who were on standard treatment. more importantly, patients on ventilator support during the critical stage of treatment responded better to dexamethasone compared to patients just receiving oxygen therapy. the outcome of this study is considered a breakthrough in the fight against covid-19 because dexamethasone is a commonly available drug and cost effective. however, further evidence is required to use dexamethasone in covid-19 patients. another drug that gained much attention for the treatment of covid-19 is hydroxychloroquine (hcq, plaquenil), an anti-malarial compound, which is also widely used for attenuation of systemic lupus erythematosus (sle), rheumatoid arthritis (ra), juvenile idiopathic arthritis (jia) and sjogren's syndrome [136] . several clinical studies, including trials from nih (nct04358068), are testing this drug for covid-19 treatment, either alone or in combination with azithromycin [137] . the treatments with hydroxychloroquine alone (400 mg by mouth twice daily for 1 day followed by 200 mg by mouth twice daily for 4 days) or in combination with azithromycin (500 mg by mouth or intravenous daily for 5 days) lead to a prolongation of the qt interval, possibly increasing the risk of sudden cardiac death [137] (table 1) . another retrospective multicenter cohort study was conducted involving 1438 patients admitted across various hospitals in the city of new york who were diagnosed with covid-19 (between 15-28 march 2020), those receiving either hcq alone (dose ranges: 200-600 mg; once or twice a day) or in combination with azithromycin (dose ranges: 200 mg to 500 mg; once or twice a day) or azithromycin alone. the results from the study showed that the probability of death for patients receiving hcq + azithromycin was 25.7% (189 out of 735), while patients receiving hcq alone was 19.9% (54 out of 271) and 10.0% (21 out of 211) in azithromycin alone group. cardiac arrest was significantly high in patients receiving hcq + azithromycin combination than treatment with placebo or hcq alone [138] . another cohort study performed at an academic tertiary care center in boston, massachusetts, showed similar high risk of qt prolongation with subsequently developed other ventricular arrhythmias in the hcq alone (400 mg, twice on day 1, then 400 mg daily on days 2 through 5) or with azithromycin-treated patients with covid-19 [139] . an observational study of 1446 admitted patients to the hospital with covid-19 (between 7 march and 8 april 2020) in new york, revealed that hcq administration alone was not associated with either a greatly lowered or an increased risk of the composite end point of intubation or death [140] . the treatment regimen of hydroxychloroquine was a loading dose of 600 mg twice on day 1, followed by 400 mg daily for 4 additional days. however, recently, the u.s. food and drug administration (fda) revoked its approval to use hcq for covid-19 treatment due to disappointing results [141] . data from randomized clinical trials suggest that hcq had no beneficial effects compared to placebo and was not successful in decreasing the mortality rate or in hospital stay (based on fda report, updated on 1 july 2020) [142] . therefore, rigorous, and large-scale studies with careful risk assessment of hcq should be conducted prior to initiating covid-19 therapeutics, with close monitoring cardiac manifestations including evaluation of cardiac biomarkers, routine electrocardiograms and electrolyte monitoring. there is an urgency for the development of a safe and effective vaccine for covid-19; however, no specific vaccines against sar-cov-2 are currently available [40] . multiple inactivated vaccine candidates for sars-cov-2, such as dna-, rna-based formulations, recombinant-subunits containing viral epitopes, adenovirus-based vectors and purified inactivated virus are under development [143, 144] . several candidate vaccines are still in the preliminary stage of phase i clinical trial. the mrna-based vaccine prepared by the usa national institute of allergy and infectious diseases against sars-cov-2 is under phase 1 trial [145] . ino-4800, a dna-based vaccine, is also in pipeline and will soon be available for human trial. preliminary results from pilot studies and clinical trials on new vaccine are encouraging and gives hope for a successful availability of an effective vaccine by end of 2020. several pharmaceutical companies, including pfizer, novartis and astrazeneca and moderna, are testing their candidate vaccine. university of oxford in collaboration with astrazeneca are in the development of covid-19 vaccine and expect to produce 30 million doses in uk by september 2020. jenner institute, oxford, uk is a leader in this effort and launched a phase iii clinical trial of more than 6000 people in may. however, due to the suspected adverse event in a person receiving the vaccine in the united kingdom, the clinical trials have been temporarily paused. moderna, a usa-based company in collaboration with switzerland's lonza, released positive outcomes from its phase i clinical trial of their mrna1273 vaccine for sars-cov-2 [146] . preliminary results are very promising, showing good immune response, and due to effectiveness and safety profiles, this vaccine is approved by the u.s. food and drug administration (fda) for phase ii and phase iii studies [147, 148] . novartis announced its plans to initiate a phase iii clinical trial to study effects of canakinumab, an interleukin (il)-1β blocker, in covid-19 patients with pneumonia [149] . they aim to rapidly enroll 450 patients at multiple medical centers across france, germany, italy, spain, uk and the usa and randomize them to receive either canakinumab or placebo on top of standard of care (soc) [150] . pfizer, in partnership with biontech (bnt), has initiated its phase i/ii clinical trial in the usa for its mrna-based vaccine, the bnt162 prevent covid-19 [151] . sinopharm, a wuhan, china-based pharmaceutical company received approval from the national medical products administration (china) and conducting phase ii clinical trials for its inactivated vaccine bbibp-corv. the company already tested 2000 doses of this vaccine and expect to release in the marker by the end of the year 2020. sinovac is planning to enter its phase iii clinical trial in collaboration with instituto butantan in brazil after observing positive results in its preclinical trail with the vaccine coronavac [144] . ad5-ncov, an adenovirus type 5 vector-based vaccine developed by cansiobiologics, china is also in phase iii clinical trial and demonstrated promising effects in the early phase of testing on 108 participants [152] . inovio pharmaceuticals in collaboration with university of pennsylvania and center for pharmaceutical research, kansas city, missouri, is testing its dna-based vaccine ino-4800 [153] . preclinical experiments conducted in guinea pigs showed antibody titer against ace2 receptor/sars-cov2 binding protein. when countries all over the world are racing to develop their own vaccine against covid-19, russia has already approved a vaccine candidate for public use named sputnik v, that was developed in collaboration with gamaleya research institute of epidemiology and microbiology in moscow [154] . the vaccines comprise either recombinant adenovirus type 26 (rad26) or recombinant adenovirus type 5 (rad5) vectors, which contain the gene for sars-cov-2 spike glycoprotein (rad26-s and rad5-s). initial results from the ongoing phase i and ii clinical trials are promising, which include total population size of 76 healthy adult volunteers [155] . among them 38 volunteers were intramuscularly vaccinated with gam-covid-vac lyo (lyophilized vaccine formulation) and other 38 participants were subjected to gam-covid-vac (frozen vaccine formulation) [155] . both heterologous recombinant adenoviral (rad26 and rad5) vector-based covid-19 vaccines induced a strong humoral and cellular immune responses with reported safety profiles in participants. however, further investigations with larger scale population (including different underlying medical complications) are needed to demonstrate the effectiveness of this vaccine for prevention of covid-19. nevertheless, scientists globally have serious concerns about unforeseen adverse effects of this vaccine without the outcomes of the phase iii trial. even though, for the development of an efficient vaccine for covid-19, extensive preclinical studies and clinical trials are essential to carefully evaluate the adverse effect of vaccine, the aforementioned fast-paced preclinical data are encouraging for advancing the preventive strategies against covid-19. several other treatment options such as convalescent plasma therapy (cpt) and monoclonal antibody therapy have been evaluated with some moderate success. cpt is a traditional method where plasma containing the antibody from recovered patients infected with covid-19 was transfused to the severely ill covid-19 patients [25, [156] [157] [158] . studies showed that cp therapy was effective, and the level of neutralizing increased as high as 1:640 times in patients infected with sars-cov-2 [25] . transfusing antibodies from covid-19 survivors into high-risk patients to neutralize sars-cov-2 could provide a quick treatment option until an optimistic vaccine will arrive to prevent this viral infection. efforts are also underway to design a monoclonal antibody that can target the specific epitope on the spike protein of sars-cov-2 and block the virus entry in to the host cell [108, 159, 160] . such efforts are still in their preliminary stage [161] and are time consuming; however, they could provide a long-lasting solution for dealing with sars viruses in general. recently, stem cell therapies with secreted extracellular vesicles (evs) offer a potential therapeutic benefit in covid-19 patients by attenuating inflammation with regeneration of the damaged lung. mesenchymal stem cells (mscs)-derived evs-based therapy could be the most promising reparative strategy in people with covid-19, because of its high proliferation rate, low invasive nature, and the immunomodulatory, antioxidant and anti-inflammatory properties of mscs [162] . there are several promising clinical trials with msc-derived evs underway, which could reveal convincing evidence in the encouraging prospect of msc-based therapies for respiratory complications of covid-19 patients [163, 164] . despite the above-mentioned beneficial effects of different therapeutics, the safety profiles of these therapies have not been proficiently identified. specifically, the potential adverse cardiovascular effects of these drugs in covid-19 patients need urgent attention before rushing the approval of any new drug into clinical application. for most effective treatments for covid-19, it is important to pay attention to emerging evidence about potential harmful risk of drug interactions. due to the highly transmissible novel coronavirus, sars-cov-2, the covid-19 outbreak has become an unprecedented worldwide pandemic with a record number of infected individuals and an excess of mortality. the desperate need for effective therapeutics for covid-19 during this pandemic integrated scientist around the world across multiple research fields while sharing their research findings and knowledge to fast-track the process of drug discovery. considering the high mortality of covid-19 patients with cardiovascular comorbidities, it is important to understand whether it is attributable to underlying cardiovascular disease (cvd) or if cvd is the consequence of inflammatory response to sar-cov-2 infection or severe respiratory symptoms. the precise mechanisms linking cvds and worsened prognosis or higher mortality rate in covid-19 patients remain unknown. recent therapies under investigation for severe multi-organ failure in covid-19 patients may have adverse cardiovascular effects, while their clinical efficacy for combating covid-19 is yet to be established. new advanced technological tools, like information technology based on smart phone apps, social media, artificial intelligence (ai), machine learning, etc., accelerate the diagnosis/screening of patients with virus, analysis of available literature, and identification of potential therapeutic targets and other specific clinical features to tackle covid-19 pandemic. moreover, ai, particularly, plays an important role in predicting the harmful interaction between cardiovascular consequences with the drugs used for covid-19, by automated interpretation of collected meta-data from various sources. in the context of disease progression with cardiovascular complications, the researchers are focusing on developing new drugs in parallel to repurposing already clinically approved drugs to avoid a massive surge of covid-19 patients with a prevalence of cvd. therefore, urgent understanding of molecular mechanism as well as retrospective and prospective studies with robust diagnosis of cardiovascular impairments will be crucial for development of advanced therapies for the treatment of sars-cov-2 virus, which could mitigate the adverse cardiovascular events among covid-19 patients and save humankind around the globe from this deadly pandemic. the authors declare no conflict of interest. angiotensin a new coronavirus associated with human respiratory disease in china the continuing 2019-ncov epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in wuhan first case of 2019 novel coronavirus in the united states the covid-19 pandemic in the usa: what might we expect? first known person-to-person 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for development of rbd protein as a viral attachment inhibitor and vaccine a human monoclonal antibody blocking sars-cov-2 infection non-coding rnas in mesenchymal stem cell-derived extracellular vesicles: deciphering regulatory roles in stem cell potency, inflammatory resolve, and tissue regeneration combating covid-19 with mesenchymal stem cell therapy can stem cells beat covid-19: advancing stem cells and extracellular vesicles toward mainstream medicine for lung injuries associated with sars-cov-2 infections this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord-284890-s73hljz9 authors: kang, lijun; ma, simeng; chen, min; yang, jun; wang, ying; li, ruiting; yao, lihua; bai, hanping; cai, zhongxiang; xiang yang, bing; hu, shaohua; zhang, kerang; wang, gaohua; ma, ci; liu, zhongchun title: impact on mental health and perceptions of psychological care among medical and nursing staff in wuhan during the 2019 novel coronavirus disease outbreak: a cross-sectional study date: 2020-03-30 journal: brain behav immun doi: 10.1016/j.bbi.2020.03.028 sha: doc_id: 284890 cord_uid: s73hljz9 the severe 2019 outbreak of novel coronavirus disease (covid-19), which was first reported in wuhan, would be expected to impact the mental health of local medical and nursing staff and thus lead them to seek help. however, those outcomes have yet to be established using epidemiological data. to explore the mental health status of medical and nursing staff and the efficacy, or lack thereof, of critically connecting psychological needs to receiving psychological care, we conducted a quantitative study. this is the first paper on the mental health of medical and nursing staff in wuhan. notably, among 994 medical and nursing staff working in wuhan, 36.9% had subthreshold mental health disturbances (mean phq-9: 2.4), 34.4% had mild disturbances (mean phq-9: 5.4), 22.4% had moderate disturbances (mean phq-9: 9.0), and 6.2% had severe disturbance (mean phq-9: 15.1) in the immediate wake of the viral epidemic. the noted burden fell particularly heavily on young women. of all participants, 36.3% had accessed psychological materials (such as books on mental health), 50.4% had accessed psychological resources available through media (such as online push messages on mental health self-help coping methods), and 17.5% had participated in counseling or psychotherapy. trends in levels of psychological distress and factors such as exposure to infected people and psychological assistance were identified. although staff accessed limited mental healthcare services, distressed staff nonetheless saw these services as important resources to alleviate acute mental health disturbances and improve their physical health perceptions. these findings emphasize the importance of being prepared to support frontline workers through mental health interventions at times of widespread crisis. in november 2019, a novel coronavirus disease was first reported and then became widespread within wuhan, the capital city of hubei province of china (chan et al., 2020) . the disease rapidly psychological distress among medical staff appeared gradually: fear and anxiety appeared immediately and decreased in the early stages of the epidemic, but depression, psychophysiological symptoms and posttraumatic stress symptoms appeared later and lasted for a long time, leading to profound impacts (chong et al., 2004; wu et al., 2009) . being isolated, working in high-risk positions, and having contact with infected people are common causes of trauma (wu et al., 2009; maunder et al., 2003) . these factors may have impacted medical and nursing staff in wuhan, leading to mental health problems. the experience of medical staff responding to sars shows that the effects on medical staff members' mental health have not only shortterm but also long-term impacts and that the value of effective support and training is meaningful (maunder et al., 2006) . efficient and comprehensive actions should be taken in a timely fashion to protect the mental health of medical staff. the chinese government has made various efforts to reduce the pressure on medical and nursing staff in china, such as sending more medical and nursing staff to reduce work intensity, adopting strict infection control, providing personal protective equipment and offering practical guidance. based on previous responses to middle east respiratory syndrome (mers), medical staff tend to believe that such measures help protect their mental health (khalid et al., 2016) . in addition, to reduce the psychological damage of covid-19 among medical and nursing staff, mental health workers in wuhan are also taking action by establishing psychological intervention teams and providing a range of psychological services, including providing psychological brochures, counseling and psychotherapy (kang et al., 2020) . at the same time, television news and online media are also disseminating information about coping strategies for psychological self-help. however, evidence-based mental health services are preferable, and it is necessary to assess the quality of mental health services (aarons et al., 2012) . therefore, we explore the mental health status of medical and nursing staff in wuhan, the efficacy of the psychological care accessed, and their psychological care needs. we recruited doctors or nurses working in wuhan to participate in this survey from january 29, 2020, to february 4, 2020. this study was approved by the clinical research ethics committee of renmin hospital of wuhan university (wdry2020-k004). data were collected through wenjuanxing (www.wjx.cn) with an anonymous, selfrated questionnaire that was distributed to all workstations over the internet. all subjects provided informed consent electronically prior to registration. the informed consent page presented two options (yes/ no). only subjects who chose yes were taken to the questionnaire page, and subjects could quit the process at any time. the questionnaire consists of six parts: basic demographic data, mental health assessment, risks of direct and indirect exposure to covid-19, mental healthcare services accessed, psychological needs, and self-perceived health status compared to that before the covid-19 outbreak. basic demographic data include occupation (doctor or nurse), gender (male or female), age (years), marital status (unmarried, married or divorced), educational level (undergraduate or lower, postgraduate or higher), technical title (primary, intermediate, or senior), and department (divided into high-exposure departments and non-highexposure departments according to the possibility of exposure to confirmed patients; high-exposure departments included the fever clinic, emergency department, general isolation ward, and intensive care unit). we used four scales to assess the mental health status of medical and nursing staff. the 9-item patient health questionnaire (phq-9), the 7item generalized anxiety disorder (gad-7), the 7-item insomnia severity index (isi) and the 22-item impact of event scale-revised (ies-r) were used to evaluate depression, anxiety, insomnia and distress, respectively. the phq-9 is a self-report measure used to assess the severity of depression, with the total scores categorized as follows: minimal/no depression (0-4), mild depression (5-9), moderate depression (10-14) , or severe depression (15-21) (kocalevent et al., 2013) . the gad-7 is a self-rated scale to evaluate the severity of anxiety and has good reliability and validity. the total scores are categorized as follows: minimal/no anxiety (0-4), mild anxiety (5-9), moderate anxiety (10-14), or severe anxiety (15-21) (löwe et al., 2008) . the isi is a measure of insomnia severity that has been shown to be valid and reliable. the total scores are categorized as follows: normal (0-7), subthreshold (8-14), moderate insomnia (15-21), or severe insomnia (22-28) (morin et al., 2011) . the ies-r is a self-report measure used to assess the response to a specific stressful life event and has extensive reliability and validity. the event used for this questionnaire was the occurrence of covid-19. the total scores are categorized as follows: subclinical (0-8), mild distress (9-25), moderate distress (26-43), and severe distress (44-88) (daniel and weiss, 2007) . exposure to covid-19 was determined with the following questions asked to medical and nursing staff: have you been diagnosed with covid-19? do you manage patients diagnosed with covid-19? has your family been diagnosed with covid-19? have your friends been diagnosed? have your neighbors (people living in the same community who may or may not know each other) been diagnosed? then, participants were asked whether there was anyone living with them with suspected symptoms. the answer to each question was yes or no. the following question was used to determine which psychological services the subject had accessed. have you ever received the following services: psychological materials (leaflets, brochures and books provided by mental health workers and distributed to staff in the hospital), psychological resources available through media (psychological assistance methods and techniques provided by psychologists through online media or tv news or various online platforms) (supplementary material), and counseling or psychotherapy (including individual or group therapy)? three areas were assessed regarding the psychological services that participants hoped to receive in the future: what kind of mental health service content were participants most interested in (including knowledge of psychology, ways to alleviate their own psychological reactions, ways to help others alleviate their psychological reactions, or ways to seek help from psychologists or psychiatrists); what kind of resources were most anticipated (including psychological materials, psychological resources available through media, group psychotherapy, individual counseling and psychotherapy, uninterested or other); and who participants would prefer to receive care from (including psychologists or psychiatrists, family or relatives, friends or colleagues, do not need help, or other). health status was determined by asking participants to compare their current health status to their health status before the outbreak of covid-19: how do you perceive your current health status compared to your health status before the outbreak? (answer options included l. kang, et al. brain, behavior, and immunity xxx (xxxx) xxx-xxx getting better, almost unchanged, worse, or much worse). data analysis was performed using ibm spss statistics for windows (version 23.0) and mplus (version 7.4). descriptive analysis was used to describe the general data and currently accessed psychological services. for count data, frequencies and percentages were used. the k-means clustering method was used to cluster the phq-9, gad-7, isi, and ies-r scores (ball, 1967) . with the euclidean square root distance as the measurement index, the patients were divided into 4 groups by the ward method. according to this grouping, exposure to covid-19 and the current state of mental healthcare services were compared. the chisquare test was used to compare the data for different categorical variables. a structural equation model (sem) was constructed via mplus to explore the relationship among the four components, namely, exposure, accessed mental healthcare services, mental health status (phq-9, gad-7, isi, and ies-r scores) and self-perceived health status compared to that before the covid-19 outbreak. the estimation method used weighted least squares with mean and variance adjustment test statistics (distefano and morgan, 2014) . we used a monte carlo method with 1000 guided resamplings to construct a confidence interval for the estimation effect (bauer et al., 2006) . in sem, several criteria, such as root mean square error of approximation (rmsea) values < 0.08 and comparative fit index (cfi) and tucker-lewis index (tli) values > 0.90, indicate acceptable models (hu and bentler, 1998) . p values < 0.05 indicated that a difference was statistically significant. in total, 994 participants, including 183 (18.4%) doctors and 811 (81.6%) nurses, completed the survey. a total of 31.1% worked in highrisk departments. the participants tended to be female (85.5%), be aged 25 to 40 years (63.4%), be married (56.9%), have an educational level of undergraduate or less (85%), and have a junior technical title (66.3%), as shown in table 1 . of all participants, 36.3% had received psychological materials, 50.4% had obtained psychological resources available through media, and 17.5% had participated in group psychological counseling, as shown in table 2 . according to the phq-9, gad-7, isi, and ies-r scores, the 994 participants were divided into 4 groups. thirty-six percent of the medical staff had subthreshold mental health disturbances (mean phq-9: 2.4, gad-7: 1.5, isi: 2.8, ies-r: 6.1), 34.4% had mild disturbances (mean phq-9: 5.4, gad-7: 4.6, isi: 6.0, ies-r: 22.9), 22.4% had moderate disturbances (mean phq-9: 9.0, gad-7: 8.2, isi: 10.4, ies-r: 39.9), and 6.2% had severe disturbances (mean phq-9: 15.1, gad-7: 15.1, isi: 15.6, ies-r: 60.0). there were significant differences in the phq-9, gad-7, isi, and ies-r scores among the four groups, as shown in table 3 . in contrast, there were no significant differences in demographic data among the four groups, as shown in table 4 . for medical and nursing staff, exposure to people around them who were infected varied among the different groups. the group with subthreshold mental health disturbances had contact with fewer people confirmed or suspected to be infected with the virus. each group with a higher level of distress had a more extensive scope of exposure. there were also significant differences in mental healthcare services among the four groups; those with severe disturbances had accessed fewer psychological materials and psychological resources available through media. in addition, the perception of current health status compared to that before the outbreak of covid-19 was also different among the groups, as shown in table 5 . we established an sem of the associations between the four areas. first, exposure as a risk factor for mental health, including the confirmed diagnosis of patients, the participants' themselves, family, friends, colleagues, neighbors, and coresidents with suspected symptoms, was analyzed in the previous step. second, the mental healthcare services accessed consisted of psychological materials and psychological resources available through media. third, mental health consisted of the phq-9, gad-7, isi, and ies-r scores. the fourth area was the subjective feelings of the staff regarding whether their physical conditions were worse than before the epidemic. the chi-square test of model fit yielded a value of 129.1, with degrees of freedom = 72, pvalue = 0.000, rmsea = 0.028, cfi = 0.978, and tli = 0.973, indicating a good fit. the results showed that the risk factors of exposure affected mental health and that mental health affected subjective physical health perceptions. mental healthcare services only partially l. kang, et al. brain, behavior, and immunity xxx (xxxx) xxx-xxx mediated the relationship between exposure risks and mental health. mental healthcare services regulated the relationship between the risk of exposure and subjective physical health perceptions by affecting mental health. the results are shown in fig. 1 and table 6 . 3.6. psychological care needs of medical and nursing staff in terms of the content of interest, namely, psychological care, medical and nursing staff with subthreshold disturbances most wanted to obtain skills to help alleviate others' psychological distress, whereas other medical and nursing staff most wanted to obtain self-help skills. medical and nursing staff with higher levels of mental health problems were more interested in skills for self-rescue and showed more urgent desires to seek help from psychotherapists and psychiatrists. medical and nursing staff differed in terms of how they wanted to obtain services based on their levels of mental health problems. medical and nursing staff with subthreshold and mild disturbances preferred to obtain such services from media sources, while staff with heavier burdens wanted to seek services directly from professionals. apart from medical and nursing staff with subthreshold disturbances who did not think they needed help from others, the other workers saw a greater need to obtain help from professionals than from close family and friends. the results are shown in table 7 . this is the first mental health investigation in the wake of the coronavirus epidemic in wuhan, china that aims, in part, to explore the demand for mental healthcare services in this context. when cities are struck by deadly, large-scale disasters of various types, the characteristics of mental health problems that arise can differ across different periods (shioyama et al., 2000) . we therefore chose to survey a set of people (health care providers) in the discrete window of time soon after the initiation of a chaotic event (the outbreak of coronavirus infections). to conduct a comprehensive analysis, we used multiple different scales to evaluate the mental health of medical staff. our study has revealed the limits in the availability of mental healthcare services provided by psychologists and psychiatrists and thus the limits in access points for psychological care for distressed individuals, including less personalized sources of support such as publication-style psychological materials and psychological resources available from media. these latter methods can nonetheless contribute positively to alleviating mental health problems and physical discomfort caused by risk factors such as the exposure of close contacts to covid-19. such exposure is known to be mentally injurious in epidemic settings: when the sars epidemic hit, not only did the direct exposure of the work environment affect the mental health of medical staff, but the infection of friends or close relatives generated psychological trauma (wu et al., 2009) . we found that subthreshold and mild mental health disturbances accounted for a large proportion of disturbances. people with such levels of disturbances may be more likely than those with more severe disturbances to take action and be motivated to learn the necessary skills and to adapt in productive ways to respond to diverse challenges. these skills have been shown in previous retrospective studies to be protective for later mental health (maunder et al., 2006) . in addition, we note that people with subthreshold and mild mental health disturbances want to find ways to better help others, which is beneficial for health care teams. in terms of physiology, positive coping has been seen to increase immune function when victimized subjects report high mental demands, leading to a better state of response (sakami et al., 2004) . however, there are negative consequences of stimulation caused by pressure, as acute psychological stress is known to activate the sympathetic adrenal medulla system and hypothalamus-pituitary adrenal axis, and this two-component stress response impacts physical and mental health and has disease consequences (turner et al., 2020) . in summary, continuous mental healthcare services are necessary even for subthreshold and mild psychological reactions during this epidemic to attenuate the possibility of escalating complications. multiple features were found for the group of untreated clinical l. kang, et al. brain, behavior, and immunity xxx (xxxx) fig. 1 . in this model, the solid line represents a significant relationship between the two, while the dotted line represents the relationship is not significant. kang, et al. brain, behavior, and immunity xxx (xxxx) xxx-xxx personnel who had serious psychological problems. first, compared to less severely affected groups, they had accessed fewer printed psychological advice materials (e.g., office brochures) and had accessed less psychological guidance publicized through digital media. second, they were more likely to desire personalized, one-on-one counseling as a therapy option. one might speculate a cause-and-effect relationship wherein more frequent exposure of the other groups to the noted materials in some way protected them from reaching the most severely impacted category, but our cross-sectional results are, by nature, correlational. this study limitation does not detract, however, from the importance of widely implementing prevention and monitoring strategies; mildly to moderately impacted personnel expressed interest in having access to psychological guidance materials, which provides evidence of the importance of prevention strategies. the number of people suffering from mental health impacts after a major event is often greater than the number of people who are physically injured, and mental health effects may last longer. nonetheless, mental health attracts far fewer personnel for planning and resources (allsopp et al., 2019) . thus, the lancet global mental health commission's observation that the use of nonprofessionals and digital technologies can provide a range of mental health interventions may indicate an opportunity (patel et al., 2018) . our data are consistent with a model in which psychological advice and guidance in print resources and disseminated in the media can provide a level of protection for medical and nursing staff, improving mental health by reducing the stress impacts caused by high risk of infection. clearly, there is a role, nonetheless, for therapist-driven sessions, as previous research showed that a convenient group course intervention for doctors reduced depersonalization, improved views on the meaning of work, and achieved sustained results (west et al., 2014) . we anticipate similar benefit for covid-19 staff in wuhan based on our findings contained herein. interestingly, previous studies on medical staff and other infectious agents have repeatedly emphasized that mental health impacts are related to department and occupation (hawryluck et al., 2004; wu et al., 2009) . health care workers with professional knowledge about differences in the relative exposure patterns and transmission of different infectious diseases could gain some degree of comfort and control over their situations (chowell et al., 2015) . for example, over the decades, although hepatitis viruses and hiv have often caused lethal infections, radiologists, pathologists and nurses knew that their risk of exposure was low as long as they exercised caution in their contact with bodily fluids. the situation has been different in wuhan due to the pernicious characteristics of covid-19. many infected individuals exhibit minimal or no symptoms while contagious, for example, early in the course of infection (bai et al., 2020) . these individuals may thus visit a variety of different hospital departments in an infectious but asymptomatic state, unknowingly spreading the disease directly through aerosolized droplets or indirectly through skin contact with handled surfaces. these features of the infectivity of coronavirus involve a substantial risk of exposure for medical workers, regardless of their hospital department, job title or building location; thus, any workerwhether doctor or nurse, specialist or generalistis at substantial risk. the resultant stress due to concerns about infection risk thus indiscriminately affects large numbers of personnel. there is a need to better recognize mental health needs as an important component of mobilizing a large-scale therapeutic response to sudden city-scale crisis scenarios. a large rapid response team in crisis situations should include mental healthcare workers. local medical and nursing staff at the epicenter of a crisis are pivotal to the overall response, and care for these caregiverswhether through face-to-face counseling or comparable support through digital platforms such as cell phone interfacesis essential in efforts to extend their immediate efficiency and to better protect their mental health in the long term. our research also has some limitations. first, compared with faceto-face interviews, self-reporting has certain limitations. second, the study is cross-sectional and does not track the efficacy of psychological services. due to changes in posttraumatic mental health, dynamic observation is necessary. a randomized prospective study could better determine correlation and causation. third, a larger sample size is needed to verify the results. in summary, the results demonstrate that a strikingly large portion of health care providers in virus-plagued wuhan are suffering from mental health disturbances. they would benefit from greater availability of personalized mental health care from psychotherapists and psychiatrists, wherein different mental health groups could focus on providing specialized mental healthcare services. among the steps needed to better prepare for future infectious disease outbreaks would be a greater investment in the mental health tools in society's medical arsenal to protect and care for future medical and nursing staff who find themselves unexpectedly on the dangerous front lines of disease response. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. the organizational social context of mental health services and clinician attitudes toward evidence-based practice: a united states national study responding to mental health needs after terror attacks presumed asymptomatic carrier transmission of covid-19 a clustering technique for summarizing multivariate data conceptualizing and testing random indirect effects and moderated mediation in multilevel models: new procedures and recommendations a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster psychological impact of severe acute respiratory syndrome on health workers in a tertiary hospital transmission characteristics of mers and sars in the healthcare setting: a comparative study the impact of event scale: revised a comparison of diagonal weighted least squares robust estimation techniques for ordinal data sars control and psychological effects of quarantine fit indices in covariance structure modeling: sensitivity to underparameterized model misspecification the mental health of medical workers in wuhan, china dealing with the 2019 novel coronavirus healthcare workers emotions, perceived stressors and coping strategies during a mers-cov outbreak standardization of the depression screener patient health questionnaire (phq-9) in the general population validation and standardization of the generalized anxiety disorder screener (gad-7) in the general population the immediate psychological and occupational impact of the 2003 sars outbreak in a teaching hospital long-term psychological and occupational effects of providing hospital healthcare during sars outbreak the insomnia severity index: psychometric indicators to detect insomnia cases and evaluate treatment response the lancet commission on global mental health and sustainable development positive coping up-and down-regulates in vitro cytokine productions from t cells dependent on stress levels the mental health of school children after the great hanshin-awaji earthquake: ii. longitudinal analysis psychological stress reactivity and future health and disease outcomes: a systematic review of prospective evidence intervention to promote physician well-being, job satisfaction, and professionalism: a randomized clinical trial second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak the psychological impact of the sars epidemic on hospital employees in china: exposure, risk perception, and altruistic acceptance of risk this work was supported by grants from the national key r&d program of china (grant numbers: 2018yfc1314600) and the national natural science foundation of china (grant numbers: 81771472). wrote and contributed to the writing of the manuscript: zl, cm, lk and sm. supplementary data to this article can be found online at https:// doi.org/10.1016/j.bbi.2020.03.028. key: cord-119576-8qp8o2g2 authors: xu, liyan; zhang, hongmou; deng, yuqiao; wang, keli; li, fu; lu, qing; yin, jie; di, qian; liu, tao; yin, hang; zhang, zijiao; du, qingyang; yu, hongbin; liu, aihan; jiang, hezhishi; guo, jing; yuan, xiumei; zhang, yun; liu, liu; liu, yu title: cost-effectiveness analysis of antiepidemic policies and global situation assessment of covid-19 date: 2020-04-16 journal: nan doi: nan sha: doc_id: 119576 cord_uid: 8qp8o2g2 with a two-layer contact-dispersion model and data in china, we analyze the cost-effectiveness of three types of antiepidemic measures for covid-19: regular epidemiological control, local social interaction control, and inter-city travel restriction. we find that: 1) intercity travel restriction has minimal or even negative effect compared to the other two at the national level; 2) the time of reaching turning point is independent of the current number of cases, and only related to the enforcement stringency of epidemiological control and social interaction control measures; 3) strong enforcement at the early stage is the only opportunity to maximize both antiepidemic effectiveness and cost-effectiveness; 4) mediocre stringency of social interaction measures is the worst choice. subsequently, we cluster countries/regions into four groups based on their control measures and provide situation assessment and policy suggestions for each group. coronavirus disease 2019 (covid -19) has been recognized as a pandemic by the world health organization in march 2020 (1) . nonetheless, on march 18, mainland china observed their first day with zero increase of local cases since the outbreak (2) . this indicates that, aside from the imported cases, the pandemic has been locally close to the end. many experiences and lessons can be shared by the rest of the world from the trajectories of the outbreak and the control strategies in mainland china. one question that is of particular importance is the costeffectiveness of different antiepidemic measures. drawn from the chinese experiences and lessons, three categories of measures have been implemented: a) "regular" epidemiological control and prevention measures, including identification of infected cases, tracing their close contacts, and quarantines for both; b) in-city activity restrictions, including work-from-home, shutdown of schools and public spaces, cancellation of events, and lock-down of residential neighborhoods; c) inter-city travel restrictions, including temperature screening at all transportation terminals, cancellation of flights and trains, and eventually travel bans from/to certain cities. specifically, (b) and (c) are considered "irregular," which contain the spread of disease in an aggressive manner through the suppression of all possible social interactions. however, these measures lead to enormous economic loss, which may mean higher unemployment rates, and shortage of food, medical services, and other necessities. those chain effects may also endanger the lives of certain social groups. fundamentally this is a trolley dilemma, and the life and health of human beings can hardly be evaluated using monetary values. nevertheless, a comprehensive understanding of the cost of each measure-including the opportunity cost of the shutdown economic activities-and the effectiveness of lifesaving can still help policy makers to compare different antiepidemic strategies in a more operable way. further, with these insights, we can then perform a cross-sectional assessment of the situation of the global antiepidemic campaign regarding the aforementioned measures in different countries/regions, such that typical policies can be clustered and prescriptive policy suggestions can be provided accordingly, which also echoes the argument in (3) . in prior research, scholars have used deductive models to find that the timing of lockdown, including both inter-city travel restrictions and social distancing, significantly changes the size of infected population and the spatial extent of spread (4) (5) (6) (7) . nonetheless, all prior research only focused on specific instances of policies without discussing generalizable impacts of different measures and lacked a cost-effectiveness assessment of each measure (8) (9) (10) . in this article, based on the transmission pattern of covid-19 in china, we build a two-layer contactspread model ( fig. 1) to recover the whole spatio-temporal transmission process, especially the early-stage numbers and distribution of cases at the prefecture level (see sm 1, 2, and 4 ). with this model as a generalizable baseline, we conducted a comprehensive sensitivity analysis for all antiepidemic measures (fig. 2) and concluded the following assessment on the effectiveness of the measures, in terms of number of infected cases, and number of infected cities. 1. containing daily social interaction, parameterized in the model as ! , " for the infected and the exposed populations, is the most effective measure for controlling both the number of infected cases and the spatial extent of the spread. more specifically, we find that a) the controls of ! and " show comparable and substitutable effects in containing the spread of disease, with different elasticity in different stages of the epidemic. controlling " is more effective when the number of cases is small (e.g., fewer than 10 in a city), and ! is more effective when the number of cases is sufficiently large. the implication is that at the early stage of transmission, comprehensive epidemic surveys and contact tracing, alongside with strict quarantine and social distancing, should be used to prioritize the reduction of the social interaction levels of the exposed population ( " ), while after the number of cases has increased to a sufficiently high level, comprehensive testing and identification of all infected cases should be prioritized in order to reduce the social interaction levels of the infected population ( ! ). b) stricter control of social interaction for both ! and " have diminishing returns in reducing the number of cases, but increasing returns in limiting the spatial extent of spread. for example, in one month of simulation, when daily social interaction drops from 100% to 90% of the normal level, the number of infected cases drops by 10%-25% (depending on the stage of epidemic), while the number of cities with infected cases drops only by 0-1%; when daily social interaction drops from 10% to 0, however, the number of cases drops only by 0.05%-0.5% for infected cases versus 2%-35% for cities with infected cases. an exception is at the ending stage of the epidemic, when controlling social interaction has increasing returns in both effects. c) the effects of the epidemiological and social interaction control measures are monotonic for the reduction of infected cases and the spatial extent of spread: the stricter they are enforced, the lower number of infected cases and the narrower spatial extent of spread can be observed. 2. the time of reaching turning point is independent of the current number of infected cases but is only related to the stringency of epidemiological and social interaction control measures, i.e., the relative change of ! , " . when the two parameters are 1/4-1/3 of the normal everyday values, the turning point comes in two weeks and the clearance of cases happens in two to three months; when ! , " are larger than 1/2-2/3 of the normal values, the turning point will never come, i.e., the peak value of case numbers will remain the same as if there are no such measures, but they only delay the time of peak. 3. except at the early stage and the ending stage, inter-city travel restriction has only minimal effect on both the reduction of infected cases and control of disease spread in a city network. overall, compared with in-city epidemiological and social interaction control measures, the contribution of inter-city travel restrictions to the reduction of the number of infected cases and the spatial spread of disease is much smaller-lower by two orders of magnitudes. when the number of cases is sufficiently large, inter-city travel restriction even exacerbates the situation since it limits the social interaction of infected cases, and "condenses" # locally (11) . this finding is consistent with that in prior research (12, 13) . therefore, to national or regional governments who manage a city network, and to international antiepidemic collaboration, travel restriction should only be regarded as an auxiliary measure at the beginning and ending stage of the spread to protect cities which have not been infected at all, or only with a sufficiently small number of cases. in the latter case epidemiological and social interaction control measures should also be implemented simultaneously to get the health care system and other prevention measures prepared. the simulation-based formal analysis above is consistent with the empirical evidence in china. the lockdown of wuhan, and nationwide strict enforcement of epidemiological control and social distancing policies around january 23, including the cancellation of all chinese new near gatherings mark the key move of the antiepidemic campaign. at that time point, all other cities in china were at early stages of the epidemic, which guaranteed the effectiveness of the wuhan travel ban. in addition, with aggressive social interaction control in all cities the turning point of the number of cases arrived in two weeks outside of wuhan. in wuhan, the key move was the functioning of 16 fāngcāng hospitals (mobile cabin hospitals) in early february which enabled citywide comprehensive quarantine of the infected population (14) . this measure reduced the social interaction of infected cases to almost zero, and together with strict social distancing they effectively reversed the trend of spread after two weeks. in terms of inter-city travel restrictions, since they were during the chinese new year and the extended holidays, and overlapped with social distancing measures, the net effect could not be easily isolated empirically. nonetheless, since mid-february the economy had re-opened. by the end of march, the inter-city migration in southern and eastern chinese cities had recovered to the same level as in previous years (15) , but most cities still observed almost zero increase of infected cases. this further supports that the effectiveness of travel restriction is very limited for the cities with small numbers of cases. another evidence to support this point is the 300,000 people who left wuhan right before the lockdown night (16) . this "escaped" population did not significantly change the effectiveness of the national antiepidemic effort. further analysis on the cost-effectiveness of the measures shows more irregularity and non-linearity, leading to more nuanced relationships (detailed in sm 5). here we summarize the most critical general patterns as follows: 1. the measures which can achieve both high antiepidemic effectiveness (low number of cases and narrow spatial spread) and high cost-effectiveness (smaller loss of economic outputs) only exist at the early stage of transmission. at the early stage, if epidemiological and social interaction control measures can be strictly enforced (sufficiently low ! and " ), it is possible to keep the spread at a low level, with a loss of economic outputs only up to 4%. the intuition is as follows: based on the assumptions of this article, the early-stage measures only include comprehensive testing, close contact tracing, and quarantine, but do not include indiscriminate restrictions of in-city social interaction and inter-city travel, which incurs high costs. the policy implication is straightforward: for early-stage cities and regions, it is critical to practice epidemiological control interventions, but not to necessarily mobilize the whole society into social interaction reduction. this finding is consistent with the suggestions in (6). 2. except for the early stage, it is impossible to simultaneously achieve both high antiepidemic effectiveness and high cost-effectiveness. except for a few "plateaus," the effectiveness of epidemiological and social interaction control measures monotonically increases with the stringency of control measures. however, the cost and cost-effectiveness functions are non-monotonic and there usually exists more than one peak (see details in sm 5), which in most cases do not coincide with the effectiveness peak. typically, the costs are the lowest when the control measures are at sufficiently low or sufficiently high levels. while the latter case has been explained in the last point, the sufficiently low control measure scenario basically leaves the whole population to be infected. therefore, the tradeoff between sufficiently low and sufficiently high levels of control measures depend on many technological factors, including the short-term and long-term capacity of healthcare systems, long-term uncertainty of virus mutation, and development of vaccines, as well as many non-technological factors, including the risk averse attitudes for the short term and the long term, the mental discounting between short-term and long-term tradeoffs, and the fundamental value judgement on the "value of lives," the discussion of which are beyond the scope of this article, and will be left for discussion at the end of this article. 3. lastly, although it is difficult to choose the optimal control strategy, the worst choice is explicit: mediocre control of social interaction, e.g., social distancing with leakage. this choice still incurs 20-60% loss of economic outputs, but only achieves 30-40% reduction in the number of cases, an extent which is insufficient to overturn the epidemic curve. except for moderately delaying the spread of disease which may be taken advantage of to get the healthcare system prepared, this strategy is the worst choice in all other dimensions. with the formal results above, we can now perform a cross-sectional assessment of the global situation of the antiepidemic campaign from a transmission-prevention policy perspective. among the three types of measures (epidemiological control measures, social distancing, and travel restriction), we disregard the travel restriction measure as our results clearly show that it is ineffective for most countries/regions under the current situation (we will discuss the exceptions later). rather, we use two datasets (17, 18) which codified the antiepidemic measures chosen by countries/regions as of april 7 (due to the lack of testing data, we use wuhan as a proxy for mainland china), and for the countries/regions analyze the relationship of their two stringency indices, $ and % , i.e., the activity levels of the infected and exposed populations, and the respective effectiveness on the reduction of infected cases. based on the stringency of the two dimensions of antiepidemic measures, we can divide all countries/regions into three groups (fig. 3) , each with a different antiepidemic "strategy": elimination, control, and delay. more than 100 countries/regions are not included because of the lack of data. we will also discuss the implications of this fact. 1. the "elimination" group: this group (up right corner of fig. 3 ) consists of only a few countries/regions, including mainland china (represented by wuhan), hong kong sar, vietnam, uae, bahrain, etc., all with # ≪ 1, such that the epidemic could be expected to dwarf within a reasonably short time period. mainland china is the most prominent example of this group, where aggressive measures have been taken on both dimensions to reduce the activity of the infected population as well as the exposed population. the measures include effective epidemiological control interventions, such as comprehensive testing and close contact tracing, and also aggressive social distancing measures, such as shutdown of schools, workplaces, and public transport, cancellation of events, and mass disease control education. these measures incur 40%-90% loss of economic outcome in a month, and the loss accumulates as the epidemic is not completely "eliminated". obviously, the underlying value judgment of the elimination strategy is an overwhelmingly high weight on health and lives over any cost-control or costeffectiveness reckoning. although the treasuring for lives is always respectable, long-lasting economic tightening also constitutes a threat to society, especially to the disadvantaged social groups. due to the existence of asymptomatic carriers, false-negative test results, and international imports of cases, a complete elimination of the epidemic is extremely difficult. thus, if the aim is to literally eliminate all cases, the economic losses are highly likely to accumulate to an unbearable level. therefore, we suggest that countries/regions which have followed the elimination strategy consider turning to the "control" strategy (elaborated below) to avoid excess economic losses on the condition that the active number of infected cases has been reduced to a sufficiently low level. we also suggest that these countries/regions keep the travel restriction measures-the most effective measure at this stage of the epidemic indicated by our simulation results. 2. the "control" group: this group includes south korea, singapore, qatar, norway, slovenia, russia, and new zealand, etc., all with # < 1, but still not sufficiently small, such that the epidemic can be reduced to a lower level (but not eliminated), depending on the stringency of intervention measures. the singapore in february was the most prominent example within this group, where antiepidemic measures have been mild enough not to affect everyday life by aggressive social distancing. through regular epidemiological control practices, they were managed to maintain a daily increase of infected cases fewer than 10, and only suffered 0.5%-4% loss of economic outcome in a month. the control strategy requires a highly capable epidemic control system. given the aforementioned long-term uncertainties, even with such a capable system, the strategy is still a tightrope-walking game with the risk of abrupt system overload by accidentally untracked surges of infection, which, unfortunately, appears to be the case in singapore in early april. under such circumstances, a timely turn to the "elimination" strategy may be necessary. 3. the "delay" group: all other countries/regions in fig. 3 belong to the third group, which appears to follow the "delay" strategy, with # > 1, such that the epidemic will continue to grow. this is often referred to as the "flatten the curve" strategy, which aims not to reduce the epidemic to an as-low-as-possible level within a short period of time, but only to delay its growth through mediocre epidemiological control and social distancing measures. our results show that this is usually the worst scenario in terms of cost-effectiveness. a country/region may opt to this strategy because their tradeoff between short-term certainty (economic loss avoidance) and longterm uncertainty (possible disappearance of the epidemic in the summer, development of vaccines, etc.) leans towards the former. unless they have strong evidence to justify the tradeoff, we strongly suggest they reconsider. moreover, our results show possible directions to improve-enhancing the social interaction control for the infected population through more comprehensive testing or enhancing the social interaction for the exposed population through stricter social distancing measures, whichever sees fit based on the location of the country/region on fig. 3 . rest of the world: more than 100 countries/regions do not appear in fig. 3 due to the lack of data, most of which are third-world countries/regions. although little information is available to us about the situations in these places, we conjecture that they may at this moment be pursuing cost-effectiveness of their antiepidemic interventions because of their limited availability of resources, which we call the "worth every penny" strategy. as our results show that the most cost-effective measures are usually neither the most effective one (actually they are usually very ineffective), nor the least costive ones, the "worth every penny" strategy is not a good option either. if a country/region opts to this scenario solely because of the lack of resources, it should be viewed as a humanitarian disaster, and we call for international aid in this situation. at the end, we acknowledge the extreme difficulty of even trying to lay out the comparison between human lives and economic activities, or the tradeoffs of lives between different social groups. we believe that the ethical discussion should be open to the whole society and hope that this article can contribute to the discussion. (19) and a network transmission layer based on inter-city migration. through inter-city travel, the numbers of exposed and infected populations are adjusted daily. the model is calibrated using the migration data and the number of reported cases in china. see materials and methods for model specifications. (a) gradient of the first effectiveness function (with the number of infected cases as the metric for effectiveness) at the peak/inflecting stage, displaying decreasing margins, as well as the reverse of the effect of the inter-city travel level as ! and " decreases. (b) gradient of the second effectiveness function (with the number of cities with infected cases as the metric for effectiveness) at the accelerating stage, displaying firstly increasing and then decreasing margins as ! and " decreases. (c) gradient of the second effectiveness function (with the number of cities with infected cases as the metric for effectiveness) at the ending stage, displaying monotonically decreasing margins as each dot represents a country/region. the sizes of the dots indicate the number of infected cases on april 7, 2020. classical seir model characterizes the dynamics of the susceptible, exposed, infected, and removed population, assuming a certain population size and transmission rate. in closer scrutiny, the fixed transmission rate assumption requires contact-based transmission process (19) . from the perspective of spatial interaction, this requirement is contradictory to the prior assumption of fixed population. due to the high mobility of modern society, fixed population requires a large spatial scale of the model, e.g., the national scale. moreover, contact-based assumption is valid only at the scale of human daily activities-such scale should not exceed the urban scale to incorporate multiday intercity travels. at a larger spatial scale, human activity is featured by the "return-explorer" dichotomy (20) . the former spreads outbreaks through daily contact, while the latter "diffuses" the epidemic through long-distance travels. the order of magnitude of the intercity long-distance migration can be massive in china, and related studies have also discussed the effect of this population flow on the spread of covid-19 outbreak (8, 9, 21, 22) . thus, the covid-19 outbreak is actually subject to a "contact-spread" two-step transmission process. therefore, the classic seir model is insufficient to accurately describe the epidemic dynamics in the urban network and needs to be expanded. thereupon, we constructed a series of seir models for all cities, coupled with an intercity network. the node-edge structure of the model corresponds to the above-mentioned contactspread process; and the required data (epidemic parameters of each city, and intercity spatial interaction) are relatively simple. here, the choice of appropriate spatial resolution is critical. on the one hand, while prior research have adopted similar model design, they conducted the analysis mostly at the provincial resolution (5, 23, 24) . according to the analysis above, the provincial level is not the best choice to reflect the intercity-spread mechanism. on the other hand, at too fine spatial scales, such as 1 km-grid, township, or census blocks, modeling results can hardly be verified due to the lack of data, and random errors can be large. attempting to make a compromise between simplicity and completeness, interpretability and prediction accuracy, data spatial accuracy and verifiability (25) (26) (27) , we took cities (administratively called prefectures in china) as the unit of analysis and built a model which we call the spatial-temporal explicit seir model (stex-seir). this model can not only be used to analyze the number of infected cases, spatial range of infection, and dynamics of the covid-19 outbreak, but can also be used to reveal the arrival time of the first case in each city. we calibrate the model with chinese case statistics. although it does not cover the entire globe, it is still informative to other countries since china has gone through the whole process of the epidemic. the stex-seir model relies on the following assumptions: 1) intra-city population is homogeneous, i.e., it is a "meta-population," which is a common practice in the absence of real demographic data; 2) omitting the impact of foreign imports and exports of covid-19 cases: the proportions of imported and exported cases during the covid-19 outbreak in china are extremely small and can be omitted over the study period. 3) virus remains unmuted: although a very large number of mutations have been recorded (28) , the transmission patterns of the virus have not noticeably changed so far. first step: update the immigrated and emigrated populations, the exposed population, and the infected population (assuming that the inputs and outputs of n, e, and i across cities are completed instantly at the beginning of time t). • ,-./01 : lockdown on january 23; • 0-*(2-. : measures taken on january 20; human-to-human transmission was confirmed on that day. : the proportion of the susceptible turning into the exposed status. second step: seir model in each city: in the above equations: s (unimmune and susceptible population) may turn into infected by contacting infected individuals; e (exposed) is the population who are in the incubation period after being infected; i (infected) is the population being symptomatic and infectious; r (removed) is the population who died or have been cured-they can neither infect others nor be infected again. n: total population in the city, subject to = + + + . other notations: • " : probability that a susceptible is infected and becomes an exposed person; • ! : probability that a susceptible is infected by an exposed person; • : probability that an exposed person turns into infectious status; • : probability of being cured; • : probability that an infected person dies; • " : probability that an exposed person is infectious; • ! : the number of susceptible persons who an infectious individual contact during each step of simulation; • " : the number of susceptible persons who an exposed individual contact during every step of simulation. the case data used in this article come from the national and provincial health commissions in china (29) . wuhan is the city hit hardest by the epidemic, accounted for 61.87% of the total number of cases. the number of cases in hubei province other than wuhan accounted for another 22.03%. therefore, wuhan and hubei province have very different medical conditions, prevention and control measures from other cities and provinces in china. thus, we assigned different initial parameters for wuhan, other cities in hubei, and cities in other provinces. the initial number of cases in wuhan was set to be 1, and the initial numbers in other cities in hubei and in other provinces was set to be 0. according to the national report, the first confirmed infected case in wuhan can be traced back to december 8, 2019. thus, we chose december 8, 2019 as the starting point for the simulation. according to other studies (30) , this date is as close as possible to the real starting point of the pandemic, and epidemiological data are only available from this point to calibrate model. the endpoint of model calibration is february 26, when the epidemic in china was almost over and the model has converged by that time. we will simulate the spread of the covid-19 epidemic from that date until the end of april as verification and prediction (by the time of writing this article). we used chinese national, provincial, and municipal reports as the baseline to calibrate our model, so that the fitted number of cases would match with the surveyed data. on the one hand, the assumption, based on case statistics, is reliable. reports are released separately by more than 300 cities nationwide and updated daily. panel data from different provinces are inter-validated with other and are also supported by data from other sources (e.g., total mortality rate of the population, or mortality data of similar symptoms such as influenza, pneumonia, etc.). thus, it is extremely unlikely that the data are fabricated continuously without being noticed. on the other hand, research shows that due to delayed diagnosis at the early stage of outbreak, the actual onset date of most confirmed cases is actually one week ahead of the report date (30, 31) . considering the incubation period, we pushed the outbreak curve from the reported dates backwards by a few days, thus yielding the baseline for model calibration. the calculation and initial values of , , 3 , 4 , , , , " , ! , " , and ∆ were articulated in section 4 of the supplementary material. among the three basic dimensions of epidemic control (control of the source of infection, cutting off transmission, and protection of the susceptible), we focus on the transmission cuttingoff dimension. specific measures belonging to this dimension can be further divided into three categories: 1) "regular" epidemiological control measures; 2) in-city social interaction control and 3) intercity travel restrictions. these measures can be directly mapped to the three key parameters ! , " , and ∆ (denoted as tl henceforth) in the stex-seir model (table s1) , and thus empower the quantitatively evaluation of the effectiveness and cost-effectiveness of various scenarios. regular epidemiological control measures include thorough epidemiological surveys, close contact tracing, and quarantines of all the infected individuals and their close contacts as early and as possible-especially the close contacts, who may be potential carriers. these measures are reflected in the model by tuning the values of ! and " . it is noteworthy that the limits of the effectiveness of regular epidemiological control measures: • it is very difficult for the close-contact tracing and quarantines to be exhaustive, so they cannot reduce " to 0, indicating an effectiveness "roof"; • close contact tracing is a tedious work and is heavily manpower dependent. given that the epidemiological control system in regular practice usually has limited capacity. under outbreaks the system could be overloaded and becomes dysfunctional. under these circumstances, more aggressive measures are needed to reduce " . in-city social interaction control measures include work-from-home, shutdown of schools, workplaces, public transit, and public spaces, cancelation of public events, lockdown of residential neighborhood, etc. the effects of these measures are to reduce the chance of close contact between the infected/exposed and susceptible individuals, and are represented in the model by the values of ! and " , especially " , with contributions of different measures aggregated to a final value. we collected the measures adopted in different prior papers and coded them to estimate the final values of ! and " . it needs to be noted that the effects of specific measures are clearly overlapping with each other. for example, when social distancing both at the work and home ends are effectively implemented, the marginal "contribution" of an additional control on public transit usage would be minimal. also, despite of the nominal public orders, the actual stringency of the measures could be flexible in practice. for simplicity, we utilize expert knowledge to estimate the overall efforts, i.e., the values of ! and " . intercity travel restriction includes suspending inter-provincial and intercity buses, trains and flights, closing highways and roads, etc. the purpose is to reduce the intensity of personnel exchanges across cities, thereby reducing the transmission of the infected/exposed individuals. this is represented in the model by the reduction of spatial interaction parameter tl, or ∆ " and ∆ ! . in this paper we use two indicators to evaluate the effectiveness of disease control measures: the number of infected cases, and the spatial extent (represented by the number of cities with infected cases). minimizing the total infected population is a self-explanatory goal from the perspective of epidemic control. since e will eventually be converted to i with a fixed probability, we only need to focus on the infected population i and use the relative change of i over the simulation period (one month) as one indicator of effectiveness. the total antiepidemic effect in all cities is the summation: aside from the total number of infected cases, the spatial extent of the epidemic is also an indicator worth noticing. if the epidemic can be contained within a narrow spatial extent, the medical resources in other cities can be diverted to the infected cities to help, which actually happened in china where medical teams across the country were sent to wuhan for support. we also use the relative change of the number of cities with infected cases during the simulation period (one month) to quantify the effect: the total effect in all cities is the summation: we used the opportunity cost of economic output as the indicator for the cost of the antiepidemic measures. for simplicity, we only used the work-hour loss as a proxy for the economic output loss and did not convert it to monetary values of goods and services. travel restriction leads to reduction in the total number of personnel exchanges between cities. in particular, the outbreak of covid-19 in china overlapped with the spring festival holidays, and travel restriction apparently caused the migrant workers who previously travelled back hometown not be able to return to cities where they had worked after the holidays. while the impact on economic output is affected by factors such as the productivity difference between the migrant workers and local workers, we can use wages as a proxy for productivity and estimate the differences (32) (33) (34) . calculations show that the average income of migrant workers in 2017 was 100.36% of that of the local workers, or roughly the same, so we do not need to adjust for the differences in the model 1 . therefore, this study ignores the role of the above factors. factors such as employment elasticity, which are more difficult to estimate, are also omitted for simplicity. therefore, the loss of economic output of city i at time t from travel restriction is: where _normal is the urban population in the normal status, approximated by the number of urban populations in the same period last year, and " _normal is the " in the normal status. for those who are not affected by the intercity travel restriction, we argue that the indiscriminately implemented in-city social interaction control measures reduce their intensity of social interaction, which in turn reduces their productivity and thus reduces the economic output. more specifically, we used " and ! as the proxy for productivity. it should be noted that lower " or ! is not necessarily the result of indiscriminate suppression of daily interactions but could also be the result of regular epidemiological control measures. a distinction needs to be made between these two situations. it can be reasonably assumed that when the number of the infected cases is small. for example, the daily increase of the number of infected cases does not exceed a certain threshold, the goal of reducing ! and " can be achieved solely by regular epidemiological control measures. therefore, a rational administration will choose not to opt to universal in-city social interaction control measures to avoid collateral loss. what is lost in this case is the output of only those who have been quarantined, i.e., the exposed and infected cases. we admit that it is extremely difficult to estimate such a threshold, which could be highly dependent on specific contexts such as governance capability, the resourcefulness of the epidemic control system, and cultural and geographic factors. although, a numerical estimation would still be of help. there was no opportunity to observe this threshold during the outbreak in china: in the early stage of the epidemic (before january 23, 2020), no effective epidemic control practices were taken outside of wuhan, and after january 23, the country had generally turned to aggressive and universal antiepidemic measures and it is difficult to separate the net effect of the each epidemic control measure. however, the singapore situation in january and february may constitute a good example, where in most cases daily reported new infected cases were under 10. another remark is that the chinese government sets a threshold of 3 cases for reporting a newly discovered epidemic to the national cdc. in light of these numerical example, we use 10 daily new infected cases as an estimate of the capacity threshold value. therefore, the loss of economic output of city i at time t from in-city social interaction control measures is set as follows. for straightforwardness, we convert the economic output loss into to a relative value: the proportion of the output with regard to that of the baseline (the normal situation). the total output loss ratio of city i during the entire simulation period is and the ratio of total output loss of all cities during the entire simulation period is: in summary, the comprehensive cost-effectiveness function of antiepidemic measures is: particularly, if cost = 0, it is stipulated that both cost/effectiveness ! , cost/effectiveness 6 equal to 0. for simplicity, we only calculated the cost and cost-effectiveness functions at the national level (the entire city network). to discover any initial value-dependence of the cost and the costeffectiveness functions, we ran the simulation at different stages of the epidemic. based on the calibrated model, five scenarios with the following starting and ending dates are set: the model is run for 30 days for each scenario, and five indicators are calculated: number of total infected cases, number of cities with infected cases, overall cost, effectiveness/cost ratio with respect to the number of infected cases, and effectiveness/cost ratio with respect to the number of cities with infected cases. we calculated the gradient function of the five indicators with respect to " , ! , and tl to analyze the structure of the solution space. for simplicity, we calculate the gradients discretely at the following points: ! = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9}; " = {0, 2, 4, 6, 8, 10, 12, 14, 16}; tl = {1, 2, 3, 4, 5}, where the five levels of tl correspond to 0.2, 0.4, 0.6, 0.8, and 1 times of the normal intercity travel level. note that the lowest level of tl is not 0. this is because according to the situation in china (given by baidu migration data), when the tl is the lowest, the travel level is still about 20% of the normal level, and we believe that the stringency of intercity travel restriction in reality cannot be greater than this level. in contrast, aggressive in-city social interaction control measures can reduce the values of " and ! to levels very close to 0. we evaluated the antiepidemic situation of countries/regions based on the stringency of activity control policies of the infected and exposed, i.e., the degree of which ! and " are reduced. this takes 3 steps: 1) codifying policies and computation of the stringency indices; 2) mapping of the stringency indices into values of ! and " ; and 3) assessment of the antiepidemic situation based on the results of our analysis. for the exposed, effective activity control measures include close-contact tracing and social distancing. for the computation of the stringency of these measures, we used the data and method provided by the oxford covid-19 government response tracker (17) , and computed and compiled the exposed activity control stringency index with six indicators: school shutdown, workplace shutdown, public events cancelation, public transport shutdown, public information campaign, and close-contact tracing. for the infected population, quarantine is the most important measure to reduce their activities, which but also requires testing in the first place. we therefore used the comprehensiveness of testing as the proxy for the infected activity control stringency. as testing policy coding from the aforementioned source is rather coarse, we instead designed an alternative index based on two indicators: tests per 1 million population, and the ratio between cumulative cases and the number of total tests. the compiled index is gained through dividing the first indicator with the second, logarithmically transforming the quotient, and finally normalizing the result to the 0-100 range to match that of the exposed population's activity control stringency index. the logarithmic transformation is used only for visualization purposes, as very few countries/regions have much higher original indices. for the testing data, we employed sources from www.worldometers.info/coronavirus/. it should be noted that as mainland china does not publish testing data, we used the data from wuhan as a proxy. for both indices, we use the data as of april 7. a total of 99 countries/regions are present in the final dataset. analysis results show that there exist two threshold values for both ! and " that correspond to the "elimination" (r 0 << 1) and "control" (r 0 < 1) strategies, as shown in table s2 . it should be noted that the effects of the two indicators are substitutable, with the elasticity of ! to be larger. for the mapping from ! to the respective stringency index of a specific measure, it is clear that the mapping should not be linear because of the non-linear transformations we have done. we therefore employed an estimation method based on expert knowledge: to achieve 2/3 reduction of ! which is required to "eliminate" the epidemic, it is needed to quarantine as many infected cases as possible. considering that about 1/3 to 1/2 infected cases are asymptomatic (35) , this roughly means that all symptomatic cases should be tested. based on the statistics from wuhan and south korea, this requires the tests per 1 million population to be greater than 10,000, and the ratio between the number of cumulative cases and total tests to be smaller than 5%. converted from the above estimation to the respective stringency index, the value is around 70. we thus used this value as the boundary between "elimination" and "control". following similar methods, we estimated that the boundary between the "control" and "delay" policy groups to be around 60. for the mapping from " to the respective stringency index, because all six indicators' contribution to the actual stringency level are roughly equally weighted, we simply conducted a linear mapping between the composite stringency index and " . thus, the stringency index boundary between the "elimination" and "control" groups is 75, and that between "control" and "delay" is 50. epidemic parameter estimation is the first and fundamental step in the seir model. in previous studies, choices of these parameters usually adopted mathematical interpretation, such as the inverse of the incubation period or infectious period (7, 23) and thus the numbers are not physically interpretable. however, if we consider the actual characteristics of covid-19 as shown in epidemiological studies, the ambiguity of the model can be greatly reduced. we estimated these parameters based on real-world data, considering errors caused by possible concealment, omission, and late reports. we used close contact tracing data after january 28 to estimate ! , since statistical data in the early stage showed fluctuation due to the lag of reactions from the government. in the equation following, ( ) indicates the number of newly confirmed cases in a day. and ( ) indicates the number of close contacts who are still under medical observation in the same day. we averaged ! ( ) with regard to t and got 0.01986, so we set ! to 2%. in addition, we considered covid-19 to be infectious in the later stage of the incubation period: there is no evidence of weaker infectivity during the incubation period, and it is assumed that it can be as infectious as during the infected period, indicating " = ! = 2%. the incubation period is generally 2-14 days, and 3-7 days in most cases. the median incubation period is 4 days. assuming infectivity in the 1-3 days before the end of the incubation period, with an average of 2 days, the ratio of infectious exposed people ( " ) can be calculated as follows d is the average infectious day of the exposed, and e is the median of the incubation period. according to the new coronavirus pneumonia prevention and control program (second edition), suspected cases are those with similar clinical symptoms as infected people. if a suspected case tests positive for nucleic acid test or its viral gene sequencing is highly homologous with sars-cov-2, it is diagnosed as a confirmed case. considering the relationship between suspected and confirmed cases, the ratio between new confirmed cases to existing suspected cases is recorded as the ratio of the exposed cases becoming infected cases. this index is a characteristic of the disease itself and is generally the inverse of the incubation period from the mathematical interpretation. therefore, it should be uniform for all cities. this parameter has converged since january 28 and the average value is 0.1404 (14.04%). because of the presence of asymptomatic infections, only considering suspected cases can lead to overestimation. since asymptomatic infections accounted for 1.2% of confirmed cases, we scaled up the suspected cases and the revised to be 13.87%. according to the epidemiology working group of the chinese center for disease control, at least 104 cases existed in hubei province in december 2019, spread in fourteen counties. by january 10, 2020, there were 757 cases and 102 deaths in 113 cities of 20 provinces. however, in the national epidemic reporting system, the first death was not reported until january 20 in the whole country except wuhan. therefore, we took the results (table s3 ) published by the epidemiology working group and calculated the mortality rates in different regions at each stage (table s4) . we fitted the mortality rates with the following functions: wuhan: recovery rate is closely related to the capacity of local medical resources and city governments' responsiveness, so we conducted parameter fitting for each city. it is reasonable to believe that the number of cured cases published is reliable since there is no obvious reason for concealing recovery. therefore, the recovery rate is calculated as the ratio between newly cured cases and existed confirmed cases. the recovery rate has changed significantly by time. taking wuhan as an example, the abrupt outbreak led to a lack of medical resources at the beginning. then, aid resources from all over the world were sent to hubei province. in addition, huǒshénshān and léishénshān hospitals were built quickly to treat patients in severe conditions. these efforts contributed to the improvement of recovery rates (7) . to capture the time-wise changes, we fitted piecewise functions to the recovery rates based on the characteristics of each stage. among the different stages, the early recovery rate in wuhan fluctuated too heavily to fit, so we took the average value in the period as an indicator of the recovery rate. the specific fitted functions are as follows: mainland china except hubei province: close contact tracing is a common epidemiological control measure, especially when early treatment is not clear, and when vaccines are not available. this approach can identify potentially infected individuals, quickly isolate them before they turn to severe patients, and prevent the occurrence of secondary transmission (36) . social interaction intensities of the exposed and infected individuals are denoted as " and ! respectively in our model. these two parameters are highly related to local population densities. considering that the covid-19 outbreak occurred during the chinese new year, the intensity of social interaction was significantly higher than usual. wuhan, as china's large transportation hub, may have a higher per capita social interaction intensity than other cities. to address this, we used the contact rate of the infected population during sars (maximumly 12) as the initial value of ! (37). in general, the behavior of the exposed population is less restricted than the infected, so we assume that the maximum contact rate of the exposed is twice as high as that of the infected, which means that the maximum " is 24. according to the local epidemic reports, the initial values of ! and " in each area can be obtained (table s5) . then, based on the local control policies and response time, we adjusted the contact values at different stages. in january 20, 2020, zhong nanshan announced that there was a risk of human-to-human transmission of covid-19, and some people in wuhan began to consciously reduce their activities. until the citywide lockdown, the number of cases surged, and people began to realize the severity of the situation. then, strategies such as business shutdown, school shutdown, stay-at-home notices, and community shutdown were gradually implemented throughout the country to avoid contact between the susceptible and the infected population. in the late stage of the epidemic, numerous prevention and control strategies, including hospitalizing all confirmed cases and isolating all suspected cases, have greatly reduced the values of ! and " (figs.1 and 2 ). the initial value of each city's population in our model is that on december 8. then, the population changed after the new year migration, which can be calculated through the spatial interaction matrix. our research includes 368 prefectures in mainland china, with the time span from december 1, 2019 to april 30, 2020. the data collected included migration data from the baidu migration map (15), statistical yearbooks, and local covid-19 reports. the original baidu migration data is consisted of migration flows of 91,788 city pairs among 368 cities from january 1, 2020 to february 26, 2020. since there was no news of the covid-19 outbreak in december, the intensity of social activities was not affected and remained the same as normal workdays. in march and april after the outbreak, we assumed that due to the impact of the travel restrictions in most cities, residents' travel remained at a very low level. therefore, the migration data for december was set to be the same as an average workweek from january 6, 2020 to january 12, 2020, and the intercity migration after february 26 was set to be the same as between february 17 to february 23. in addition, the numbers of covid-19 cases in our model and population data for the 368 cities were collected from the national bureau of statistics of china (38) and the national health commission of china's reports. we collected the publicly announced epidemic control policies of all prefectures in china from january 23 to february 20. this dataset includes about 4,000 documents, among which 364 were issued at the provincial level. we codified the policies into 6 categories: one for longdistance travel restrictions, and the other five for in-city social interaction control measures (table s6) . we further translated the policies into their control stringency in terms of social interaction reduction based on expert evaluation on the policy terms as well as enforcement level inferred from media coverage. we lastly mapped the codified policies to the values of ! and " (figs. 1 and 2) . in the baseline (real-world) model, the initial number of cases at this stage was 53 and increased to 7,780 after 30 days. the initial number of infected cities were 23 and increased to 301 after 30 days. in terms of the reduction of infected cases, the decreases of the three coefficients, ! , " , and tl all have positive effects, but the effects are non-linear-with all returns diminishing marginally. the marginal contribution of ! and " are roughly comparable and also substitutable, with that of " slightly higher when the level of social interactions is high (i.e., the values of ! and " are high, or close to the ordinary level, which is 9 for ! and 16 for " ), and that of ! higher when the level of social interactions is low (as low as 0). however, the marginal contribution of ! and " are both 2-5 times higher than that of tl in most cases, and the latter is only significant when the values of ! and " are both very low. when ! ≤ 3 and " ≤ 4, the number of infected cases will shrink, and will be reduced to 0 after approximately two months (table s7 ). in terms of the reduction of number of cities with infected cases, the decreases of the three coefficients, ! , " , and tl all have positive and non-linear effects, but with increasing returns marginally. the marginal contribution of ! and " are roughly comparable and also substitutable, with that of " slightly higher when the level of social interactions is high, and that of ! slightly higher when the level of social interactions is low. however, the marginal contribution of ! and " are both 1-2 times higher than that of tl in most cases, and the latter is only significant when the values of ! and " are both very low. when ! ≤ 3 and " ≤ 4, the number of cities with infected cases will shrink, and will be reduced to 0 after approximately two months. since there was no baseline control at this stage, any change in the three coefficients means tighter control on social interactions, and hence a cost to economic output. first, the marginal contribution from the reduction of tl to the cost function is approximately 2-5 orders of magnitude lower than that of ! and " such that its impact is mostly negligible. second, the cost function has a ridge along the direction of ( ! = 9, " = 12) and ( ! = 0, " = 16). the global gradient between the ridge and ( ! = 0, " = 0) is moderate, and a lowest plateau appears when ! ≤ 6 where the value of the cost function is 0. on the other side, the global gradient is much steeper, with a minimal value of the cost function that is also 0 at the corner. the global cost peak appears at ( ! = 9, " = 12), at which point the peak cost slightly exceeds 4% of the total output. in terms of cost-effectiveness, as the peaks and trends of the cost function and two effect functions are different, the two cost-effectiveness functions show greater non-linearity. in terms of the cost-effectiveness with respect to the reduction of the number of infected cases, two local peaks exist. one is at the "strictest control" point i.e., ( ! = 0, " = 0), when each 0.3% reduction in the number of infected cases is associated with 1% of economic output cost within a month; another peak occurs at the "non-control" point i.e., ( ! = 9, " = 16), when each 1.7% reduction in the number of infected cases is associated with 1% of economic output cost within a month. however, in the latter case, there will be no reduction in the number of infected cases at all according to the respective effectiveness function, while the former case coincides with the effectiveness peak. in terms of the cost-effectiveness with respect to the reduction of the number of cities with infected cases, situations are similar, only that a third peak appears at ( ! = 0, " = 16), which is also a hardly effective solution. overall, the best solution considering both effectiveness and cost-effectiveness in whichever terms at this stage of epidemic is at the "strictest control" point (fig. s3 ). stage: january 16, 2020 to february 15, 2020 5. in the baseline (real-world) model, the initial number of cases at this stage was 1,059 and increased to 8,920 after 30 days. the initial number of infected cities were 178 and increased to 310 after 30 days. in terms of the reduction of infected cases, the decreases of the three coefficients, ! , " , and tl all have positive effects, but the effects are non-linear-with all returns diminishing marginally. the marginal contribution of ! and " are roughly comparable and also substitutable, with that of " slightly higher when the level of social interactions is high (i.e., the values of ! and " are high, or close to the ordinary level, which is 9 for ! and 16 for " ), and that of ! higher when the level of social interactions is low (as low as 0). however, the marginal contribution of ! and " are both up to two orders of magnitude higher than that of tl in most cases, and the latter is only significant when the values of ! and " are both very low. when ! ≤ 3 and " ≤ 4, the number of infected cases will shrink, and will be reduced to 0 after approximately two months (table s8 ). in terms of the reduction of number of cities with infected cases, the decreases of the three coefficients, ! , " , and tl all have positive and non-linear effects, but with increasing returns marginally. the patterns of marginal contribution of the three coefficients are similar with the "reduction of infected cases" case and we do not elaborate here. first, the marginal contribution from the reduction of tl to the cost function is approximately 2-4 orders of magnitude lower than that of ! and " such that its impact is mostly negligible. second, the cost function has a ridge along the direction of ( ! = 9, " = 4) and ( ! = 0, " = 16). the global gradient between the ridge and ( ! = 0, " = 0) is moderate and roughly linear, and a lowest plateau appears when ! ≤ 3 and " ≤ 4 (the "strictest control" scenario) where the cost is a small number (2%-4%). on the other side, the global gradient is much steeper with increasing margins, with a minimal value of the cost close to 0 at the corner (the "non-control scenario). one noteworthy character of the cost function is that the value of ! does not affect the position of the peak, but affects its value: keeping " the same, each 10% reduction in ! reduces the cost function by 2%-4%. the global cost peak appears at ( ! = 9, " = 4), or a "loose control" scenario, at which point the peak cost exceeds 40% of the total output. the intuition is that in this case, the control on social interactions is not sufficient to reverse the trend curve of the epidemic, and after the number of infected cases exceeding a certain threshold (the capacity "roof" of regular epidemiological measures to contain the epidemic), cities have to opt to a universal control on everyday social interactions to contain the epidemic, inflicting heavy loss on economic output. the global gradients of the cost-effectiveness function for both effectiveness metrics show similar patterns with the previous stage, only with more non-linearity, which is too complicated to be elaborated here. for more details, refer to fig. s4 . the baseline model witnessed the turning point of the epidemic, when the initial number of cases at this stage was 10,345 and reduced to 1,913 after 30 days. the initial number of infected cities were 314 and reduced to 253 after 30 days. in terms of the reduction of infected cases, the decreases of ! and " both have positive effects, but the effects are non-linear-with all returns diminishing marginally. the decrease of tl, however, have varying directions of effect dependent on the values of ! and " , with negative effect when both ! and " values are high and positive otherwise. the marginal contribution of ! and " are roughly comparable and also substitutable, with that of " slightly higher when the level of social interactions is high (i.e., the values of ! and " are high, or close to the ordinary level, which is 9 for ! and 16 for " ), and that of ! one order of magnitude higher when the level of social interactions is low (as low as 0). however, the marginal contribution of ! and " are both up to two orders of magnitude higher than that of tl in most cases, and the latter is only significant when the values of ! and " are both very low. when ! ≤ 3 and " ≤ 6, the number of infected cases will shrink, and will be reduced to 0 after approximately two months. higher values of ! and " (looser control on the level of social interactions) will not be sufficient to reverse the epidemic trend curve. and at the non-control scenario, the number of infected cases will grow to approximately 200,000, or 20 times the number at the beginning of the baseline scenario (table s9 ). in terms of the reduction of number of cities with infected cases, the decreases of the three coefficients, ! , " , and tl all have positive and non-linear effects, but with increasing returns marginally. the patterns of marginal contribution of the three coefficients are similar with the "reduction of infected cases" case and we do not elaborate here. first, the marginal contribution from the reduction of tl to the cost function is approximately 2-4 orders of magnitude lower than that of ! and " such that its impact is mostly negligible. second, the cost function has a ridge along the direction of ( ! = 9, " = 0) and ( ! = 2, " = 16). the global gradient between the ridge and ( ! = 0, " = 0) is moderate, and the lowest cost at the corner (the "strictest control" scenario) is a small number (2%-4%). on the other side, the global gradient is much steeper, with a minimal value of the cost function close to 0 at the corner (the "non-control scenario). again, the value of ! does not affect the position of the peak but affects its value: keeping " the same, each 10% reduction in ! reduces the cost function by 8%-9%. the global cost peak appears at ( ! = 9, " = 0), or a "loose control" scenario, at which point the peak cost exceeds 90% of the total output. the global gradients of the cost-effectiveness function for both effectiveness metrics show similar patterns with the previous stage, only with more non-linearity, which is too complicated to be elaborated here. for more details, refer to fig. s5 . in the baseline model, the initial number of cases at this stage was 3,886 and reduced to 22 after 30 days. the initial number of infected cities were 288 and reduced to 1 (wuhan) after 30 days. in terms of the reduction of infected cases, the decreases of ! and " both have positive effects, but the effects are non-linear-with all returns diminishing marginally. the decrease of tl, however, have varying directions of effect dependent on the values of ! and " , with negative effect when both ! and " values are high and positive otherwise. the marginal contribution of ! and " are roughly comparable and also substitutable, with that of " slightly higher when the level of social interactions is high (i.e., the values of ! and " are high, or close to the ordinary level, which is 9 for ! and 16 for " ), and that of ! 4 times higher when the level of social interactions is low (as low as 0). however, the marginal contribution of ! and " are both up to 1 order of magnitude higher than that of tl in most cases, and the latter is only significant when the values of ! and " are both very low. when ! ≤ 9 and " ≤ 10, or ! ≤ 6 and " ≤ 12, the number of infected cases will shrink, and will be reduced to 0 after approximately two months. higher values of ! and " (looser control on the level of social interactions) will not be sufficient to reverse the epidemic trend curve. and at the non-control scenario, the number of infected cases will grow to approximately 10,000, or three times the number at the beginning of the baseline scenario (table s10 ). in terms of the reduction of number of cities with infected cases, the decreases of the three coefficients, ! , " , and tl all have positive and non-linear effects, with increasing returns marginally at most times except when the values of ! and " are both very low-a noteworthy character that is different with the symmetric accelerating stage. another noteworthy character of the effectiveness function is the occurrence of plateaus when ! ≤ 9, where the change of " and tl will not affect the spatial scope of the epidemic. first, the marginal contribution from the reduction of tl to the cost function is approximately 2-4 orders of magnitude lower than that of ! and " such that its impact is mostly negligible. second, the cost function has a ridge along the direction of ( ! = 9, " = 10) and ( ! = 0, " = 10). the global gradient at both sides of the ridge drops close to 0 with increasing margins and plateaus when ! is sufficiently low or high. again, the value of ! does not affect the position of the peak, but affects its value: keeping " the same, each 10% reduction in ! reduces the cost function by 5%-8%, and when ! < 6, a plateau occurs where cost is minimal. the global cost peak appears at ( ! = 9, " = 10), or a "loose control" scenario, at which point the peak cost exceeds 20% of the total output. the global gradients of the cost-effectiveness function for both effectiveness metrics show similar patterns with the previous stage, only with more non-linearity, which is too complicated to be elaborated here. for more details, refer to fig. s6 . in the baseline model, the initial number of cases at this stage was 267 and reduced to 1 after 30 days. the initial number of infected cities were 99 and reduced to 1 (wuhan) after 30 days. in terms of the reduction of infected cases, the decreases of the three coefficients, ! , " , and tl all have positive effects, but the effects are non-linear-with all returns diminishing marginally. the marginal contribution of ! and " are roughly comparable and also substitutable, with that of " about two times higher at all times. however, the marginal contribution of ! and " are both up to one order of magnitude higher than that of tl in most cases, and the latter is only significant when the values of ! and " are both very low. when " ≤ 12, or ! ≤ 6 and " ≤ 14, the number of infected cases will shrink, and will be reduced to 0 after approximately two months. higher values of ! and " (looser control on the level of social interactions) will not be sufficient to reverse the epidemic trend curve (table s11 ). in terms of the reduction of number of cities with infected cases, the decreases of the three coefficients, ! , " , and tl all have positive and non-linear effects, this time all with decreasing returns marginally -a noteworthy character that is different with the symmetric early stage. plateaus also exist at this stage, when ( ! , " ) is to the left (smaller) side of (6, 0)-(0, 8), where any further change of the coefficients will not affect the spatial scope of the epidemic. at this stage, the shape and value of the cost function are both dominated by " . they decrease monotonically and roughly linearly along with the direction of " 's decline, and the effects of ! and tl are very small. at this stage, the epidemic at the baseline has come to an end. although the initial number of cases is roughly equivalent to the initial stage of the epidemic, the strict control at the previous stages has led to a significant reduction in the number of the exposed population. therefore, the cost function at this time is dominated by " , and the peak value of the cost function is only 0.5% of the output, a great reduction compared to those in the previous three stages. since the lift of controls on social interactions will help restore economic output, the peak cost-effectiveness at this stage all occurs when all controls are lifted, at which time economic output will be very close to the normal level (when there is no epidemic). the second highest cost-effectiveness peak appears when the controls are maintained (given the number of infected cases, the controls now are realized predominately through effective epidemiological measures, rather than universal containment of social interactions), where the maximum loss of economic output is about 0.5%. while the former appears tempting, in the long run (about two months later) it is likely to cause a rebound in the epidemic (we only run the simulation for one month, so this effect cannot be directly observed in the model. however, the situation is similar to the initial period of the epidemic, and thus the lift of controls is just equivalent to starting the entire epidemic from the beginning, such that a second outbreak is inevitable if other conditions remain unchanged). the latter, on contrary, appears to achieve a good balance between cost and effectiveness within this study's analytical framework (fig. s7) . table s2 . threshold values for ! and " of the "elimination" and "control" strategies. elimination (r 0 << 1) control (r 0 < 1) ! 1/3 of the normal value while " is the normal value 2/3 of the normal value while " is the normal value " 1/4 of the normal value while ! is the normal value 1/2 of the normal value while ! is the normal value world health organization, who director-general's opening remarks at the media briefing on covid-19 national health commission of the people's republic of china a new twenty-first century science for effective epidemic response early phylogenetic estimate of the effective reproduction number of sars-cov-2 the effect of travel restrictions on the spread of the 2019 novel coronavirus modified seir and ai prediction of the epidemics trend of covid-19 in china under public health interventions the lockdown of hubei province causing 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structural change and cyclical dynamics quantifying sars-cov-2 transmission suggests epidemic control with digital contact tracing key: cord-333581-icp0xwhx authors: aziz, muhammad; haghbin, hossein; lee-smith, wade; goyal, hemant; nawras, ali; adler, douglas g. title: gastrointestinal predictors of severe covid-19: systematic review and meta-analysis date: 2020-07-30 journal: ann gastroenterol doi: 10.20524/aog.2020.0527 sha: doc_id: 333581 cord_uid: icp0xwhx background: covid-19 pandemic has created a need to identify potential predictors of severe disease. we performed a systematic review and meta-analysis of gastrointestinal predictors of severe covid-19. methods: an extensive literature search was performed using pubmed, embase, web of science and cochrane. odds ratio (or) and mean difference (md) were calculated for proportional and continuous outcomes using a random-effect model. for each outcome, a 95% confidence interval (ci) and p-value were generated. results: a total of 83 studies (26912 patients, mean age 43.5±16.4 years, 48.2% female) were included. gastrointestinal predictors of severe covid-19 included the presence of diarrhea (or 1.50, 95%ci 1.10-2.03; p=0.01), elevated serum aspartate aminotransferase (ast) (or 4.00, 95%ci 3.02-5.28; p<0.001), and elevated serum alanine aminotransferase (alt) (or 2.54, 95%ci 1.91-3.37; p<0.001). significantly higher levels of mean ast (md 14.78 u/l, 95%ci 11.70-17.86 u/l; p<0.001), alt (md 11.87 u/l, 95%ci 9.23-14.52 u/l; p<0.001), and total bilirubin (md 2.08 mmol/l, 95%ci 1.36-2.80 mmol/l; p<0.001) were observed in the severe covid-19 group compared to non-severe covid-19 group. conclusion: gastrointestinal symptoms and biomarkers should be assessed early to recognize severe covid-19. covid-19, caused by sars-cov-2, has become a worldwide pandemic imposing a significant burden on healthcare systems around the globe. the virus causes a variety of manifestations, including pneumonia, acute respiratory distress syndrome, shock, sepsis, and death [1] . currently, no specific therapy (preventive or therapeutic) is available for this disease [2] . symptomatically, the virus leads to fever, fatigue, cough, shortness of breath, myalgias, arthralgias, nasal congestion, runny nose, sore throat, nausea/vomiting, and diarrhea [1] . the virus further causes laboratory abnormalities, including derangements of white cell count, platelet count, c-reactive protein, procalcitonin, lactate dehydrogenase, aspartate aminotransferase (ast), alanine aminotransferase (alt), total bilirubin (tb), creatinine, and d-dimer [1] . the pandemic nature of this disease necessitates emergent and early recognition of symptomatic patients to identify those at most severe risk and to provide supportive measures as needed, up to and including mechanical ventilation. gastrointestinal parameters (symptoms and laboratory findings) have been reported in the literature among patients with covid-19 [3] , but there is little comprehensive information regarding gastrointestinal symptoms in these patients. we performed a systematic review and meta-analysis a comprehensive literature search was performed from january 1 st , 2020, to may 31 st , 2020, using the following databases: pubmed/medline, embase, cochrane, web of science. the search strategy, using a predeveloped vocabulary for covid-19 [4] , was created by an experienced librarian (wls) and crosschecked by another reviewer (ma). an example search strategy using embase is highlighted in supplementary table 1. article screening and data extraction was performed by 2 independent reviewers (ma and hh) and any discrepancies in screening/extraction were resolved through mutual discussion. interobserver agreement was evaluated using % of agreement and cohen's kappa (κ) statistic. articles were selected if they reported data on covid-19 patients with respect to gastrointestinal symptoms (diarrhea, abdominal pain, and nausea/vomiting) or laboratory findings (serum ast, alt, or tb). we excluded articles if the data of interest were not reported or the article had not undergone a peer-review process. we further excluded case reports and retrospective studies/case series reporting <10 cases. we used the bibliography of the finalized articles to further broaden our literature search. we did not restrict our search according to language. severe covid-19 was defined as respiratory distress (rate ≥30 /min, oxygen saturation ≤93% at rest and/or pao 2 /fio 2 ≤300 mmhg) [1] , intensive care unit (icu) admission, and/or death. laboratory data (mean serum ast, alt and tb) were reported based on the local laboratory's reference parameters for each study. symptoms (diarrhea and nausea/vomiting) were reported based on initial presentation. data extraction was performed using microsoft excel (microsoft, redmond, wash, usa). continuous variables (using mean and standard deviation [sd] ) and proportional variables (using event and total patients) were compared using the dersimonian-laird approach or a random-effects model. the fixed effect model was used as a sensitivity tool; however, given the presumed heterogeneity of study data from diverse sources and clinical settings, the randomeffects model was considered more appropriate and results were reported using that approach [5, 6] . the mean and sd were calculated from median and interquartile range where applicable. results are displayed using forest plots for each summary estimate, i.e., mean difference (md) and odds ratio (or) for continuous and proportional variables, respectively. a 95% confidence interval (ci), p-value (<0.05 was considered statistically significant), and study heterogeneity using i 2 statistic (>50% was considered as substantial heterogeneity) were calculated for each outcome [7] . subgroup analysis was performed based on the definition of severe covid-19 (respiratory distress, icu admission, and death) if at least 3 studies reported the outcome. sensitivity analysis using leave-one-out metaanalysis was performed and point estimates were generated. meta-regression was attempted to assess the impact of moderator variables on study outcomes. the moderator variables assessed included female proportions in each study, region of study (asia, europe, north america, south america), and number of centers in each study (single center, dual center, multicenter). the statistical analysis was performed using open meta analyst (cebm, university of oxford, oxford, united kingdom) and comprehensive meta-analysis (biostat, englewood, nj, usa). we utilized the quality in prognostic studies (quips) tool for assessing the risk of bias in the observational studies [8] . publication bias was assessed qualitatively by visualizing the funnel plot and quantitatively using egger's regression analysis. we adhered to "preferred reporting items for systematic reviews and meta-analyses (prisma)" guidelines for the purposes of this manuscript. using the search strategy defined above, a total of 1525 records were generated. after the inclusion/exclusion criteria had been applied, a total of 83 published studies (all observational) remained that reported data on gastrointestinal symptoms and/or laboratory findings ( fig. 1) [1, 3, . all studies included laboratory-confirmed covid-19 patients. the percentage of agreement was >90% for both screening and data extraction and corresponding κ values of 0.72 and 0.69 (substantial agreement), respectively, were noted. of the 83 included studies, 42 reported data on disease severity with respect to symptoms and/or lab findings. study details and demographics of included patients are highlighted in table 1 . based on region, 70 studies originated from asia, 8 from north america, 1 from south america, and 4 from europe. the study duration was from december 11 th through may 5 th , 2020. based on the number of centers reporting data, 17 studies were multicenter, 6 were dualcenter, 57 were single-center, and 3 studies failed to mention the center from where the data originated. a total of 26,912 patients were included across these 83 studies. the patients' mean age was 43.5±16.4 years and the female proportion was 48.2%. the overall prevalence of diarrhea on admission among the study population was 13.0% (95%ci 10.8-15.5%; i 2 =95.1%). based on region, the following prevalences were noted: europe 16.8% (95%ci 2.9-57.8%; i 2 =98.0%), north america 26.2% (95%ci 20.1-33.3%; i 2 =90.6%), and asia 11.5% (95%ci 9.5-13.9%; i 2 =91.8%). the overall prevalence of nausea/ vomiting on admission among the study population was 9.5% (95%ci 7.9-11.4%; i 2 =92.6%). based on region, the following prevalences were noted: europe 8.9% (95%ci 2.1-30.4%; i 2 =94.1%), north america 18.7% (95%ci 14.6-23.6%; i 2 =83.9%), and asia 7.7% (95%ci 5.9-9.9%; i 2 =91.6%). the prevalence of abnormal ast findings on admission was 27 .7%). the prevalence of abnormal tb levels on admission was 10.6% (95%ci 5.0-21.0%; i 2 = 97.1%). all studies that reported abnormal tb were from asia. the odds of patients with diarrhea having severe disease were significantly greater compared to those without diarrhea (26 studies, or 1.50, 95%ci 1.10-2.03; p=0.01; i 2 =54.1%) ( fig. 2a liu, et al [12] zhang, et al [27] wang, et al [40] zhou, et al [44] chen, et al [48] nobel, et al [67] pan, et al [69] wang, et al [77] wang, et al [30] yang , et al [83] zhang, et al [85] elevated serum ast levels in patients were evaluated in 16 studies and greater odds of disease severity were noted compared to patients without elevated ast (or 4.00, 95%ci 3.02-5.28; p<0.001; i 2 =40.4%) (fig. 3a) . the results were consistent on leave-one-out meta-analysis (or 3.64-4.14) as well as subgroup analysis for disease severity defined based on respiratory distress ( only 5 studies evaluated elevated serum tb levels in association with disease severity, and elevated tb was associated with severe disease (or 2.09, 95%ci 1.36-3.21; p=0.001; i 2 =17.5%) (fig. 3c ). leave-one-out meta-analysis demonstrated a consistent association (or 1.89-2.51). a subgroup analysis and meta-regression were not possible because of the low number of studies. the mean serum ast level was significantly higher in the severe group compared to the non-severe group (32 studies, md 14.78 u/l, 95%ci 11.70-17.86 u/l; p<0.001; i 2 =97.5%) (fig. 4a) . the leave-one-out meta-analysis was consistent with a point estimate (md) ranging from 13. the mean serum alt level was also significantly higher for the severe group compared to the non-severe group (31 studies, md 11.87 u/l, 95%ci 9.23-14.51 u/l; p<0.001; i 2 =95.5%) (fig. 4b) . the results were consistent on leave-one-out meta-analysis (md 11.14-12.61 u/l) and subgroup analysis for severity based on respiratory distress ( on meta-regression, female proportions were inversely correlated with disease severity on the basis of mean tb level (p=0.03). based on quips tools, most of the studies (n=63) were at risk of bias for failing to account for confounders, while the remaining (n=20) accounted for some confounders. twenty studies lacked details of the statistical design (supplementary table 2 ). visible asymmetry was observed on a funnel plot based on the symptom of diarrhea; however, egger's regression did not reveal a significant publication bias (p=0.76) (supplementary fig. 1 ). our meta-analysis demonstrated significant correlations between gastrointestinal parameters (diarrhea, elevated serum alt, ast and tb) and severe disease outcomes, i.e., respiratory distress, icu admission, and/or death. although the most frequent manifestation of covid-19 is pneumonia, gastrointestinal signs/symptoms are seen in a significant number of patients and can be the presenting manifestations of the disease [90] . a systematic review by cheung et al reported diarrhea and nausea/vomiting in 13% and 10% of covid-19 patients, respectively [91] . we demonstrated a similar prevalence of diarrhea (13%) and nausea/vomiting (9.5%). we believe that the reported prevalence of diarrhea and nausea/vomiting is somewhat lower than in reality, as some of these patients only present with these symptoms and may not undergo covid-19 testing because they do not fulfill local hospital or laboratory criteria. the mechanism behind gastrointestinal symptoms is thought to be secondary to viral attachment and entry via angiotensin-guar, et al [1] huaig, et al [10] chen, et al [3] liu, et al [12] chai, et al [ chen, et al [3] liu, et al [12] zhang, et al [26] zhang, et al [35] wang, et al [40] zhou, et al [44] cai, et al [47] hcng, et al [57] vteng, et al [76] yang, et al [83] zhang, et al [85] zhang, et al [86] zhao, et al [87] converting enzyme 2 (ace2), readily expressed in ileal and colonic epithelium [92] . this can explain symptoms such as diarrhea and nausea/vomiting. furthermore, researchers have also identified viral rna in the stool of patients infected with covid-19, making diarrhea not only a marker for disease severity but a potential route of contagion [22] . given the association of diarrhea with severe covid-19 disease, based on our meta-analysis results, covid-19 patients with diarrhea should be stratified into a high-risk group for developing severe disease as described above and managed accordingly. several mechanisms have been postulated to explain the hepatotoxicity seen in covid-19 patients. one possible mechanism of hepatotoxicity of covid-19 is immune system activation. it has been shown that many of the respiratory viruses, including covid-19, lead to an activation of cytotoxic t cells and kupffer cells in the liver that eventually damage hepatocytes [93] . another mechanism is the triggering of a "cytokine storm, " leading to a massive surge in mediators such as interleukin-6, associated with sepsis, multiorgan dysfunction and death [8, 94, 95] . direct viral entry through the intestines and invasion of the portal system and, subsequently, cholangiocytes, is another hypothesized mechanism [96] . lastly, drug-induced hepatotoxicity should also be considered, as currently researchers are investigating all possible therapeutic options [97] . we demonstrated significantly increased elevation of alt, ast and tb in patients with severe covid-19 compared to non-severe patients, which can be attributed to some or all of the aforementioned mechanisms. several limitations exist with our analysis. the most notable was the lack of high quality randomized controlled trials and cohort studies. we relied on data from observational studies that reported admission data. observational studies have their own inherent biases that limit data interpretation, including selection, recall, and confounding bias. it is difficult to establish a temporal relation between cause and event using observational studies, as there is no follow up. however, as we reported admission data, we propose screening and riskstratifying individuals, based on their admission laboratory findings and symptoms, into severe and non-severe categories. we were not able to account for factors such as comorbidities, timing of hospitalization and routine home medications. we were also not able to account for these related gastrointestinal symptoms due to lack of stratified data. lastly, given that the major manifestations of covid-19 are respiratory symptoms (cough, shortness of breath, sputum production) and fever, gastrointestinal symptoms may have been underreported. despite the limitations, our analysis combines data from a large number of studies with a robust number of patients. we used admission data to avoid potential heterogeneity introduced by other factors, such as in-hospital medications, nosocomial infections, intubation, etc. the results of our study were consistent on both subgroup and sensitivity analysis. furthermore, we provided subgroup prevalence based on region, i.e., asia, europe and north america where applicable. in conclusion, patients presenting with 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manifestations of 2019 novel coronavirus disease in a large cohort of infected patients from new york: clinical implications digestive symptoms in covid-19 patients with mild disease severity: clinical presentation, stool viral rna testing, and outcomes the clinical course and its correlated immune status in covid-19 pneumonia clinical features and outcomes of 98 patients hospitalized with sars-cov-2 infection in daegu, south korea: a brief descriptive study gastrointestinal complications in critically ill patients with covid-19 korea national committee for clinical management of covid-19. clinical course and outcomes of patients with severe acute respiratory syndrome coronavirus 2 infection: a preliminary report of the first 28 patients from the korean cohort study on covid-19 diarrhea: an underestimated symptom in coronavirus disease 2019 prevalence and clinical presentation of health careworkers with symptoms of coronavirus disease 2019 in 2 dutch hospitals during an early phase of the pandemic epidemiological, clinical, and virological characteristics of 465 hospitalized cases of coronavirus disease 2019 (covid-19) from zhejiang province in china gastrointestinal symptoms of 95 cases with sars-cov-2 infection analysis of imported cases of covid-19 in taiwan: a nationwide study clinical time features and chest imaging of 85 patients with covid-19 in zhuhai sex-specific clinical characteristics and prognosis of coronavirus disease-19 infection in wuhan, china: a retrospective study of 168 severe patients gastrointestinal symptoms and coronavirus disease 2019: a case-control study from the united states severe obesity, increasing age and male sex are independently associated with worse in-hospital outcomes, and higher in-hospital mortality clinical characteristics of covid-19 patients with digestive symptoms in hubei, china: a descriptive, cross-sectional, multicenter study acute liver injury in covid-19: prevalence and association with clinical outcomes in a large 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characteristics of noncritically ill patients with novel coronavirus infection (covid-19) in a fangcang hospital diarrhea is associated with prolonged symptoms and viral carriage in corona virus disease 2019 clinical characteristics and outcomes of patients with severe covid-19 with diabetes epidemiological and clinical features of 200 hospitalized patients with corona virus disease 2019 outside wuhan, china: a descriptive study clinical features and short-term outcomes of 221 patients with covid-19 in wuhan risk factors for disease severity, unimprovement, and mortality in covid-19 patients in wuhan, china liver impairment in covid-19 patients: a retrospective analysis of 115 cases from a single centre in wuhan city clinical characteristics of patients with 2019 coronavirus disease in a non-wuhan area of hubei province, china: a retrospective study epidemiological characteristics and clinical features of 32 critical and 67 noncritical cases of covid-19 in chengdu effect of gastrointestinal symptoms in patients with covid-19 taste changes (dysgeusia) in covid-19: a systematic review and metaanalysis gastrointestinal manifestations of sars-cov-2 infection and virus load in fecal samples from a hong kong cohort: systematic review and metaanalysis the digestive system is a potential route of 2019-ncov infection: a bioinformatics analysis based on single-cell transcriptomes systemic viral infections and collateral damage in the liver elevated interleukin-6 and severe covid-19: a meta-analysis the association of low serum albumin level with severe covid-19: a systematic review and meta-analysis enteric involvement of coronaviruses: is faecal-oral transmission of sars-cov-2 possible? drug-induced liver injury or indigestion* or dysmotilit* or nausea* or vomit* or emesis* or hematemesis* or 'abdominal pain*' or amylase or lipase or alt or 'alanine aminotransferase*' or ast or 'aspartate aminotransferase*' or bilirubin or 'alk phos' or 'alkaline phosphatase*' or cea or 'carcinoembryonic antigen*' or 'ca19 9' or 'carbohydrate antigen 19 9' or ggt or 'γ glutamyltransferase*' or 'gamma glutamyltransferas3*' or 'y glutamyltransferase*' or 'fecal calprotectin*' or 'fecal leukocyte*' 1858951 2. (('coronavirinae'/exp or 'coronavirus infection'/de or coronavirus*:ti,ab,kw or 'corona virus*':ti,ab,kw or 'pneumonia virus*':ti,ab,kw or cov:ti,ab,kw or ncov:ti,ab,kw) and (outbreak:ti,ab,kw or wuhan:ti,ab,kw) or covid19:ti,ab,kw or #3 not ('conference abstract'/it or 'editorial'/it or 'review'/it or 'short survey'/it) /de or 'animal experiment'/de or 'animal model'/de or 'animal tissue'/de or 'meta analysis'/de or 'practice guideline'/de or 'systematic review /de or 'animal experiment'/de or 'animal model'/de or 'animal tissue'/de or 'meta analysis'/de or 'practice guideline'/de or 'systematic review'/de) and *searches for human or excluding nonhuman or animal studies were inconsistently indexed, so were abandoned as a strategy state the process for selecting studies (i.e., screening, eligibility, included in systematic review, and, if applicable, included in the meta-analysis). data collection process 10 describe method of data extraction from reports (e.g., piloted forms, independently, in duplicate) and any processes for obtaining and confirming data from investigators. data items 11 list and define all variables for which data were sought (e.g., picos, funding sources) and any assumptions and simplifications made.6 (contd...) 12 describe methods used for assessing risk of bias of individual studies (including specification of whether this was done at the study or outcome level), and how this information is to be used in any data synthesis. table 2 results of individual studies 20 for all outcomes considered (benefits or harms), present, for each study: (a) simple summary data for each intervention group (b) effect estimates and confidence intervals, ideally with a forest plot. consider their relevance to key groups (e.g., healthcare providers, users, and policy makers). limitations 25 discuss limitations at study and outcome level (e.g., risk of bias), and at review-level (e.g., incomplete retrieval of identified research, reporting bias).14 conclusions 26 provide a general interpretation of the results in the context of other evidence, and implications for future research. funding funding 27 describe sources of funding for the systematic review and other support (e.g., supply of data); role of funders for the systematic review. key: cord-303203-1kpw4ru0 authors: guo, jing; feng, xing lin; wang, xiao hua; van ijzendoorn, marinus h. title: coping with covid-19: exposure to covid-19 and negative impact on livelihood predict elevated mental health problems in chinese adults date: 2020-05-29 journal: int j environ res public health doi: 10.3390/ijerph17113857 sha: doc_id: 303203 cord_uid: 1kpw4ru0 the covid-19 pandemic might lead to more mental health problems. however, few studies have examined sleep problems, depression, and posttraumatic symptoms among the general adult population during the covid-19 outbreak, and little is known about coping behaviors. this survey was conducted online in china from february 1st to february 10th, 2020. quota sampling was used to recruit 2993 chinese citizens aged ≥18 years old. mental health problems were assessed with the post-traumatic stress disorders (ptsd) checklist for the diagnostic and statistical manual of mental disorders, fifth edition (dsm-5), the center for epidemiological studies depression inventory, and the pittsburgh sleep quality index. exposure to covid-19 was measured with questions about residence at outbreak, personal exposure, media exposure, and impact on livelihood. general coping style was measured by the brief coping style questionnaire (scsq). respondents were also asked 12 additional questions about covid-19 specific coping behaviors. direct exposure to covid-19 instead of the specific location of (temporary) residence within or outside the epicenter (wuhan) of the pandemic seems important (standardized beta: 0.05, 95% confidence interval (ci): 0.02–0.09). less mental health problems were also associated with less intense exposure through the media (standardized beta: −0.07, 95% ci: −0.10–−0.03). perceived negative impact of the pandemic on livelihood showed a large effect size in predicting mental health problems (standardized beta: 0.15, 95% ci: 0.10–0.19). more use of cognitive and prosocial coping behaviors were associated with less mental health problems (standardized beta: −0.30, 95% ci: −0.34–−0.27). our study suggests that the mental health consequences of the lockdown impact on livelihood should not be underestimated. building on cognitive coping behaviors reappraisal or cognitive behavioral treatments may be most promising. the covid-19 pandemic not only affects physical health, it might also lead to elevated levels of mental health problems such as sleep problems, depressive issues, and posttraumatic stress symptoms [1, 2] . the pandemic is, however, a multifaceted and complex type of exposure. living in the epicenter of the outbreak or having travelled to that center might make a difference in the way the the survey was conducted online from 1-10 february 2020, and the questionnaires were distributed and retrieved through a web-based platform (https://www.wjx.cn/app/survey.aspx). quota sampling was used to recruit participants. chinese citizens aged ≥ 18 years old were invited to participate. in total, 2993 participants from 31 provinces in china responded to the survey; 552 students were excluded because of their special status, which resulted in a final n = 2441 adults. to reach more subjects with high exposure to covid-19 and from somewhat lower social economic strata, we targeted recruitment to six groups that might otherwise have remained underrepresented, namely medical workers, service staff, social service workers, (school and college) teachers, blue-collar workers and farmers, and unemployed individuals and others. the convenience sampling was conducted as followed. first, several key contact persons in these specific groups were selected, for example a chief nurse, class tutor, or company manager. second, the key contact persons helped us distribute the questionnaires to the subjects through their wechat group (a very popular chinese online communication tool). third, the subjects in each wechat group were asked to send our questionnaire web link to their friends. this way data were collected from medical workers (n = 421, 14.7%), service staff (n = 259, 9.1%), social service workers (n = 230, 8.0%), (school and college) teachers (n = 648, 22.7%), blue-collar workers and farmers (n = 388, 13.6%), unemployed individuals and others (n = 488, 17.1%). almost 48% of the respondents were male, and 90.3% of the subjects were between 18-50 years old. more than half of the sample completed at least undergraduate studies, and more than 70% were married. the large majority had a middle to high income and 39% worked in the formal labor market. there were some differences between the participants within wuhan, in sub-wuhan, and outside wuhan (for details, see table 1 ). all participants gave consent after being informed about the aim of the survey and joined the study voluntarily. the study was approved by the ethics committee of peking university medical center. depressive symptoms were assessed with the 20-item center for epidemiological studies depression scale (cesd), which has been widely used to measure depression in the general population [11] . previous studies demonstrated that this scale has adequate reliability and validity among chinese respondents [12, 13] . respondents reported the frequency of each type of symptom on a 4-point scale: 0 (rarely or never; less than 1 day), 1 (some of the time; 1-2 days), 2 (a moderate amount of the time; 3-4 days), or 3 (most or all of the time; 5-7 days). the total score ranges from 0 to 60, with a higher score indicating a higher level of depressive symptoms. in this study the cronbach's alpha was 0.93. with a cut-off point at 21 [14] , respondents were divided into two categories, "depressed" or "not depressed". post-traumatic stress symptoms (ptss) ptss were assessed with the self-report post-traumatic stress symptoms disorders (ptsd ) checklist for the diagnostic and statistical manual of mental disorders, fifth edition (dsm-5), estimating the degree to which individuals had been struggling with dsm-5-related ptss symptoms in the past month [15] . respondents answered the 20 items on a 4-point rating scale from 0 (not at all) to 4 (extremely). items were summed for a total score ranging from 0 to 80, with higher scores indicating higher level of ptss. cronbach's alpha was 0.97. the 20 items were clustered in the following areas: intrusions, avoidance, negative alterations in mood and cognitions, and alterations in reactivity and arousal. the diagnostic criteria of dsm-5 require at least one "intrusion" symptom, one "avoidance" symptom, two "negative alterations in mood and cognitions" symptoms and two "alterations in reactivity and arousal" symptoms, all rated 2 or higher. sleep problems were assessed using the pittsburgh sleep quality index (psqi) [16] . the psqi consists of 19 items rated from 0 to 3 including estimation of sleep latency, duration, disturbances, and the severity and frequency of other sleep problems. the total psqi score ranges from 0 to 21 with higher scores indicating worse sleep quality. cronbach's alpha was 0.86. with a cut-off point at 7 [17] , respondents were divided into two categories, struggling with "insomnia" or "no insomnia". because of the high correlations between the scales for depression, ptss, and insomnia, ranging from r = 0.39-0.75, we decided to compute a principal component analysis. a strong first component emerged, with loadings >0.69. the aggregated scale for mental health problems was the sum of scales for ptss, depressive symptoms, and sleep problems. the question about wuhan exposure concerned living in or having travelled to wuhan, with "1" referring to living in or having had a wuhan travel history, or "0" referring to no wuhan residence or travel history. also, two questions were asked about living near wuhan city, and not living in the vicinity of wuhan city, with yes or no as possible answers. exposure to the covid-19 pandemic through watching or using the media was answered on a 4-point rating scale for frequency: very frequent, often, some, no exposure). direct exposure to covid-19 was assessed with a question about possibly having suffered or suffering from covid-19, or someone in the family, or neighborhood or among friends, with "1" for covid-19 of self, a member of the family, a friend, someone in the neighborhood, and "0" referring to no exposure). the respondents were asked to estimate the impact of the pandemic on their livelihood, with four response alternatives (none, some, relatively large, very large impact). it was measured by the simplified coping style questionnaire (scsq), developed in china [18] . the scsq is a self-report scale which comprises of 20 items with a 5-point rating scale, ranging from 1 (not used) to 5 (used a great deal). the scsq consists of two subscales: problem-focused coping and emotion-focused coping. the problem-focused coping category includes twelve items that describe positive cognitive and behavioral strategies to manage distress. the emotion-focused coping category includes eight items that describe negative cognitions and avoiding behavioral activities to manage the problem. this inventory has good internal and test-retest reliability. in the present study, cronbach's alpha of the total scale was 0.89 and that for problem-focused coping and emotion-focused coping were 0.85 and 0.93, respectively. respondents were asked how they were coping with covid-19. the questions concerned 12 specific coping behaviors, including "tell myself that everything will be better soon", "reading and watching tv", "getting more knowledge about covid-19", "wearing a mask when going outside", "staying home and following the social distancing rule", "disinfecting and deep cleaning", "crying, being angry, and yelling", "drinking", "smoking", "praying", "taking more medicine", and "taking one's temperature". the respondents were asked to rate the behaviors from 1 (not used) to 5 (used a great deal). the following covariates were measured. demographic variables included ethnicity (han, else), marriage (having no spouse, having a spouse), education (junior high school and below, high school/technical school, junior college, undergraduate, postgraduate and above), and income (low, middle, or high income). job descriptions included the seven categories mentioned above and categorized into jobs in the formal versus informal sector. following previous studies [19, 20] , health-related variables included questions pertaining to prior mental health problems (yes, no), and occurrence of two-week illnesses (yes, no), and prior exposure to potential trauma (experience of a traumatic event in the last year (yes, no)). the main analyses consisted of multiple regressions on the aggregate outcome of mental health problems in four steps, and in each step the same covariates were used: age, gender, educational level, formal or informal job, married, income, past illness, prior exposure, prior mental health problems. in model 0 each of the predictors were included separately to estimate their 'raw' contribution to the prediction of mental health problems, controlling for the covariates. in model 1 the three predictors of (potential) exposure (location, media, direct exposure) were included to examine which component would be the most powerful predictor. in model 2 the perceived impact on livelihood was added, and finally, in model 3 emotion-focused and problem-focused coping behaviors were included to explore how much variance coping would predict in mental health problems. the standardized beta's can be compared across models and predictors, lower and upper 95% confidence intervals (cis) were computed as well as the p-values. in the next series of logistic regression analyses, the odds and their 95% ci and p-values for the predictors of the three components of mental health problems were computed, again with the same four models. the components ptss, depression, and insomnia were dichotomized to differentiate between clinical and nonclinical cases. in a final set of analyses regressions with the 12 coping behaviors as predictors of mental health problems were conducted, controlling for the same set of covariates used in the previous regressions. the software for statistics and data science (stata) version 14.0 (statacorp., college station, tx, usa) was used to carry out all analyses. in table 2 the results of the multiple regressions on the aggregate outcome of mental health problems are presented. the largest variance in mental health problems was explained by coping behaviors, with more use of problem-focused coping behaviors predicting less problems (effect size beta = −0.31), and more use of emotion-focused coping behaviors predicting more problems (effect size beta = 0.50). furthermore, an important predictor was the perceived impact on livelihood. larger impacts were associated with more mental health problems and the standardized beta for the respondents feeling the largest impact amounted to a standardized beta of 0.21. finally, direct or indirect exposure to covid-19 through location, media, or infected cases predicted statistically significant variance in mental health problems, with wuhan location, very frequent media exposure, and actual direct exposure to the virus predicting elevated levels of mental health problems. standardized beta's ranged from 0.03 to 0.09 (positive or negative), thus considerably smaller effect sizes compared to those found for impact on livelihood or coping. a sensitivity analysis was conducted including formal versus informal job as a predictor of mental health problems instead of its role as a covariate but the beta in model 3 was a negligible 0.00 (95% ci: −0.04-0.03). for predicting ptss the models showed that exposure through location, media, or direct contact was less important than the impact on livelihood and coping behaviors. more impact on livelihood and more emotion-focused coping were associated with higher risk of clinical ptss levels, whereas problem-focused coping reduced this risk (see table 3 ). this was similar for the prediction of risk for depression, but living in the neighborhood of wuhan instead of within the city of wuhan lowered the risk for depression (odds = 0.50), whereas direct exposure added predictive value by elevating the risk of becoming clinically depressed (odds = 1.39, see table 4 ). direct exposure also was associated with elevated risk of insomnia (odds = 1.70, see table 5 ). the models with more predictors included in the same regressions did not make much of a difference compared to model 0 with only one predictor at a time included (and the covariates of course). only in model 3 in which coping was included in the last step the negative beta for living in the neighborhood of wuhan but not in wuhan itself was not statistically significant anymore (beta = −0.04). very frequent media exposure and direct exposure to covid-19 kept predicting elevated levels of mental health problems. the large effect sizes for impact on livelihood and coping attenuated only slightly from model 0 to model 3, and they were still substantial, in particular problem-focused and emotion-focused coping style. in figure 1 the practical coping behaviors are presented. more emotion-focused coping behaviors such as "crying, being angry, and yelling", "drinking", or "smoking" seemed to be associated with largest risk for mental health problems but more frequently "praying", "taking more medicine", or "taking one's temperature" also elevated this risk albeit to a somewhat lesser extent. most helpful in decreasing the risk for mental health problems were coping behaviors such as "telling myself that everything will be better soon", "getting more knowledge about covid-19", and "staying home and following the social distancing rule". to a somewhat lesser extent it seemed also to help when coping with "reading and watching tv", "wearing a mask when going outside", and "disinfecting and deep cleaning" were used (see figure 1a) . a similar picture emerged or the association between coping behaviors and ptss, depression, and insomnia separately (see figure 1bfigure 1 . the relationship between coping behavior and post-traumatic stress symptoms (ptss), depression, insomnia, mental health problems. (a) coping and ptss, (b) coping and depression, (c) coping and insomnia, and (d) coping and mental health score. notes: v1 refers to "tell myself that everything will be better soon", v2 refers to "reading and watching tv", v3 refers to "getting more knowledge about covid-19", v4 refers to "wearing a mask when going outside", v5 refers to "staying home and following the social distancing rule", v6 refers to "disinfecting and deep cleaning", v7 refers to "crying, being angry, and yelling", v8 refers to "drinking", v9 refers to "smoking", v10 refers to "praying", v11 refers to "taking more medicine", and v12 refers to "taking one's temperature". these 12 items were asked in a random order in the questionnaire. all confounding variables were controlled in above models. or, odds ratio. ci confidence interval. coping and depression, (c) coping and insomnia, and (d) coping and mental health score. notes: v1 refers to "tell myself that everything will be better soon", v2 refers to "reading and watching tv", v3 refers to "getting more knowledge about covid-19", v4 refers to "wearing a mask when going outside", v5 refers to "staying home and following the social distancing rule", v6 refers to "disinfecting and deep cleaning", v7 refers to "crying, being angry, and yelling", v8 refers to "drinking", v9 refers to "smoking", v10 refers to "praying", v11 refers to "taking more medicine", and v12 refers to "taking one's temperature". these 12 items were asked in a random order in the questionnaire. all confounding variables were controlled in above models. or, odds ratio. ci confidence interval. our main findings point at the significant role of direct exposure to covid-19 instead of the specific location of (temporary) residence within or outside the epicenter of the pandemic. increased mental health problems were also associated with more intense exposure through the media. most importantly, in our relatively highly educated and predominantly lower to upper 'middle-class' participants the perceived negative impact on livelihood showed the largest effect size in predicting the level of mental health problems. we also examined the effect of coping style and coping behaviors against covid-19 and found that a problem-focused coping style and positive cognitions and prosocial coping behaviors predicted reduced mental health problems. compared to wuhan, we found a lower mental health level among sub-wuhan participants. however, this difference disappeared after adjusting for coping. previous studies on earthquake survivors and on 9/11 world trade center survivors showed that participants who were living closer to the epicenter showed increased mental health issues [21, 22] . our study provides somewhat contrasting evidence for the covid-19 affected population. direct exposure, perceived impact on livelihood, and how one was coping with the pandemic seemed more important than the specific location of (temporary) residence within or outside the epicenter (wuhan) of the pandemic. for specific mental health problems some different associations were found. direct exposure to covid-19 elevated the risk for depression and insomnia but not for clinical ptss, for which the perceived impact on livelihood seemed more important. impact on livelihood was also associated with depression but not with insomnia. direct exposure to covid-19 involves higher risks for infection and severe respiratory illness, leading to more mental disorders [23] , but it is unclear why only the risks of clinical depression and insomnia but not ptss appeared to be elevated. for ptss the threat of poverty and the deterioration of economic conditions due to the outbreak seem more important. this threat to livelihood reduces social resources such as access to medical care, education, employment, and well-being for the individual and his or her family, which may cause even greater harm to mental health than the epidemic itself [24] . our findings demonstrate that coping styles are associated with mental health problems due to covid-19. a problem-focused coping style seems to relieve individuals' post-traumatic stress, depression, and insomnia symptoms, and the emotion-focused coping style seems to exacerbate mental health symptoms [25] . problem-focused coping is a positive strategy that entails some active methods such as finding out several different ways to solve the problem or seeking advices from relatives or friends. emotion-focused coping tends to emphasize passivity and powerlessness, which enhances anxious and depressed feelings. in line with positive effects of problem-focused coping, we found that practical behaviors such as emphasizing positive cognitions [26] and getting more information about the virus indeed were associated with less mental health problems. in a previous study, positive cognitions about the severe acute respiratory syndrome (sars) outbreak were shown to result in less psychological disorders [27] . it also seemed to help when participants tried to cope by following the (pro-)social distancing and hygienic rules. a recent study indicated that personal psychoneuroimmunity prevention measures such as the frequent practice of hand hygiene and wearing face masks could decrease the likelihood that individuals would experience psychiatric symptoms [28] . through knowledge acquisition and hygienic behaviors individuals actively try to alleviate their fear of uncertainty about the future. some implications may follow from these findings. first and foremost, the mental health consequences of the expectation of a large negative impact on livelihood should not be underestimated. regardless of location or exposure the economic threats of the pandemic seem to leave a rather strong imprint on mental health. as a worldwide recession has been predicted to follow the current pandemic [29] , our findings foreshadow indeed 'a crashing wave' not only of immune-system related neuropsychiatric disorders [30] , but also of a wide array of stress-related depressive symptomatology without a direct link to deficits of the immune system. the most effective coping behaviors are pointing at cognition and might suggest the potentially promising role of reappraisal interventions [31] or cognitive behavioral treatments [32] in fighting the negative mental health consequences of the pandemic. also, the positive role of following the rules of social distancing and hygiene may suggest the importance of active, prosocial involvement in the containment or slowing down of the virus infection also for coping with the mental burden of the pandemic. it may induce a collective feeling of empowerment and some control over an otherwise overwhelmingly stressful experience [33] . some limitations of this study should be mentioned. first, although it is tempting to interpret our findings causally it should be noted that the cross-sectional design without experimental manipulation does not allow for causal conclusions. it is difficult, however, to see how exposure to covid-19 might be the effect instead of the cause of elevated mental health problems, controlling for pre-existing problems. nevertheless, the associations with perceived impact on livelihood and with coping behaviors might be (partly) caused by elevated mental health problems, and longitudinal or quasi-experimental studies may throw some light on the causal direction [34] . second, because we used an internet survey in a large sample it was not possible to include a long series of scales, questions, and items. we relied for example on a simple but clear-cut question about the respondents' feelings about the impact of the pandemic on their livelihood and we want to emphasize the need for further research on this issue with more elaborated measures. our findings certainly demonstrate that this is a fruitful path to follow in the near future. third, generalizability of the results might be restricted in time, geography and sociocultural context. our data were collected at the beginning of february 2020, a moment in time where the true nature of the pandemic seemed not yet clear to the general public worldwide or even to the experts. furthermore, the study was conducted in various parts of china but surely did not have worldwide coverage and thus its findings might be (partly) specific to this geographic environment. lastly, we recruited a chinese convenience sample for which the nonresponse rate could not be established because of anonymity requirements and in which poor participants from rural areas without internet connections were underrepresented. this underrepresentation of poor participants might have led to an underestimate of the mental health consequences of worries about livelihood issues during and after the lockdown. the covid-19 outbreak in wuhan was followed by a worldwide pandemic and unprecedented lockdown of many large cities and entire countries. here we reported on the early mental health sequelae (in the 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the pittsburgh sleep quality index reliablility and validity of the chinese version of coping style scale. chin the sars (severe acute respiratory syndrome) pandemic in hong kong: effects on the subjective wellbeing of elderly and younger people risk factors for chronic post-traumatic stress disorder (ptsd) in sars survivors association between prenatal exposure to the haiti 2010 earthquake, consequent maternal ptsd and autistic symptoms in offspring substance use in adolescents 10 years after the world trade center attacks in new york city causal inference using different phenotypic traits related to trauma exposure, trauma response, and posttraumatic stress disorder social relationships and the sense of self: the consequences of an improved financial situation for persons suffering from serious mental illness. community ment dementia caregivers' coping strategies and their relationship to health and well-being: the cache county study an emotion and a vital coping resource against despair zhang, z. behavioural, cognitive and emotional responses to sars: differences between college students in beijing and suzhou is returning to work during the covid-19 pandemic stressful? a study on immediate mental health status and psychoneuroimmunity prevention measures of chinese workforce how the covid-19 recession is like world war ii? bloomberg opinion are we facing a crashing wave of neuropsychiatric sequelae of covid-19? neuropsychiatric symptoms and potential immunologic mechanisms the efficacy of stress reappraisal interventions on stress responsivity: a metaanalysis and systematic review of existing evidence the efficacy of cognitive behavioral therapy: a review of metaanalyses acute stressors and cortisol responses: a theoretical integration and synthesis of laboratory research longitudinal study on the mental health of general population during the covid-19 epidemic in china acknowledgments: we thank all the participants for their collaboration. the authors declare no conflict of interest. int. j. environ. res. public health 2020, 17, 3857 key: cord-266738-8xx1xm2d authors: feng, zhan-hui; cheng, yong-ran; chen, juan; ye, lan; zhou, meng-yun; wang, ming-wei title: chinese medical personnel against the 2019-ncov date: 2020-05-31 journal: journal of infection doi: 10.1016/j.jinf.2020.02.011 sha: doc_id: 266738 cord_uid: 8xx1xm2d nan in this journal, zhu et al. recently reported the results of their genomic analysis of multidrug-resistant klebsiella pneumoniae isolates from individual patients before and after colistin treatment highlighting the rapid emergence and multifaceted molecular mechanisms of colistin resistance in k. pneumoniae. 1 this work highlights the therapeutic and public-health challenges of colistinresistance (cr), which is increasingly used as a large resort antibiotic, despite its unattractive toxicity profile and narrow therapeutic window. 2 oral non-absorbed colistin has been proposed as a decontamination strategy in intensive care units and for patients carrying multidrug resistant enterobacterales (mdr-e). 3 , 4 the impact of decolonization strategies in terms of emergence of cr has rarely been monitored because no reliable selective medium existed and cr was not considered a public-health problem. recently, reliable universal culture media have been developed to screen for cr. 5 here, we studied the impact of non-absorbed oral colistin on the emergence of cr in the gut microbiota of patients from the rgnosis-wp3 randomized controlled trial. 6 thirty-nine subjects colonized with mdr-e were randomized to receive oral colistin sulfate 2 miu 4 times a day + neomycin sulfate 500 mg bid for 5 days followed by a fecal microbiota transplant (fmt) from healthy donors, or no intervention. stool samples were collected on visit v0 (screening sample), v2 (after 5 days of oral decontamination and before fmt for the intervention group), v3, v4 and v5, respectively 5-10 days, 30-40 days and 150-210 days later. 6 stool samples from donors and 15 subjects from the intervention group and 15 from the control group were available for this work and plated on drigalski plates (control) and superpolymyxin r plates. 5 colony forming units (cfu) counts of all gram-negative rods were determined. isolates growing on superpolymyxin r plates were identified by maldi-tof; cr was confirmed by the culture-based rapid polymyxin np test and mic determined by the microdilution method. the limit of detection was 10 2 cfu/g of stool. cr-e. coli were sequenced using the illumina hiseq technology. to determine whether cr isolates were present before the intervention, a specific mcr-1 pcr was performed on patients stool prior to intervention (v0) and on the donor's stool. 7 electroporation of plasmids was performed to localize the gene conferring resistance to colistin and neomycin and molecular typing of the electroporants was performed using pcr based replicon typing (pbrt). ✩ université de paris, iame, inserm, umr-1137 no patient or donor included in the trial carried cr isolates on v0. among the 15 patients in the intervention group two (13.3%, [ic90 −1; 3], p = 0.24) carried cr isolates at least at one visit after the intervention ( fig. 1 ) . no cr-enterobacterales was detected in the stools of subjects from the control group. among both subjects with cr-enterobacterales, one carried 10 log cfu/g of hafnia paralvei , a species which is intrinsically resistant to colistin (mic = 8 mg/l), also resistant to neomycin (mic = 32 mg/l) on visit 4 and the other carried 1 log cfu/g and 3 log cfu/g cr-e. coli at visits 4 and 5, respectively, with a colistin mic at 8 mg/l. relative abundance of cr-e. coli increased between v4 and v5 from 0.01% to 1% of the total enterobacterales population. the cr-e. coli recovered at v4 and v5 both belonged to phylogroup c st23 group and carried the serotype o176:h9. a plasmid-borne mcr-1.1 gene encoding for cr as well as a aph(3 )-ia gene conferring resistance to neomycin were identified, both being co-located on the same inchi2 plasmid. in addition, resistance genes conferring resistance to hygromycin b ( aph(4)-ia ), sulfonamides ( sul2 ), tetracyclines ( tet(a) ) and phenicols ( flor and cata1 ), all antibiotics used in veterinary medicine, were evidenced. for both subjects, cr strains could not be retrieved in the initial stool of the subject or in the donor's stool. pcr experiments performed with specific primers to detect mcr-1 gene directly on the pre-therapeutic stool were also negative. to our knowledge, this is the first report of the in-vivo selection of cr-enterobacterales in the gut microbiota of patients after oral decontamination by colistin. the selection of cr strains (a naturally-resistant h. paralvei and a mcr-1 producing e. coli ), both resistant to colistin and neomycin, may be the result either of the enrichment process by sod of preexisting cr strains that had not been initially detected because of very low abundances, or of an exogenous acquisition, either from other individuals or through fmt. 8 indeed the transmission from fmt of mdr strains from positive donors is a potential risk. 8 despite our efforts to decrease the limit of detection of mcr producers by using a pcr technique directly on the pre-therapeutic stool sample and the donors' stools, we failed to detect the parental strain, either because cr strains were in intestinal niches, the limit of detection remained too high, or the strain was acquired exogenously. however, the mcr-1 -positive e. coli is likely of animal origin according to its genetic features and its co-resistance profile. 9 indeed, phylogroup st23 is frequently encountered among avian pathogenic e. coli (apec) and co-resistances to many antibiotics used specifically in veterinary medicine is striking. 10 furthermore, the aph(3 )-ia gene confers resistance to neomycin and paromomycin, the latter commonly used in cattle and pigs. the selection of the mcr-1 producer is an illustration of the "one health" problem of resistance: a strain likely to have been selected by veterinary antibiotics among animals ended up in a patient's gut, later enriched by the use of colistin and neomycin as decontaminant. although the small number of subjects is a clear limitation, this observation is a "proof-of-concept" of the risk of selection of cr-enterobacterales after oral colistin treatment and fmt, at a time when colistin is one of the last resort antibiotics to treat mdr-enterobacterales infections. the selection of commensal cr-e. coli is especially worrying, given the pathogenic potential of e. coli and its ability to widely colonize animals and humans. given the controversial results of oral decontamination by colistin, we believe it should only be used with precautions and with thorough monitoring of cr. we read with interest a recent paper in this journal by luzatti and colleagues, 1 who explored the significance of the presence of herpes simplex virus (hsv) dna in lower respiratory tract (lrt) specimens for the diagnosis of hsv pneumonia in immunocompromised patients. the authors underlined the difficulty in gauging the clinical relevance of such a laboratory finding in the absence of histopathological data, as hsv shedding in the lrt may occur in the absence of disease. the interpretation of real-time pcr results for diagnosis of pneumocystis jirovecii (pj) pneumonia (pjp) faces an analogous challenge, since the presence of pj dna in lrt may reflect colonization (carriage) rather than infection. 2 there is limited information on the clinical value of pj real-time pcr in diagnosing pjp in patients with hematological diseases; 3-6 this is exceedingly challenging as the sensitivity of direct examination procedures is suboptimal due to low fungal burdens. 3 here, we report on our experience on this matter. a total of 219 episodes of pneumonia occurring in 192 consecutive patients with hematological disorders in which pjp was considered in the differential etiological diagnosis were included. of these, 127 episodes developed in patients undergoing either allogeneic hematopoietic stem cell transplantation-allo-hsct-( n = 86) or autologous-hsct ( n = 19), and 92 in non-transplant patients (acute leukemia, n = 61; lymphoma, n = 16; chronic leukemia, n = 8; others, n = 2). the patients were attended at the hospital clínico universitario-hcu-( n = 100) or at the hospital universitario politécnico "la fe" -hlf-( n = 92) between june 2014 and august 2019. no patients in the cohort tested positive for hiv. this study was approved by the respective hospital ethics committee and informed consent was obtained from all patients. a single specimen per episode was available for diagnosis (bal fluids, n = 179; sputa, n = 22; ta, n = 17 and bronchial biopsy, n = 1). the realcycler pjir kit r (progenie molecular, spain) was used at hcu, and the pneumocystis jirovecii real time pcr detection (certest biotech; zaragoza, spain) was employed at hlf (see footnote in table 1 ). both assays target the large sub-unit of ribosomal (mtlsu) rna gene. preliminary experiments using 5 bal specimens indicated that both assays yield comparable pcr cycle thresholds (c t s) (median, 28.2, range, 26.4-32.3 vs. median 27.5; range, 26.3-33.1, respectively; p = 0.89). all specimens tested negative by direct examination for pj, whereas 27 were positive by real-time pcr (bal, n = 18; sputa, n = 7, and ta, n = 2); following stringent clinical, microbiological and imaging criteria ( table 1 ) , pjp was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. no histopathological confirmation of pjp was available for any patient. pcr c t values inversely correlate with fungal burden in the sample. 6 which is higher in patients with pjp than in colonized individuals. 2 here, overall, pj pcr c t s in specimens from patients with pjp tended to be lower than in pj carriers ( p = 0.39); when only bal fluid specimens were considered, the difference reached statistical significance (median, 29.0; range, 26.4-34.7 vs. median 34.6; range, 30.0-41.0; p = 0.04). this finding is likely related to use of more standardized procedures for bal fluid sampling. receiver operating characteristic (roc) curve analysis showed that a threshold c t value of 30.0 in bal specimens displayed a sensitivity of 85.7% (95% ci, 45.0-100%) and a specificity of 80% (95% ci, 40.8-100%) for pjp diagnosis. a number of studies have established different c t s cut-offs for that purpose, [6] [7] [8] [9] . in our view, however, the variability in the performance of different pcr assays and sampling conditions, heterogeneity of patient populations, and in particular the lack of a pj international standard material for pcr result normalization precludes defining a consensus universal threshold nowadays. the absence of anti-pj prophylaxis, treatment with corticosteroids and serum ldh levels ≥400 u/l have been shown to be associated with pjp. 3 here, patients not undergoing anti-pj prophylaxis were more likely to display a clinically significant pj pcr result ( table 1 ). in turn, roc curve analysis indicated that a cut-off ldh value ≥400 u/l had a sensitivity of 81.8% (ci 95%, 59.0-100%) and specificity of 67% (95% ci, 34.0-99.3%) for pjp diagnosis. in univariate regression logistic models, serum ldh values ≥400 u/l were associated with a clinically significant positive pcr pj result (or, 9.0; 95% ci, 1.2-63.8; p = 0.02). in contrast, corticosteroid use within the month before sampling was not different between the probability of pneumocystis jirovecii (pj) pneumonia (pjp) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented pj presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-pjp treatment; (v) absence of alternative diagnosis. the efficacy of therapy was assessed on a daily basis. pjp was ruled out if real-time pcr for pj tested negative, or if clinical recovery occurred in the absence of pj-targeted antimicrobial therapy. pj colonization (carriage) was the most likely possibility when patients did not meet the above criteria and an alternate diagnosis was made. b frequencies were compared using the χ 2 test (fisher exact test) for categorical variables. two-sided exact p values were reported and p values ≤ 0.05 were considered statistically significant. the data were analyzed with the spss (version 20.0) statistical package. c respiratory tract specimens were obtained following conventional procedures. specimens were examined for presence of ascus or trophic forms of pj by microscopy following blue toluidine, calcofluor white or grocott's methenamine silver staining. cytospin preparations were prepared from bal specimens for direct examination. sputa and ta samples were mixed v/v with sputasol (oxoid, uk) and vortexed for 5 min. all samples were centrifuged at 30 0 0 g for 10 min, and the pellets were resuspended 1/10 in 0.9% nacl for further processing. for real-time pcr, dna was extracted from 200 μl of specimens using the qiaamp dna blood mini kit (qiagen, hilden, germany) on either qia symphony or ez-1 platforms (qiagen), following the manufacturer's instructions. at hcu, a commercially-available real-time pcr assay previously evaluated by others, the realcycler pjir kit r (progenie molecular, spain), which targets the mitochondrial large sub-unit of ribosomal (mtlsu) rna gene, was used according to the manufacturer's instructions ( http://www.progenie-molecular.com/pjir-u-in.pdf ). at hlf, the commercially-available pneumocystis jirovecii real time pcr detection. (certest biotech; zaragoza, spain), which also targets the large sub-unit of ribosomal (mtlsu) rna gene, was employed following the manufacturer instructions ( https://www.certest. es/wpontent/uploads/2019/02/viasure _ real _ time _ pcr _ pneumocystis _ jirovecii _ sp1.pdf ). at both centers pcr were performed in the applied biosystems 7500 fast real-time pcr platform (applied biosystems, ca, usa). pcr results were reported as positive or negative. for positive samples, threshold cycle (c t ) values were also recorded. no standard curve was generated with a positive control for quantitative estimations. d antimicrobial prophylaxis for pjp was performed with trimethoprim-sulfamethoxazole (tmp/smx), one double-strength tablet (160 mg tmp/800 mg smx) given 2 (in allogeneic hsct patients) or 3 times a week with oral folic acid (15, 16) . patients with suspicion of pjp according to the attending physician were treated with tmp/smx 15-20 mg/kg (tmp) 75-100 mg/kg (smx) per day for 2-3 weeks. e in all these cases, death was attributable to pjp. patients with clinically significant pj detection and pj carriers ( table 1 ) . detection or recovery of other microbial agents (one or more) was documented in 17 of the 27 specimens testing positive by pj pcr ( table 2 ). in line with a previous report, 9 this microbiological finding was significantly less frequent ( p = 0.001) in specimens from patients with pjp than in colonized patients; in fact, microbial co-detection was inversely associated with pjp in univariate logistic regression models (or, 0.024; 95% ci, 0.002-0.26; p = 0.002). strengths of the current study are the following: (i) clinical categorization of pjp was based upon stringent criteria defined by a multidisciplinary team; (ii) only hematological patients were included; (iii) a comprehensive routine investigation of microbial causes of pneumonia other than pj was conducted; (iv) the experience of two centers was collected. in addition to its retrospective nature, our study also has some limitations: (i) we cannot completely rule out that some patients categorized as being pj carriers did in fact have pjp, as most of these patients received full courses of tmp/smx in combination with antimicrobials targeting other microbial agents. the lack of standardized criteria for pjp diagnosis makes clinical misclassification of patients a potential drawback in studies such as ours, particularly when no positive microscopy or histopathology findings are available; (ii) although we evaluated bal, bronchoalveolar lavage; pjp, pneumocysis jirovecii pneumonia; ta, tracheal aspirate. a as per our routine protocol, all specimens were examined by gram and acid-fast bacilli stain. samples were also examined for presence of respiratory viruses (rvs) using either the luminex xtag rvp fast assay (luminex molecular diagnostics, austin, tx,usa) at hcu, or the clart® pneumovir assay (genomica, coslada, spain) at both centers, as previously reported. 10 semiquantitative (sputa) and quantitative (bal and ta) cultures for bacteria were performed on conventional media: bacterial loads > 10 4 cfu/ml or > 10 5 cfu/ml were deemed to be clinically relevant on bal fluids and ta samples, respectively. specimens were cultured on bcye-alpha agar, bd (becton dickinson) mgit® ( mycobacteria growth indicator tube)/lowenstein-jensen agar slants and sabouraud agar for recovery of legionella pneumophila, mycobacterium spp., and other fungal organisms, respectively. the platelia tm aspergillus ag kit (bio-rad, hercules, ca, usa) was used for quantitation of aspergillus spp. galactomannan in bal fluid and serum specimens. all bal fluid specimens underwent cytomegalovirus (cmv) pcr testing using the realtime cmv pcr assay (abbott molecular) at hcu or the cmv r-gene® assay (biomerieux) at hlf, as previously reported. 10 over 200 patients, only 12 presumptively had pjp; (iii) two different commercially-available pcr assays were used across centers. nevertheless, we found them to yield rather comparable c t s. in summary, we found that a positive pj pcr result in respiratory specimens from transplant and non-transplant hematological patients with pneumonia frequently reflects colonization rather than infection; pcr c t values in bal fluids, serum ldh levels and lack of co-detection of other microorganisms potentially involved may be helpful in clinical categorization in the absence of positive by pj microcopy results. we have no conflict of interest to declare. dear editor , poller et al., in this journal, provided a useful consensus for use of personal protective equipment for managing high consequence infectious disease 1 . although this was driven largely by recent ebola virus disease emergencies, we should remind your readers of the continuing problem of lassa fever (lf) in west africa. lf is a febrile infectious disease caused by lassa virus. the clinical presentation of the disease is nonspecific and includes fever, fatigue, hemorrhage, gastrointestinal symptoms, respiratory symptoms, and neurological symptoms 2 . the observed case fatality rate among patients hospitalized with severe lf is 15-20% 3 , 4 . the disease is mainly spread to humans through contamination with the urine or faeces of infected rats 2 . human-to-human transmission can occur through contact with the body fluids of infected per-sons. therefore, health care workers are at high risk for infection when the standard precautions for infection prevention and control including appropriate personal protective equipment are inadequate 5 . it is estimated that there are approximately 30 0,0 0 0 lf cases annually, resulting in approximately 50 0 0 deaths in west african countries 4 . in 2018, nigeria had a large lf outbreak, and we previously reported epidemiological characteristics of the outbreak, analyzing data collected between january and may 2018. 6 however, information on laboratory-negative suspected cases was not enough to conduct a case-control study to fully determine the risk factors and clinical characteristics of the disease. nigeria had a lf outbreak in 2019 as well. 7 here we report the epidemiological and clinical characteristics of the outbreak including case-control analysis against laboratory-negative suspected cases using data collected between 1st january 2018 and 6th october 2019. from january to december 2018, there were 3498 suspected cases, including 633 laboratory-confirmed lf cases. in 2019, there were 4019 suspected cases reported by 6th october, including 721 laboratory-confirmed lf cases. details on the case definition, laboratory test, surveillance, and data collection have been described previously. 6 of the confirmed lf cases, there were 171 fatalities (case fatality rate, 27.0%) in 2018 and 154 fatalities (case fatality rate, 21.4%) in 2019. the number of laboratory-confirmed lf cases and positivity rate peaked in the dry season (january-march) in both 2018 and 2019 ( fig. 1 (a) ). the largest number of laboratory-confirmed lf cases were reported from the neighboring edo and ondo states in both 2018 and 2019 ( fig. 1 (b) ). there were laboratory-confirmed lf cases in states such as kebbi and zamfara that had no reported cases previously, in 2019. during the study period, the detailed demographic and clinical information was collected for 1305 laboratory-confirmed lf cases (of 1354 cases, 96.4%) and 3350 laboratory-negative suspected cases (of 6163 cases, 54.4%). chi-square tests were conducted to compare the distribution of age, sex, and each symptom between the laboratory-confirmed lf cases and laboratory-negative suspected cases ( table 1 ). the proportion of children was significantly lower in laboratory-confirmed lf cases compared with that in laboratory-negative suspected cases. the proportion of males was significantly higher in laboratory-confirmed lf cases than that in laboratory-negative suspected cases. fever was the most prevalent symptom in both laboratoryconfirmed lf cases and laboratory-negative suspected cases, followed by headache ( table 1 ) . gastrointestinal symptoms, such as abdominal pain, vomiting, and diarrhea, were observed in more than 30% of laboratory-confirmed lf cases, whereas hemorrhaging was observed in 21.1% of laboratory-confirmed lf cases. while the prevalence of face/neck edema was low even in laboratoryconfirmed lf cases (6.4%), nonetheless, the odds ratio of having face/neck edema was 6.0 times high for laboratory-confirmed lf cases. we here reported the lf outbreak in 2018-2019 largest recorded in history. while previous studies have focused on laboratory-confirmed lf cases and mainly compared fatal cases and survived cases, 6 , 8 , 9 our observation revealed the difference between laboratory-confirmed lf cases and laboratory-negative suspected cases. the age and sex distribution differed significantly between laboratory-confirmed lf cases and laboratory-negative suspected cases. fever, headache, and gastrointestinal symptoms were the most common symptoms in laboratory-confirmed lf cases, which are similar to those reported previously. 6 , 8 however, these symptoms were also prevalent in laboratory-negative suspected cases. clinical guidelines for lf state that edema in the face and neck is a specific sign of the disease. 10 the present study found that the symptom had a significantly high odds ratio for confirmed lf although the prevalence of this symptom was low. unfortunately, we did not determine the differential diagnosis for the laboratory-negative suspected cases. laboratory tests for the differential diagnoses are now underway for the lf-negative samples collected during the outbreak. the results would provide us further insight for better clinical management of patients with febrile illnesses in lf-endemic areas. in addition to the standard precautions for infection prevention and control including appropriate personal protective equipment pointed out by poller et al., 1 it is important to know epidemiological and clinical characteristics of high consequence infectious diseases such as lf. that would help healthcare workers and public health officers increase an index of suspicion of the diseases, further leading to better clinical management and surveillance. the authors have declared that no conflicts of interest exist. this work was partially supported by the leading initiative for excellent young researchers from the ministry of education , culture, sport, science & technology of japan and the japan society for the promotion of science (grant number, 16809810 ). the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 1 these authors contributed equally to this article. accepted 31 december 2019 available online 15 january 2020 https://doi.org/10.1016/j.jinf.2019.12.020 © 2020 the british infection association. published by elsevier ltd. all rights reserved. recently, several studies in this journal have demonstrated the threat of animal-derived viruses to humans. [1] [2] [3] since 2018, an increase in human pseudorabies virus (prv) infection cases has been reported in china, indicating a new animal-derived virus threat to human health. porcine pseudorabies (pr), also known as aujeszky's disease, is one of the most economically important viral diseases in pigs globally. its causative agent is prv, which is classified into the genus varicellovirus of subfamily alphaherpesvirinae , family herpesviridae . prv is almost always fatal in newborn piglets, is frequently accompanied by neurological symptoms, and may cause abortions and/or stillbirths in pregnant sows. prv primarily infects members of the suidae family and can also infect other domestic and wild mammals, including horses, cattle, sheep, goats, dogs, cats, etc. currently, vaccination is the most effective strategy for pr prevention and control in pigs worldwide. in china, prv infections in pigs were first recorded in 1947. in the 1970s, an inactivated vaccine consisting of the bartha-k61 vaccine strain was imported into china. since then, this vaccine has been widely used in pig vaccination for pr prevention and control. before 2011, no large pr outbreaks were reported in pigs in china. however, after late 2011, novel prv wild-type variants emerged in nearly all regions of china and affected a number of swine herds vaccinated regularly with the bartha-k61 vaccine, resulting in significant economic losses. 4 subsequent animal experiments indicated that the bartha-k61 vaccine could not provide complete protection for pigs against a challenge with novel prv wild-type variants in china. for control and eradication of pr, the disease was listed in the "mid-and long-term animal disease prevention and control program in china (2012-2020)" by the chinese government, with the aim of eliminating pr in china by 2020 ( http://www.gov.cn/zwgk/2012-05/25/content _ 2145581.htm ). however, vaccination for prv is still voluntary and not required in china. a nationwide epidemiological investigation in 2014 demonstrated a high prevalence of 23.26% of prv among swine herds in china. 5 humans were previously regarded as refractory for prv infection, although serological prv antibody positivity was found in three cases. in 2018, the first human prv infection case with direct molecular evidence was reported in china (case 1, table 1 ). 6 in this case, the eyes of a 46-year-old woman were directly exposed to sewage on a hog farm. in the following two weeks, symptoms of fever, headache, coma, and endophthalmitis were observed in the patient. next-generation sequencing (ngs) indicated that prv dna was detected in her vitreous humor samples but not in her cerebrospinal fluid (csf). after surgery, the patient was discharged, but her vision remained impaired. in a subsequent study, zhao et al. table 1 clinical characteristics and other information on the twelve human prv infection cases in china. analyzed csf samples from four patients with encephalitis of unknown etiology using ngs (cases 2-5, table 1 ) and found molecular evidence of prv infection. 7 in addition, retinitis and blindness was observed in two cases (cases 2, 5, table 1 ), and the patient in case 3 died. the occupation of the four patients was all associated with pork production/sale/cooking. in 2019, six other human prv infection cases involving encephalitis were reported in china, and all patients were pork/pig handlers or veterinarians. [8] [9] [10] it was noted that all patients still suffered from various sequelae after discharge, except for in one case where the patient died. increasing reports on human prv infection cases in china have recently indicated that prv poses a significant threat to public health in china, especially in people in close contact with sick pigs and/or related pork products/contaminants. to reduce the risk of prv infection in susceptible workers, it is necessary to promulgate relevant policies by the chinese government to promote pr vaccine development to protect pigs from infection with novel prv wild-type variants currently circulating in china. in addition, relevant policies should be updated by the chinese government to monitor vaccination status and virus variation in pigs nationwide. moreover, it seems that prv can infect humans via injury to the skin or eyes. until now, no effective drugs to prevent the progression of the disease caused by prv infection have been reported. therefore, it is necessary to improve biosafety and self-protection awareness in susceptible populations that have contact with sick pigs and work in jobs related to handling pork products/contaminants. promoting drug development for curing prv-related disease in infected patients may also help reduce the currently increasing threat of prv to human health in china. all authors declare that they have no competing interests. dear editor, the emergence and spread of gram-negative bacteria, for example, klebsiella pneumoniae , co-producing carbapenemases and mobilized colistin resistance ( mcr ) genes limit our choice for treating multidrug-resistant infections, posing significant threats to public health. herein, we reported the discovery of mcr-9 gene in 28 k. pneumoniae strains isolated from patients in eight european countries, including belgium ( n = 2), denmark ( n = 1), montenegro ( n = 13), poland ( n = 1), romania ( n = 1), serbia ( n = 1), slovenia ( n = 1), and spain ( n = 7). notably, the co-existence of mcr-9 and the carbapenemase-encoding genes, ndm-1, vim-1, and oxa-48 were confirmed in k. pneumoniae isolates of human origin. phylogenetic analysis suggested that mcr-9 -carrying k. pneumoniae isolates, including 23 carbapenem-resistant and five susceptible k. pneumoniae strains, show a highly geographically clustered pattern. genetic environment analysis revealed the presence of insertion element is903, is1 or a cupin fold metalloprotein, wbuc, in the mcr-9 flanking. taken together, these findings indicated that mcr-9 has existed for a long time and already spread among crkp isolates of human origin in europe since 2013, further increasing the significant threat of public health through either the nosocomial spread or environmental routes. the mobilized colistin resistance ( mcr ) gene mcr-9 was detected in 28 human gut microbiomes, which has been disseminating across three continents, including asia, europe and america, recently published in the journal of infection. 1 the rapid increase in carbapenem resistance among gram-negative bacteria worldwide has greatly compromised the efficacy of carbapenem antibiotics, which has gotten renewed attention to the importance of polymyxin antibiotics for multidrug-resistant (mdr) infections. recently, sophia david and colleagues 2 reported the epidemic of carbapenem-resistant klebsiella pneumoniae (crkp) in europe, which raised concern that mobile carbapenemase resistance determinants were widely spread in european hospital settings, and inter-hospital spread is far more frequent within, rather than between, countries. however, limited information regarding the co-occurrence of carbapenemases and mcr genes in the klebsiella pneumoniae ( k. pneumoniae ) isolates have been provided. plasmid-mediated resistance genes mcr as well as tet (x3/x4) have been widespread in bacterial species of animal, human, and environment origin as well as human and animal gut microbiomes worldwide, where is a huge arg reservoir with a high horizontal gene transfer possibility. 1 , 3 -5 several studies 6 -8 illustrated that the newly described mcr-9 has spread beyond the united states into europe and asia, and into other enterobacteriaceae species. of clinical concern is the inevitable spread of a plasmid harboring the mcr-9 gene into a crkp isolate, which has been listed by the world health organization as a critical priority antibiotic-resistant bacterial pathogen for which new antibiotics are urgently needed. 9 in response to this potential clinical problem, we download > 1717 k. pneumoniae genomes isolated from 244 hospitals in 32 european countries 2 and the 14,764 complete bacterial genome sequence (accessed 26 july 2019), and explored the distribution of plasmid-mediated resistance genes mcr and tet (x3/x4). we are surprised to find that the complete mcr-9 gene (nucleotide = 100%) was present in 28 k. pneumoniae isolates of 1717 k. pneumoniae strains from belgium ( n = 2), denmark ( n = 1), montenegro ( n = 13), poland ( n = 1), romania ( n = 2), serbia ( n = 1), slovenia ( n = 1), and spain ( n = 7) (table s1 ). additionally, 23 of the 28 k. pneumoniae isolates of human origin were crkp strains and only five were carbapenem-susceptive isolates (table s1 ). as reported, these mcr-9 -harbouring strains were isolated from patients in europe between 2013 and 2014. these results suggest that mcr-9 gene might have been presented in europe for a long time and already spread to the crkp isolates, which is a major cause of both hospital-and community-acquired infections. 2 to further analyze these mcr-9 -positive k. pneumoniae isolates, the resistome of the draft genome was analyzed using the comprehensive antibiotic resistance database. 10 interestingly, the mcr-9 gene was co-existed with various carbapenemase-encoding genes: in eleven isolates with ndm-1, eight with vim-1, and two with oxa-48 ( fig. 1 (a) ). it should be noted that the mcr-9 -and ndm-1-carrying isolates were distributed in denmark ( n = 1), montenegro ( n = 8), romania ( n = 1), and serbia ( n = 1), as well as several other beta-lactam resistance determinants (for example, tem-1, cmy-16, oxa-10 and shv-11) ( fig. 1 (a) and table s1 ). moreover, the mcr-9 -and vim-1-harbouring isolates were dominant in spain ( n = 7) and slovenia ( n = 1), as well as two beta-lactamase-encoding genes (non-carbapenemases) (ctx-m-9 and shv-11) ( fig. 1 (a) and table s1 ). it is worrying that a crkp isolate from spain in 2014 was carrying mcr-9 , vim-1, and oxa-48 genes simultaneously. the presence of mcr-9 in crkp isolates from patients is of critical importance as mcr-9 could be present in hospital-borne outbreaks cre strains in the future. from whole-genome shotgun (wgs) data of the 28 mcr-9 -positive k. pneumoniae isolates, sequences types (sts) were extracted and assigned to nine different types, i.e. , 274, 461, 15, 16, 416, 1890, 37, 1942, and 147 ( fig. 1 (a) ). phylogenetic analysis suggested that mcr-9 -carrying k. pneumoniae isolates show a highly geographical clustering pattern 2 ( fig. 1 (a) ). isolates from patients in the same hospital were clustered into one clade, for example, in spain and montenegro. overall, the k. pneumoniae isolates from different countries were genetically diverse, suggesting that the mcr-9 -positive k. pneumoniae isolates were also genetically diverse and that mcr-9 could disseminate among different k. pneumoniae isolates, mainly by nosocomial transmission. 2 nowadays, all known mcr genes have been detected in various gram-negative bacterial species, whereas a small number of studies have shown the presence of mcr-1, mcr-3, mcr-7 , and mcr-8 in k. pneumoniae isolates from animal and human origin at relatively low detection rate. 11 -14 the presence of mcr-9 in the crkp isolates indicated that this novel mcr gene may already be widely spread among k. pneumoniae isolates of human origin in europe. we subsequently searched mcr-9 gene in 14,764 complete bacterial genome sequence and ncbi-nr database (14 october 2019) in the ncbi, to fully understand the prevalence of mcr-9 gene in klebsiella species isolates. interestingly, the mcr-9 gene (identity > 99% and 100% query coverage) was present in various bacterial genomes, including three klebsiella species isolates consisting of k. pneumoniae ( n = 4), k. quasipneumoniae ( n = 1), and k. oxytoca ( n = 3) (table s3) . therefore, further studies focusing on the epidemiology and transmission mechanism of mcr genes, in particular mcr-9 in klebsiella species of human origin are warranted to better understand the public health threat of emergence of antibiotic resistance among clinical k. pneumoniae . contigs carrying mcr-9 in 28 k. pneumoniae isolates could be classified into two groups (for example, gca_900513855.1 and gca_900501685.1) (table s2) . genetic environments analysis indicated that the presence of insertion element is903 and wbuc (a cupin fold metalloprotein), in the mcr-9 (gca_900513855.1, ∼28 kb) upstream and downstream flanking, respectively, similar to (identity > 99%) the plasmid sequences of pme-1a, pctxm9_020038, and pmrvim0813, and contigs from of e. coli isolate 68a and nz_naan010 0 0 063 from salmonella 15 ( fig. 1 (b) ). additionally, mcr-9 in another contig ∼8.7 kb was in the upstream of two insertion element is1 and is30 0 0, as well as a beta-lactamase-encoding resistance gene ctx-m-9, which similar to the plasmid sequence of pmrvim0813. we did not detect the downstream regulatory genes (qsec and qseb) found in the isolates that harbor mcr-9 . 8 , 16 moreover, we were unable to determine whether a complete is903 element is upstream due to a short mcr-9 -bearing contig that is available for comparison ( fig. 1 (b) ). therefore, a long-read sequencing coupled with a hybrid assembly method is needed to fully evaluate and monitor the transfer and development of args, especially mcr-9 among crkp isolates. although two unique plasmid-mediated tigecycline resistance genes firstly discovered in bacteria of animal origin in china and subsequently identified in many bacterial isolates of human, animal and environment origin, including klebsiella species, as well as human and animal gut microbiomes, 1 , 4 , 5 none of them was detected in the 1717 k. pneumoniae strains in europe. in summary, we reported the discovery of mcr-9 gene in 28 clinical k. pneumoniae strains of human origin in eight european countries. importantly, the mcr-9 gene was co-existed with different carbapenemase-encoding genes in the same strains. the spread of mcr-9 , ndm-1, vim-1, and oxa-48 and other beta-lactam resistance determinants (non-carbapenemase) carrying by crkp appears likely to be by plasmid dissemination, as the genes identified in isolates belonging to a diverse set of sts distributed in different hospitals in europe. it is noteworthy that all these mcr-9 -positive crkp strains were isolated between 2013 and 2014, highlighting an earlier presence of mcr-9 among crkp around the world than previously known. these findings raise the likelihood of ongoing undetected mcr-9 gene spread among cre strains. therefore, further study is urgently needed to understand the prevalence and dissemination of mcr-9 , especially in cre and crkp strains, and effective measures should be taken to control its spread. g.f.g. designed the study. y.n.w. and f.l. collected and downloaded the datasets. y.n.w., f.l., y.f.h., b.l.z., g.p.z., and g.f.g. analyzed and interpreted the data. y.n.w. and g.f.g. wrote the draft of the manuscript. all authors discussed, reviewed and approved the final report. supplementary information is available for this paper. correspondence and requests for materials should be addressed to g.f.g. the authors declare no competing interests. the interesting systematic review by amin-chowdhury and colleagues provides information about outbreaks of severe pneumococcal disease (spd) in closed settings that occurred in the conjugate vaccines era 1 . it shows that vaccine-type spd outbreaks are still occurring and it highlights the lack of consensus on how to manage such outbreaks. in the following, we will describe how we managed a recent outbreak of spd in norway. in march 2019, møre and romsdal hospital trust notified the norwegian institute of public health (niph) about a cluster of spd amongst men working in shipyards in møre and romsdal county. serotype data from niph were available for nine of the cases -all were serotype 4. the majority of cases had been working at one specific shipyard. municipal medical officers (mmo), the norwegian labour inspection authority (nlia), and niph formed a multidisciplinary outbreak team to investigate and control the outbreak. we formed specific case definitions: each case had to have resided in møre and romsdal county in the period from 1. january 2019 onwards and: confirmed : had invasive pneumococcal disease (ipd) with serotype 4 isolated from a normally sterile site. probable : worked at the specific shipyard and had a clinical presentation compatible with lower respiratory tract infection or ipd, but without microbiological confirmation or serotype 4 isolated from a non-sterile medium (e.g. nasopharyngeal swab or sputum culture). we identified 20 cases, ten confirmed and ten probable in the period between 28. january and 3. april ( fig. 1 ). all available isolates were serotype 4 (10 confirmed, 7 probable) and were susceptible to penicillin. fifteen isolates were sequence type (st) 801, while two were a single locus variant of 801, st 15,063. all cases were men between 20 and 60 years, with a mean age of 47 years. fifteen were hospitalized. four were norwegian citizens, the remaining came from other european countries. seven cases smoked. one case had an underlying medical risk condition. immunization history against pneumococci were unknown for all. the cases had several professions; mostly related to interior outfitting and metal welding. approximately 1800 individuals worked at the shipyard in the time period. many of them lived in temporary accommodation. at an on-site inspection of the shipyard, nlia observed a polluted atmospheric work environment and little use of personal protective equipment. several measures were put in place to control the outbreak, including information and advice to raise symptom awareness and to reinforce hand and respiratory hygiene, vaccination and occupational corrections. local medical clinics and hospital were alerted about the outbreak and advised to have a low threshold to admit and treat suspected cases. mmo held information meetings with shift leaders, and written information about spd in several languages was distributed to workers to increase spd awareness. intensified hygiene measures were implemented at the ship yard and housing quarters. nlia ordered immediate occupational corrections related to controlling the atmospheric work environment. niph recommended vaccination with the 13-valent conjugate vaccine (pcv13) to interrupt transmission and prevent disease. both the pcv13 and the 23-valent polysaccharide vaccine provide protection against serotype 4, but pcv13 was preferred as this may also affect colonization. as several work tasks were conducted in parallel process in confined spaces with suboptimal ventilation, we were unable to identify a single target group for vaccination. hence, the shipyard offered vaccination to all workers. occupational health service promptly vaccinated all workers during a four-day period. contrary to the majority of studies included in the systematic review, niph did not recommend chemoprophylaxis. as the workers were otherwise healthy (i.e. no high risk group like old age, immunocompromising conditions etc.), and since it was impossible to target a specific group of workers, niph deemed it undesirable to distribute antibiotics to 1800 asymptomatic workers, with the possibility of inducing antimicrobial resistance and possible side effects. due to high turnover of personnel it was not possible to calculate an attack rate. we did not find any new cases after control measures were implemented. no deaths have been reported in relation to the outbreak. this outbreak closely resembles one of the outbreaks described in the systematic review; between april and june 2015, an outbreak with serotype 4, st 801 occurred at a shipyard in belfast 2 . we are also aware of an outbreak this fall, 2019, at a shipyard in finland with serotype 4 (st 801), 8 and 12f 3 . although welders are a known risk group for spd, 4 in all these three outbreaks, people who worked closely alongside welders were also infected. in addition to exposure to welding fumes, the crammed and poorly ventilated working conditions, and possibly housing conditions, may have increased the risk of developing spd and facilitated the transmission of pneumococci in this closed setting. overall, this norwegian outbreak extends the knowledge about how to manage and control outbreaks of spd in closed settings. none. in this journal brunet and colleagues 1 discussed reactivation of latent infections in the context of chronic disease, solid organ transplantation or long-term immunosuppressive treatment. we recently observed the reactivation of leishmania infection in a 46-year-old patient receiving methotrexate for psoriasis, who was diagnosed with visceral leishmaniasis (vl) showing a mucocutaneous involvement. we analyzed the epidemiologic and clinical characteristics of all cases of leishmaniasis in patients with psoriasis found through a review of the literature. our patient was admitted into the infectious disease unit of paolo giaccone hospital, in palermo, with a painless and ulcerated lesion onto the oral mucosa ( fig. 1a ) , two nodular ulcerated lesions on the right knee and another one on instep of the right foot appeared one month before ( fig. 1b ) . the patient did not travel outside italy during the last year. he had been suffering from lowgrade fever in the last month. considering the above findings leishmaniasis was suspected and a needle aspiration of oral and cutaneous lesions was arranged in order to perform microscopy and leishmania-pcr, which were positive for leishmania. laboratory tests exhibited: wbc 4970/mmc, hb 13.9 g/dl, c reactive protein, 26.9 mg/l; positive serology for leishmania (igg 1/3200) and positive leishmania-pcr test on peripheral blood. abdominal us examination revealed splenomegaly (14 cm); methotrexate was suspended and liposomal amphotericin b, 4 mg/kg per day for 10 days, followed by two further administrations two weeks later was started. cutaneous and mucosal lesions improved at the end of the first 10 days of therapy and completely vanished after two further administrations, 40 days from the beginning of treatment. leishmania-pcr on peripheral blood after 10 days of therapy was negative. table 1 shows the literature data about characteristics, therapy and outcome of patients with psoriasis and leishmaniasis. leishmaniasis is a vector-born chronic infectious disease caused by protozoa of the genus leishmania and transmitted to humans by the bite of phlebotomine sandflies. in europe, the mediterranean countries are the most affected areas. leishmania parasite establishes chronic intracellular parasitism, survives for an infected person's lifetime and, in the event of major immune deficiency, may be reactivated from sites of latency. leishmaniasis can present with a spectrum of clinical manifestations and three patterns of infection are described: cutaneous (cl), mucosal or mucocutaneous (ml or mcl) and visceral leishmaniasis (vl). the infecting species of leishmania is very important in determining the clinical manifestations and the host immune response is crucial in determining the clinical outcome of infection 2 . today, non-hiv related immunosuppressive conditions are becoming increasingly prevalent, mainly because of better medical care of patients with chronic illnesses and the therapeutic use of immunosuppressive drugs. in the field of rheumatology, leishmaniasis has been reported in association with the use of various immunosuppressive drugs. 3 the introduction of tumor necrosis factor-alpha (tnf-α) antagonist drugs has received much attention recently and several cases of vl have been reported in rheumatic patients who do anti-tnf α drugs. 4 psoriasis is a chronic inflammatory autoimmune disease affecting 2-3% of the world's population and characterized by an aberrant hyper-proliferation of keratinocytes. the pathogenesis of psoriasis is complex. genetic susceptibility, environmental triggering factors and an over-reaction of local innate immune response initiate inflammation. subsequent involvement of adaptive immune response with production of th 1 cytokines, chemokines and growth factors lead to epidermal hyperplasia. 5 recently, a functional role of interleukin-17-producing t helper cells (th17) in psoriasis has been suggested by their reduction during successful anti-tnf treatment. 6 it is also known that th17 lymphocytes play an essential role in protecting against intracellular protozoa and in the successful clearance of leishmania by strengthening the th1 response. 7 in view of this, it could be argued that psoriasis may represent a protective factor for leishmania infection. indeed, in our review we did not found any case of leishmaniasis in psoriatic subjects who were not under immunosuppressive therapies. biological agents, which are powerful immunosuppressive drugs, have been more and more used in rheumatic patients and leishmania infections have been reported among anti-tnf-agents users. 8 recently maritati et al. found higher prevalence of subclinical leishmaniasis in patients with inflammatory rheumatic diseases receiving biological drugs than those treated with other immunosuppressive drugs. 9 however, leishmaniasis has also been reported in psoriatic patients not receiving biological drugs, as occurred to our patient ( table 1 ) . diagnosis of cl in psoriatic patients is challenging, as it mimics many other infections or a flare-up of psoriasis itself that can lead to ineffective and harmful changes of therapy. immunosuppressive therapies cause atypical manifestations of leishmaniasis with large lesions spread over large cutaneous areas and associated to a possible mucosal involvement. ml by l. infantum is very rare and only sporadically described in patients receiving powerful immunosuppressive therapies or in hiv-coinfected patients. mcl is mostly observed in latin america where l. braziliensis accounts for most cases, but l. panamensis, l. guyanensis, and l. amazonensis have also been implicated. only rarely cutaneous lesions extend to areas of skin distant from the mucosa involved, as in our case in which two lesions on the foot and knee were associated with the oral lesion. in the context of impaired immunity, it is also advisable to rule out vl by pcr-leismania on peripheral blood so as to establish the most appropriate therapy: intralesional or intravenous. finally, there is no agreement on appropriate screening for leishmaniasis before immunosuppressive treatments and on the strategy to be followed after the diagnosis of leishmaniasis in rheumatic patients taking immunosuppressive drugs. 10 molecular methods are highly sensitive and specific tools for the diagnosis of visceral leishmaniasis and a screening with leishmania-pcr in immunosuppressed patients living in endemic areas could be useful to identify patients at highest risk of reactivation. 9 specific leishmaniasis treatment followed by suspension of the immunosuppressive therapy was adopted by most of the authors. overall even if the treatment response is not as good as seen in the immunocompetent population, our review reports a good outcome in all cases and patients remained relapse-free without maintenance therapy and despite the ongoing use of immunosuppressive medication. in conclusion physicians must be alert to the possibility of development of leishmaniasis in immunosuppressed rheumatic patients. adequate screening for vl should be incorporated into the list of baseline studies to carry out before initiating biologic therapies, at least in endemic areas. the authors declare that there is no conflict of interest. as demonstrated in several studies in journal of infection , herpesviruses pose an increasing threat to human health. [1] [2] [3] according to international committee on taxonomy of viruses (ictv), equine herpesviruses (ehvs) belong to the family herpesviridae . until now, a total of 9 ehv species types have been determined in equines, viz. ehv1-ehv9. 4 among them, ehv1 and ehv4 are the most relevant herpesviruses affecting equines. both ehv1 and ehv4 infection are associated with upper respiratory tract disease, but only ehv1 infection could cause abortion and myeloencephalitis. ehv1 and ehv4 are prevalent in equines on all continents and have considerable economic impact on the horse industry. 5 in china, the number of equines is very large, reaching to be ∼ 6.8 million in 2018 ( http://www.stats.gov.cn/tjsj/zxfb/ ). ehv infection in equines was first reported in china in 1980, and the epidemiological investigation since then indicated ehv was prevalent in the equine population in all the studied 16 provinces in mainland china, with a seroprevalence ranging 8% −92%. [6] [7] [8] vaccination is commonly used to prevent and control ehv. however, china has not developed a commercially available ehv vaccine so far. ehv vaccine has a limited market application potential in china currently. due to the lack of relevant knowledge on ehv, most of the chinese horse owners always erroneously identified it as other common pathogen of equine respiratory diseases, and didn't realize its potential threat to equine health and reproduction. although the number of equines in china is large, most of them are labor/farming horses. to the best of our knowledge, even for racehorses, vaccination with ehv vaccine has not been performed in mainland china. considering the wide distribution and high prevalence of ehv in china, it is urgently to popularize knowledge on ehv in horse owners and promote market application prospects of ehv vaccine. in china, few veterinary researchers are currently investigating equine virus, including ehv. this is mainly caused by the change of equines' historical role. in the last century, a great number of equines were used for military in china. however, there is only one military equine farm in mainland china at present. considering a more important economic role of other domestic animals (e.g., pigs, chickens, and cattle) compared with equines, investigating equine virus (including ehv) is not a priority in the related guide policies issued by the chinese government. though epidemiological studies on ehv in china are limited, it still could be concluded that epidemic status of ehv is very complicated in china, which increases the difficulty in ehv vaccine development. in most provinces, ehv1 and ehv4 were co-circulating in equines with a high seroprevalence. 8 until now, a total of 7 ehv1 strains have been isolated from tissue samples of aborted equine fetuses (5 from farming horses in northeast china in 1980, 1 from asian wild horses in western china in 1999, 1 from farming horses in western china in 2016). 6 , 8 in addition, a novel ehv8 strain was isolated from one horse with serious respiratory disease in northern china in 2010. 9 recently, our laboratory firstly determined the molecule evinces for ehv4 and ehv5 in racehorses in sothern china (data not shown). however, a more large-scale and surveillance of ehv in equines is necessary to fully understand epidemic status of ehv in china, which could establish a foundation for updating the composition of ehv vaccine developed in china in future. in other countries, much effort has been made to develop ehv vaccine, and modified-live and inactivated virus vaccines have been registered for sale. 10 before an ehv vaccine is developed successfully in china by itself, it is necessary to vaccinate the susceptible equine population with an ehv vaccine commercially available from other countries to prevent and control ehv in china. however, a well-designed case-control animal challenge study still needs to estimate the protective efficacy of different vaccines against the field prevalent ehv strains in china. all authors declare that they have no competing interests. a recent review article on the treatment of hepatitis c with directly-acting antiviral (daa) drugs, makes numerous recommendations for baseline drug resistance testing. 1 in our local practice, we have been performing baseline drug resistance testing for some years now, prior to the publication of these guidelines. we present a recent retrospective hcv kinetics analysis of these patients' changing viral loads in response to daa therapy below. such studies have been used previously to compare viral suppressive responses in different hcv genotypes and treatment regimens. 2 , 3 the patients were a mixture of treatment-naive and treatment-experienced (including with interferon-based, ns3 protease inhibitor-based and daa-based regimens) cases. the current standard of care for hepatitis (hcv) patients is a combination of direct acting antivirals (daas), for which there are three different hcv viral protein targets (ns3, ns5a and ns5b). table 1 ns3, ns5a, ns5b resistance associated substitutions (ras), by hcv genotype, found in this patient cohort at baseline drug resistance testing (viral sequencing performed at imperial college, london, uk). the patients included a mixture of treatment-naïve and treatment experienced (i.e. interferon-based, ns3 protease inhibitor-based and more recent daa-based regimens) cases. resistance associated substitution (ras) by hcv genotype treatment with daas cure the vast majority of hcv-infected patients, with oral regimens having > 95% efficacy in most patient groups. 1 , 4 , 5 treatment failure currently affects approximately 5% of treated patients and is often associated with the selection of resistance associated substitutions (ras). 1 we performed hcv drug resistance testing both retrospectively (following treatment failures) and prospectively (prior to treatment) in our cohort of hcv genotype (g) 1-3-infected patients, during march 2015-june 2018. viral extraction, pcr and sequencing were performed at imperial college, using qiagen viral rna mini kits (qiagen pn:52906, qiagen ltd., manchester, uk), and inhouse pcr and sanger sequencing methods on an abi prism 3100-avant genetic analyser (thermo fischer scientific, loughborough, uk). the prediction of hcv genotype and drug sensitivities is derived from the geno2pheno algorithm [ www.geno2pheno.org ]. 6 treatment regimens used during this period complied with contemporaneous nhs rate cards: for non-cirrhotic or compensated cirrhotic patients: g1-treatment-naive: omb/par/rit + das + r; g1-treatment-experienced: elb/grz + /-r; g2-treatmentnaive/experienced: gle/pib; g3-treatment-naive/experienced: gle/ pib; g1-decompensated cirrhotic patients sof/led + r; g2/g3decompensated cirrhotic patients: sof/vel + r. we assessed the impact of any ras across g1-g3 on hcv rna kinetics by analysing viral load (realtime hcv viral load, abbott m20 0 0, abbott molecular uk, maidenhead, england) decline rates. we applied linear mixed regression to model the viral loads and assumed a linear decline (log 10 scale) over time, using sas statistical software (sas institute inc., nc, usa). in this cohort of 54 patients (n: g1 = 21, g2 = 6, g3 = 27), hcv ras were found as shown in table 1 . hcv rna viral load decline rates were found to be similar and not statistically different ( p = 0.760) at: −2 log 10 and −1.8 log 10 per month, respectively, for g1 and g2/g3 ( fig. 1 ). this suggests that these viral load decline rates were similar across g1-g3 infections despite baseline differences in viral load, ras profile, or a history of any previous treatment (i.e. interferon-based, older ns3 protease inhibitor-based, or more recent daa regimens). these results demonstrate similar hcv rna clearance efficacies of the various daa treatment regimens for g1-g3, in this patient cohort. although other studies on hcv kinetics have been published, they do not usually compare multiple hcv genotypes. 7 similar studies on patients infected with g4-6 viruses, and/or undergoing other daa treatment or retreatment combinations, 8 , 9 will be with great interest we have read the report of zhang et al. concerning the increased susceptibility to pertussis in chinese adults at childbearing age, as determined in a comparative seroprevalence study using samples collected from 2010 to 2016. 1 the authors describe that about 5% of the individuals had pt-igg antibodies, which is indicative of a recent infection. in the adults 20-39 years of age, 29.1% subjects had undetectable pt-igg antibodies in 2010 but 57.4% in 2015/2016. it is well known that adolescents and adults have become the reservoir of pertussis and an important source of transmission to vulnerable infants. bordetella pertussis is commonly associated with atypical pneumonia as determined in hospitalized children. 2 several seroprevalence studies conducted in different regions of china indicate that the incidence of pertussis is most likely underestimated. 3 , 4 this may be due to the use of insensitive diagnostics. at present, the diagnosis of pertussis in china is mainly based on culture. however, both the cdc and the world health organization (who) use pcr as the gold standard for diagnosis, in addition to culture. 3 oropharyngeal or nasopharyngeal swabs were obtained from 17,104 inpatients aged between 10 days and 14 years of age with clinical suspicion of pertussis, enrolled from march 2014 to february 2018 in shenzhen children's hospital. more than 50% of all patients were younger than 6 months of age. the hospitalized patients included 10,894 males and 6210 females (sex ratio, 1.75). all patients recovered after the treatment. a real time pcr assay targeting ptxa-pr was used to detect b. pertussis . of the 17,104 samples, 772 (4.51%) tested positive for b. pertussis by rt-pcr. our results indicate that despite vaccination pertussis remains a major health problem in china, since the prevalence of infection by b. pertussis in hospitalized children was high. the majority of patients were admitted because of pneumonia. the detection rate in hospitalized patients was lower than the rates reported earlier in shanghai and ji'nan. 3 , 4 this may be due to lower number of samples collected in these studies and due to the use of serology or culture methods. the overall prevalence rates were 3.97% and 5.48%, respectively. however, b. pertussis infection in female patients was significantly higher than in male patients (x 2 = 20.913, p < 0.001). this has earlier been reported by the ecdc 5 and haberling et al. 6 and may point to a genetic association with susceptibility to b. pertussis . the detection rates were dependent on age in patients (x 2 = 139.8, p < 0.001). the prevalence decreased with age: 8.71% newborns, 5.33% in infants, 2.39% in toddlers, 1.28% in (pre-) schoolers ( fig. 1 ) . the high vulnerability of newborns and young infants for b. pertussis infection may be related to a combination of insufficient herd immunity and suboptimal protection against b. pertussis infection in children too young to be fully vaccinated. since vaccination rates in infants are already at 99%, it will be difficult to improve this further. therefore, other measures must be considered, including booster vaccination at pre-school age and vaccination during pregnancy. because young infants are mainly cared for by mothers and other adults, the most important cause of infection with b. pertussis is their close contact with parents and siblings. 7 in general, b. pertussis was detected more often during seasonal changes, especially from late summer to early autumn. in hospitalized children the number of b. pertussis infections increased in march and september as compared to other months ( fig. 2 ) . the seasonal infection rates were 4.66% in spring, 4.75% in summer, 4.62% in autumn and 4.00% in winter, respectively. the prevalence in the winter season was lower but not statistically different than in other seasons (x 2 = 3.388, p = 0.336). in this study, we used real-time pcr, the most accurate method to detect b. pertussis . the detection rate may be significantly lower than the actual level, because oropharyngeal samples in most patients were collected instead of nasopharyngeal samples, and the pcr target gene was ptxa-pr instead of is4 81. is4 81 is present in high-copy numbers in b. pertussis whereas ptxa-pr is a single-copy target. however, the ptxa-pr pcr is more specific and will not detect b. parapertussis , which contributes to more than 5% of pertussis cases. 8 many studies have shown that adolescents and adults with b. pertussis infections, causing chronic cough, are an important reservoir for transmission, putting newborns at high risk. 9 maternal pertussis immunization prevents infant pertussis, as recently shown by amirthalingam et al. vaccine effectiveness against infant deaths was estimated at 95%, and disease incidence in infants < 3 months of age has remained low. 10 according to our results, vaccination of pregnant women and adults, especially those in close contact with infants and young children, may help to prevent pertussis in infants and young children in china. the authors have declared that no competing interests exist. this study was supported by the sanming project of medicine in shenzhen ( szsm201512030 ) and by the shenzhen science and technology project ( jcyj20170303155012371 ). tang and colleagues reported in this journal their experience with covid-19 disease 1 , the outbreak of which began in december 2019 in wuhan, hubei province, china 2 , 3 with spread to 33 additional countries 4-8 as of the 21st february 2020. here we report the clinical features and outcome of the first two cases of disease caused by sars-cov-2 infection in the united kingdom (uk) -the first imported and the second associated with probable person-toperson transmission within the uk. public health management will be reported separately. the index case (a) entered the uk on 23/01/20 from hubei province in china. initially asymptomatic, this individual, a 50 year-old female with no past medical history and on no regular medications, developed symptoms of fever and malaise on 26/01/20, accompanied by sore throat and dry cough. she had travelled with her partner and reported no infectious contacts prior to travel. on 28/01/20, a close household contact of the index case, a resident of the uk, developed symptoms of fever (38.5 °c), followed the next day by diffuse myalgia and a dry cough. this patient (case b) is a previously fit and well 23 year-old male. he had returned to the uk from hubei province on 06/01/20. case b promptly sought advice via the national health service (nhs) self-referral service nhs 111, and he and case a were assessed as being possibly at risk of covid-19, and were admitted to the regional infectious diseases unit at castle hill hospital, hull university teaching hospitals for isolation, assessment and diagnostic sampling. they were managed in separate negative pressure cubicles with anterooms. nursing and medical staff donned personal protective equipment (ppe) as recommended by public health england (phe). the clinical observations of each of the patients, together with their initial blood tests, are shown in table 1 . ( fig. 1 ) . clinical examination findings were unremarkable. initial investigations revealed only mild lymphopenia and elevation of crp, with mild neutrophilia in case b. periodic fever of 38-38.5 °c was observed in case b until d3 of admission. repeat blood tests in this individual on d3 demonstrated mild acute kidney injury (aki, serum creatinine 144 μmol/l). the aki was thought most likely due to dehydration, and resolved within 24 h with administration of intravenous infusion of crystalloid at 125 ml/h. cxr was normal. empirical oral antibiotic therapy (co-amoxyclav 500/125 mg p.o. t.d.s.) was administered on d3, to cover the possibility of secondary bacterial infection, but was subsequently discontinued. symptoms resolved in case a by d3 and in case b by d4 of admission. pcr testing of sars-cov-2 from nose and throat swabs taken daily was negative from d2 onwards in case a and from d5 in case b (throat swabs from this individual were negative throughout). there was no clinical indication for the use of experimental antiviral therapies. patients were deisolated according to current phe guidance, based on complete resolution of symptoms and two sequential negative respiratory pcr tests at least 24 h apart. rooms were decontaminated with 0.1% hypochlorite followed by uv light treatment. the contact of these individuals remained asymptomatic throughout the 14 days incubation period but was isolated as a precaution and to be close to family these first cases of sars-cov-2 are informative for clinicians caring for suspected and confirmed cases in the uk and elsewhere. reassuringly, illness in both individuals was relatively mild and short-lived, with no evidence of parenchymal lung disease (reflected by normal oxygenation and the absence of radiological infiltrates) or of the late-stage deterioration that has been reported in case series 9 , possibly due to the absence of comorbidities. experimental antiviral therapeutic options for severe disease were not considered necessary given the mild clinical nature of the illness. clinical illness correlated with the presence of viral rna in upper airway samples ( fig. 1 ) , with no evidence of prolonged asymptomatic shedding, although discordance between nose and throat samples in case b highlights the need to sample both areas. it was reasonably assumed that the source of infection in case b was close contact with symptomatic case a, given that the time from travel to china to onset of symptoms in case b was 22 days, although this cannot be proven. based on this assumption, the period from exposure to disease onset appeared short, at approximately 48 h, consistent with recent reports of the incubation period of sars-cov-2 6 . co-occurrence of respiratory viral infection, as we observed in case b with rhinovirus, has been described in the context of sars-cov-2 ( https://www.medrxiv.org/ content/10.1101/2020.02.12.20022327v1 ) as it has with many other respiratory viruses spread by similar routes, and may have contributed to the increased symptomatology in case b. interestingly the partner of case a, who was a close household contact, remained asymptomatic throughout and had negative tests for sars-cov-2 shedding. it will be of interest to investigate the serological responses in this individual to ascertain evidence of subclinical infection. isolation, minimisation of contacts and use of appropriate ppe is a cornerstone of management of high consequence respiratory viral infection. in the cases reported here, phe recommendations for ppe were followed 10 and there were no breeches in ppe or nosocomial transmission. this should provide reassurance to healthcare workers managing patients with suspected covid-19 in the uk that current ppe is both feasible and effective. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. dear editor , as reported in this journal 1 and elsewhere, 2 an outbreak of atypical pneumonia caused by the zoonotic 2019 novel coronavirus (sars-cov-2) is on-going in china and has spread to the world. as of feb 16, 2020 (24:00, gmt + 8), there have been 70,548 confirmed patients and more than 1700 deaths from sars-cov-2 infection in china, and 58,182 confirmed patients and 1696 deaths in the most affected province, hubei province. much research progress has been made in dissecting the evolution and origin of sars-cov-2 and characterizing its clinical features. [3] [4] [5] [6] [7] while the outbreak is on-going, people raise grave concerns about the future trajectory of the outbreak, especially given that the working and schooling time has been already dramatically postponed after the chinese lunar new year holiday was over (scheduled on jan 31). in particular, a precise estimation of the potential total number of infected cases and/or confirmed cases is highly demanding. earlier studies based on susceptible-exposed-infectious-recovered metapopulation and susceptible-infected-recovered-dead models revealed the number of potentially infected cases and the basic reproductive number of sars-cov-2. 3 , 8 , 9 these traditional epidemiological models apparently require much detailed data for analysis. 3 , 8 here we explored a simple data-driven, boltzmann functionbased approach for estimation only based on the daily cumulative number of confirmed cases of sars-cov-2 (note: the rational for boltzmann function-based regression analysis is presented in supporting information (si) file). we decided to collect data (initially from jan 21 to feb 10, 2020) in several typical regions of china, including the center of the outbreak (i.e. wuhan city and hubei province), other four most affected provinces (i.e., guangdong, zhejiang, henan, hunan) and top-4 major cities in china (i.e., beijing, shanghai, guangzhou, shenzhen). during data analysis on feb 13, 2020, the number of new confirmed cases on feb 12 in hubei province and wuhan city suddenly increased by 14,840 and 13,436, respectively, of which 13,332 and 12,364 are those confirmed by clinical features (note: all the number of confirmed cases released by feb 12 were counted according to the result of viral nucleic acid detection rather than by referring to clinical features). we thus arbitrarily distributed these suddenly added cases to the reported cumulative number of confirmed cases from jan 21 to feb 14 for hubei province by a fixed factor (refer to table s1 ), assuming that they were linearly accumulative in those days. it is the same forth with the data for wuhan city. regression analyses indicate that all sets of data were well fitted with the boltzmann function (all r 2 values being close to 0.999; figs. 1 a, b, s1 , and table 1 ). the potential total number of confirmed cases for mainland china, hubei province, wuhan city, and other provinces were estimated as 72,80 0 ±60 0, 59,30 0 ±60 0, 42,10 0 ±70 0 and 12,80 0 ±10 0; respectively; those for provinces guangdong, zhejiang, henan and hunan were 1300 ±10, 1170 ±10, 1260 ±10, 1050 ±10, 1020 ±10 and 940 ±10, respectively ( table 1 ) ; those for beijing, shanghai, guangzhou and shenzhen were 394 ±4, 328 ±3, 337 ±3 and 397 ±4, respectively. in addition, we estimated the key date, on which the number of daily new confirmed cases is lower than 0.1% of the potential total number as defined by us subjectively (refer to table 1 ). the above analyses were performed assuming that the released data on the confirmed cases are precise. however, there is a health commission, the state administration of traditional chinese medicine, the academy of chinese medical sciences, 29 provinces and cities, as well as the army ( fig. 1 ) . huoshenshan hospital is a specialized hospital established in the wuhan staff sanatorium. patients with confirmed coronavirus pneumonia have been admitted to our hospital. it has a total of 10 0 0 beds, and includes an intensive care unit, an ordinary care unit, a laboratory, and radiology and other auxiliary departments. according to the national health commission of the people's republic of china, the related design scheme of the institute was completed on january 24, 2020. construction of the hospital began on january 29th, and the hospital was completed and put into use on february 2nd. the chinese people's liberation army has transferred 1400 medical personnel to undertake the task of helping people infected with the virus. we firmly believe that chinese medical 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www.gov.uk/government/publications/wuhan-novelcoronavirus-infection-prevention-and-control/wuhan-novel-coronavirus-wncov-infection-prevention-and-control-guidance accessed 3rd emergence of a novel coronavirus causing respiratory illness from wuhan a novel coronavirus outbreak of global health concern epidemiological and clinical features of the 2019 novel coronavirus outbreak in china a new coronavirus associated with human respiratory disease in china a pneumonia outbreak associated with a new coronavirus of probable bat origin genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding clinical characteristics of 2019 novel coronavirus infection in china nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study data-based analysis, modelling and forecasting of the novel coronavirus (2019-ncov) outbreak a data driven time-dependent transmission rate for tracking an epidemic: a case study of 2019-ncov emergence of a novel coronavirus causing respiratory illness from wuhan early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features of patients infected with 2019 novel coronavirus in wuhan the novel coronavirus originating in wuhan. china: challenges for global health governance emergence of sars-like coronavirus poses new challenge in china we are indebted to all colleagues who contributed to this substudy in paris and geneva. in particular, we would like to thank no public or private funds were used for the current study. eliseo albert holds a río hortega research contract from the carlos iii health institute (ref. cm18/00221 ). estela giménez holds a juan rodés research contract from the carlos iii health institute (ref. jr18/0 0 053 ). we thank all the staff of the domestic and international organizations who fought against this outbreak, including those at the various health care facilities, lassa fever diagnostic laborato-ries, nigeria centre for disease control, world health organization, african field epidemiology network, public health england, ehealth africa, pro health international, university of maryland baltimore, us centers for disease control and prevention, alliance for international medical action, médecins sans frontières, and numerous other partners. we also express our sincerest condolences to the families and friends of those who died during the outbreak. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2019.12.016 . this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sector. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2020.01.019 . this work was supported by the national natural science foundation of china ( 31702271 ), and the guangdong provincial natural science foundation ( 2017a030310367 ). we are grateful to the patients for providing their written informed consent to publish this report. our thanks go to nursing, laboratory and medical colleagues in hull university teaching hospitals nhs trust and the newcastle upon tyne hospitals nhs foundation trust who contributed directly and indirectly to patient care, and to many colleagues in public health england and across the hcid network who contributed their time and expertise to the management of these cases. cjad is supported by a clinical research career development fellowship from the wellcome trust ( 211153/z/18/z ). we thank graduate students (boyan lv, zhongyan li, zhongyu chen, yu cheng, mengmeng bian, shuang zhang, zuqin zhang, and wei yao; all from prof. xinmiao fu's research group at fujian normal university) for data collection. this work is support by the national natural science foundation of china (no. 31972918 and 31770830 to xf). the reported cumulative number of confirmed cases may have uncertainty. assuming the relative uncertainty follows a single-sided normal distribution with a mean of 1.0 and a standard deviation of 10%, the potential total number and key dates were estimated at 95% ci. for detail, refer to the methods section and figs. 1 c, d, s2 and s3.b key date is determined when the number of daily new confirmed cases is less than 0.1% of the potential total number. tendency to miss-report some positive cases such that the reported numbers represent a lower limit. one typical example indicating this uncertainty is the sudden increase of more than 14 0 0 0 new confirmed cases in hubei province on feb 12 after clinical features were officially accepted as a standard for infection confirmation.another uncertainty might result from insufficient kits for viral nucleic acid detection at the early stage of the outbreak. we thus examined the effects of such uncertainty using a monte carlo method (for detail, refer to the methods section in si file). for simplicity, we assumed that the relative uncertainty of the reported data follows a single-sided normal distribution with a mean of 1.0 and a standard deviation of 10%. under the above conditions, the potential total numbers of confirmed cases of sars-cov-2 for different regions were estimated ( figs. 1 c, d, s2 and s3 ) and summarized in table 1 16 ,092), respectively, indicating that overall the outbreak may not be so bad as previously estimated. 9 such uncertainty analysis also allowed us to estimate the key dates at 95% ci. as summarized in table 1 , the key dates for mainland china, hubei province, wuhan city, and other provinces would fall in (2/28, 3/10), (2/27, 3/10), (2/28, 3/10) and (2/27, 3/13), respectively.finally, the ongoing sars-cov-2 outbreak has undoubtedly caused us the memories of the sars-cov outbreak in 2003. we thus collected the data from the who officiate website for analysis, and found that the cumulative numbers of confirmed cases of 2003 sars-cov both in china and worldwide were fitted well with the boltzmann function, with r 2 being 0.999 and 0.998, respectively ( figs. 1 e and f) .in summary, we found that all data sets, including both the on-going outbreak of sars-cov-2 in china and the 2003 sars-cov epidemic in china and worldwide, were well fitted to the boltzmann function ( fig. 1 and s1 ). these results strongly suggest that the boltzmann function is suitable for analyzing the epidemics of coronaviruses like sars-cov and sars-cov-2. one advantage of this model is that it only needs the cumulative number of confirmed cases, somehow as simple as the recently proposed model. 10 in addition, the estimated potential total numbers of confirmed cases and key dates may provide valuable guidance for chinese central and local governments to deal with this emerging threat at current critical stage. none. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2020.02.019 . we appreciate the work tang et al. have report emergence of a novel coronavirus in china. 1 the 2019-ncov broke out in wuhan, china at the end of 2019, and has attracted worldwide attention. [2] [3] [4] although the chinese government has taken active measures to control this epidemic, the virus is very infectious. according to the real-time data of the national health commission of the people's republic of china up until february 5, 2020, within a short period of half a month, the number of confirmed cases and the number of deaths were 24,443 and 493, respectively. the epidemic is progressing rapidly. 2019-ncov poses new public health challenges in china. 5 in wuhan, china, the number of local medical staff is insufficient for the demand resulting from the explosive increase in the number of infected patients. therefore, many medical personnel are needed to devote themselves to the front line of combating the virus.medical personnel throughout the country are led under the unified leadership of the chinese government. although the epidemic in wuhan is serious, a large number of medical staff rushed to wuhan to supplement the shortage of manpower in wuhan hospitals. this is a battle without smoke, the heroes of which are our medical staff. according to the national health commission of the people's republic of china, as of january 30, 2020, hubei province opened 11,0 0 0 isolated patient beds, and about 170,0 0 0 healthcare professionals from all kinds of medical institutions are working on the front lines and providing care for patients with fevers, and for suspected or confirmed patients. in this time of emergency, under the unified deployment of the chinese government, there are 52 medical teams including 6097 medical personnel from the national key: cord-309001-erm705tg authors: liu, q.; song, n. c.; zheng, z. k.; li, j. s.; li, s. k. title: laboratory findings and a combined multifactorial approach to predict death in critically ill patients with covid-19: a retrospective study date: 2020-06-30 journal: epidemiol infect doi: 10.1017/s0950268820001442 sha: doc_id: 309001 cord_uid: erm705tg to describe the laboratory findings of cases of death with coronavirus disease 2019 (covid-19) and to establish a scoring system for predicting death, we conducted this single-centre, retrospective, observational study including 336 adult patients (≥18 years old) with severe or critically ill covid-19 admitted in two wards of union hospital, tongji medical college, huazhong university of science and technology in wuhan, who had definite outcomes (death or discharge) between 1 february 2020 and 13 march 2020. single variable and multivariable logistic regression analyses were performed to identify mortality-related factors. we combined multiple factors to predict mortality, which was validated by receiver operating characteristic curves. as a result, in a total of 336 patients, 34 (10.1%) patients died during hospitalisation. through multivariable logistic regression, we found that decreased lymphocyte ratio (lymr, %) (odds ratio, or 0.574, p < 0.001), elevated blood urea nitrogen (bun) (or 1.513, p = 0.009), and raised d-dimer (dd) (or 1.334, p = 0.002) at admission were closely related to death. the combined prediction model was developed by these factors with a sensitivity of 100.0% and specificity of 97.2%. in conclusion, decreased lymr, elevated bun, and raised dd were found to be in association with death outcomes in critically ill patients with covid-19. a scoring system was developed to predict the clinical outcome of these patients. since the outbreak of disease caused by a new virus in wuhan, china in december 2019, hundreds of thousands of people have been infected with the virus. as of march 2020, the cumulative number of confirmed diagnoses on the chinese mainland has been over 80 000, but there has been no new domestically transmitted case reported for several days, which indicates that the epidemic in china has been basically controlled. however, the viral disease has swept into at least 190 countries and killed tens of thousands of people. over the last few weeks, the number of cases of this disease outside china has increased dozens of times. therefore, the world health organization (who) had made an assessment on 11 march that the disease could be characterised as a pandemic [1] . the pathogen of the disease was first isolated by chinese scientists on 7 january 2020, and was identified as a new type of coronavirus [2] , which was initially known as 2019-ncov and recently named sars-cov-2 [3] . it has the characteristics of a typical coronavirus family and belongs to the beta coronavirus 2b lineage. although the initial epidemiological investigation suggested that it was transmitted to humans through wildlife, the distinct human-to-human transmission phenomenon has been confirmed in subsequent studies [4] . full-genome sequencing and phylogenic analysis suggest that it is similar in structure to severe acute respiratory syndrome (sars) virus, and mainly causes respiratory tract infections in humans [5] , which was designated as coronavirus disease 2019 (covid-19) later by who. several descriptive studies have confirmed that most infected patients were mildly symptomatic or even asymptomatic [6, 7] . however, there were still many patients who developed severe pneumonia or even death [8, 9] . the relevant indicators of this part of the patients, especially the patients who died, need to be of significant concern. a data-driven analysis stated the hubei province (except wuhan) has an estimated case-fatality rate (cfr) of 1.41% [10] , which was also confirmed by a recent retrospective study involving 1099 patients [11] . however for critically ill patients, the mortality rate is much higher. a study from jin yin-tan hospital of wuhan compared the critically ill and non-severe patients, and the results showed that the mortality of critically ill patients with covid-19 was considerable [9] . however, there is still no specific and effective treatment except for meticulous supportive care for this disease. no solid evidence proved any antiviral agents could improve outcomes in covid-19. even lopinavir−ritonavir treatment, previously thought to be effective, has been shown by studies that no benefit was observed in hospitalised adult patients with severe covid-19 [12] . in such cases, critically ill patients could rapidly develop acute respiratory distress syndrome (ards), organ dysfunction and other serious complications and eventually death. therefore, it is significant to estimate risk factors for severe disease and death, so that we could more efficiently focus on medical resources to treat patients who may have poor prognoses in efforts to reduce mortality. although there have been previous articles describing the clinical course of the disease or some factors that predicted death [13] [14] [15] because many patients were still in the middle stage of the disease at the time of the study and did not reach their clinical outcome, the collected clinical data were inevitably incomplete, and the results were less accurate. under the situation that the epidemic is basically under control, most patients have their definite outcomes, either cured or died, so that the research would be more accurate, which was why we conducted this research study at this time. in addition, we used a combined predictive system with several variables, which also ensures the validity of the prediction. in this research study, we collected the clinical data of patients with covid-19 admitted in the hospital, encompassing laboratory indexes and their clinical outcomes (cure or death). we aimed to describe laboratory findings of cases of death, compare them with cured patients, and finally design a multifactor prediction model, which is expected to provide early identification for patients with clinically severe covid-19. this single-centre, retrospective, observational study included adult patients (≥18 years old) with severe or critically ill covid-19 admitted in two wards of union hospital, tongji medical college, huazhong university of science and technology in wuhan. all patients were diagnosed with covid-19 according to who interim guidance and they all had a definite outcome (death or discharge) between 1 february 2020 and 13 march 2020 ( fig. 1 ). demographical data, laboratory indexes, medical history, underlying diseases and outcome data were extracted from the blood screening test and electronic medical records. all data were examined by one independent physician through the patient's paper charts. the study was conducted in accordance with the principles of the declaration of helsinki. informed consent was not obtained from patients as all data were retrieved retrospectively from the laboratory testing information system and no additional blood samples were taken. this study was approved by the ethics review board of wuhan union hospital. the presence of sars-cov-2 in respiratory specimens was detected by next-generation sequencing or real-time rt-pcr methods to confirm the diagnosis of covid-19 as described in the previous article [16] . underlying diseases included hypertension, cardiovascular disease, diabetes, malignancy, cerebrovascular disease, chronic obstructive pulmonary disease (copd), chronic kidney disease, chronic liver disease, organ transplant history and undergoing general anaesthesia surgery within 1 month. the duration from the onset of disease to hospital admission was recorded. the neutrophil ratio (neur), is the percentage of neutrophils to the total number of all white blood cells (wbcs). similarly, the lymphocyte ratio (lymr) is the number of lymphocytes as a percentage of the number of wbcs. statistical analyses were performed by spss 17.0 (spss inc, chicago il, usa). continuous and categorical variables were presented as median, interquartile range (iqr) and n (%), respectively. the mann−whitney u test, χ 2 test or fisher's exact test were used. binary logistic regression was conducted further. we used both single variable and multivariable logistic regression to verify those factors. variables with statistically significant differences in the single variable analysis were included in the multivariable analysis, and several variables with potential for bias were excluded. this was followed by a backwards stepwise logistic regression. the final model was used to predict death and that sensitivity/specificity/roc curves were produced. a p-value < 0.05 was considered statistically significant. the study included 336 adult patients with severe or critically ill covid-19 eventually. the median age was 65 years (iqr, 51-69), and 169 (50.3%) were men. the median duration from first symptoms to hospital admission was 2 days (iqr, 1-4). in a total of 336 patients, 182 (54.2%) had one or more underlying conditions. in all, 34 (10.1%) patients died during hospitalisation while 302 (89.9%) were discharged. compared with survivors, non-survivor patients were significantly older with a median age of 74 years (iqr, 64-78) vs. 64 years (iqr, 51-68) ( table 1) . (1) laboratory findings laboratory parameters of all patients were recorded on day of hospital admission, then divided into survivor or non-survivor groups according to their clinical outcome. the levels of wbc count, neutrophil (neu), neutrophil ratio (neur), blood urea nitrogen (bun), d-dimer (dd) and c-reactive protein (crp) were higher in non-survivor patients, together with the reduction of lymphocyte ratio (lymr) ( table 1) . (1) results of logistic regression analysis in single variable analysis, age, wbc count, lymr, neur; serum albumin (alb), bun; prothrombin time (pt), fibrinogen (fib), dd; and crp were associated with death (table 1) . wbc, lym, lymr, are all related to the wbc count, and may affect each other or have contained relationships. to avoid bias in the prediction model due to correlation, it is better for the variables in a model to be completely independent of each other. similarly, fib, pt and dd all reflected the coagulation function, and we chose only one to represent it. therefore, we excluded wbc, pt and fib in the subsequent analysis. this was followed by table 2 . eventually, we found that lymr, bun and dd at admission were closely related to death. (1) combination of predictors and development of predictive model three laboratory indicators were combined to provide a predictive probability value for the outcome of death in covid-19 patients, which was expressed in terms of pre. the roc curve was then used to evaluate the predictive efficiency of the combined predictor and individual factors for the outcome of death, which is shown in figure 2 . according to it, the area under the curve (auc) and cut-off values of the three factors were calculated ( table 3) . as demonstrated, the optimal thresholds of lymr, bun and d-dimer were 8.615%, 5.95 mmol/l and 1.56 μg/ml. on the basis of the logistic regression model and the roc curves, the scoring system for prediction of death was developed with three variables including lymr, bun and dd. when lymr < 8.615%, 1 point is counted, otherwise 0 points are counted. similarly, when bun ≥ 5.95 mmol/l or d-dimer ≥ 1.56 μg/ml, 1 point is counted, otherwise 0 points are counted. the total score for each patient was calculated by summing points of each risk factor. we also drew the roc curve of the combination for predicting risk of death in patients with severe or critically ill covid-19 in figure 2 . the combined prediction model had the auc of 0.994 (95% ci 0.979-0.999), with specificity/sensitivity of 97.24%/100.00% and positive predictive value (ppv)/ negative predictive value (npv) of 81.0%/100.0% (table 3 ). the cut-off value of it was 0.115. (1) comparison of the above three indicators of patients who died at different time points to further investigate the changes in d-dimer, bun and lymr in the progression of disease in patients who died, we compared table 4 and figure 3 , the results showed no significant differences among the three time points for these indicators. for example, bun was not significantly different in patients who died at the beginning of hospital admission, at the beginning of mechanical ventilation and before death, which means this indicator did not change significantly during the progression of disease in patients who died. since the outbreak of covid-19, many studies have revealed its virological characteristics, transmission characteristics, clinical manifestations, but there were few studies on patients who died. it is now clear that sars-cov-2, a kind of coronavirus, belongs to the β-coronavirus family, and could cause severe coronavirus disease similar to severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) [17] . at the same time, based on previous research, the virus can spread rapidly from person to person. its basic reproductive number (r 0 ) is estimated to be 2.2, which means that each patient has transmitted the infection to 2.2 other people on an average [4] . the clinical manifestations of the disease are variable. in previous studies, most patients had mild symptoms such as fever, fatigue and dry cough [8] , with lower overall mortality than sars and mers [11] , but the mortality rate of severe patients was higher than those two diseases [9] . therefore, in this research study, we analysed the laboratory examination indicators of patients who died and hoped to find out the risk factors that could predict the outcome of death. through analysis, we screened three indicators of dd, lymphocyte ratio and bun as predictors of the outcome of death. dd, as a commonly used clinical and simple test, effectively reflects the activation of the coagulation system. in our study, dd higher than 1.56 μg/ml was closely related to fatal outcome of covid-19. it has been proved that high levels of dd are significantly related to 28-day fatality in patients with infection or sepsis detected in the emergency department [18] . the cohort study from jin yin-tan hospital and wuhan pulmonary hospital (wuhan, china) also found that dd greater than 1 μg/ml was the risk factor of death in covid-19 patients. meanwhile, dd is an activation marker of coagulation cascade, which is considered an early event in patients with infection and sepsis [19] . therefore, elevation of dd may indicate severe infection or sepsis, which is often the cause of death in patients with covid-19. as mentioned in previous studies, lymphocytopenia occurred in most severe patients [8, 9] . this laboratory abnormality is similar to it previously observed in patients with sars and mers [20, 21] . consistent with these research studies, our findings showed that lymphocyte ratio lower than 8.615% was highly associated with death of covid-19 patients. therefore, we speculated that the virus may mainly affect lymphocytes, leading to their apoptosis, thereby triggering immune dysfunction in patients, which may be the reason why some patients rapidly develop sepsis and multiple organ failure. some studies have shown that a drastic reduction in the total number of lymphocytes indicates that the coronavirus could consume many immune cells and suppressed the cellular immune function [22] , suggesting that injury of t lymphocytes may be an important factor leading to worsening of the patient's condition. hence, application of immunomodulators may improve infection status in critically ill patients. bun often implies acute kidney injury and is also considered an important predictor of organ failure. our analysis showed that elevated blood urea was closely related to the poor prognosis of patients with covid-19, which was also mentioned briefly in other studies [8] . we suspected that the elevation of bun may be related to acute kidney injury, which may be caused by the invasion of the virus itself, insufficient tissue oxygen supply and shock. in other research studies, older age has been reported as a favourable risk factor of mortality [9, 13] , but through multivariate analysis, our study excluded age as a predictor of death. the reason was that the main objective of previous research was the comparison between severe and non-severe patients, but our study mainly focused on the cases of death in severe patients, in which case the effect of age may be relatively small. we further collected laboratory indexes performed during the hospitalisation of these patients who died and before their death. the timing of mechanical ventilation in these deceased patients was also the time of their worsening condition, so we chose to retrospectively analyse changes in the corresponding indicators at these time points in order to explore the relationship between these indicators and progression of disease. by comparing the above three indicators at different time points, we found that the difference was not significant (table 4 , fig. 3 ). this may mean that relevant indicators of these patients have not changed obviously from the early stages of admission to the clinical outcome, and existing treatment may not significantly slow the deterioration of the disease. it also implies that these deceased patients showed signs of developing a severe outcome at the beginning of hospital admission, indicating the rationality of our prediction using the initial admission data as well as suggesting that patients with this trend could be screened out early and need to be focused on treatment to reduce the covid-19 morbidity rate. to our knowledge, this is the largest number of studies involving severe covid-19 patients, and it is also one of the few studies focusing on patients who died. compared with single-factor predictions in other studies [13] , our designed multifactor scoring system is significantly more accurate. the roc curve also shows that this method has extremely high specificity and sensitivity. at the same time, the three indicators required by this prediction method are easy to obtain at the time of admission and can be implemented in other medical centres. our study also has some limitations. firstly, there is a certain bias due to retrospective research. some indicators that may be meaningful are not routinely tested in the clinic, such as cytokines, lactic acid, transferrin and so on. secondly, the research sample size is still too small. it is still a single-centre study and could not represent the overall situation well. thirdly, the scoring system is established and evaluated using the same group of patients, which makes the evaluation results may be less accurate, and a prospective research cohort needs to be established to further validate its accuracy. we found that three factors including decreased lymphocyte ratio, elevated bun and raised d-dimer were related to death outcomes in critically ill patients with covid-19. a combined multifactorial prediction model with high accuracy was developed to predict the clinical outcome of these patients. world health organization declares global emergency: a review of the 2019 novel coronavirus (covid-19 a novel coronavirus from patients with pneumonia in china sars-cov-2 is an appropriate name for the new coronavirus early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a pneumonia outbreak associated with a new coronavirus of probable bat origin epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study. the lancet respiratory medicine early estimation of the case fatality rate of covid-19 in mainland china: a data-driven analysis clinical characteristics of coronavirus disease 2019 in china a trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study analysis of factors associated with disease outcomes in hospitalized patients with 2019 novel coronavirus disease association of radiologic findings with mortality of patients infected with 2019 novel coronavirus in wuhan, china clinical features of patients infected with 2019 novel coronavirus in wuhan understanding of covid-19 based on current evidence evaluation of a novel prognostic score based on thrombosis and inflammation in patients with sepsis: a retrospective cohort study d-dimer is a significant prognostic factor in patients with suspected infection and sepsis multiple organ infection and the pathogenesis of sars middle east respiratory syndrome coronavirus efficiently infects human primary t lymphocytes and activates the extrinsic and intrinsic apoptosis pathways t-cell immunity of sars-cov: implications for vaccine development against mers-cov acknowledgements. the authors thank all participants for their contribution to the study.financial support. this research received no specific grant from any funding agency, commercial or not-for-profit sectors. ethical standards. the study was conducted according to the principles of the declaration of helsinki. the ethics review board of wuhan union hospital approved this study. informed consent for individual patient was not obtained since all data were retrieved retrospectively from the laboratory test information system without additional blood samples or laboratory analysis.data availability statements. the data that support the findings of this study are available from union hospital, tongji medical college, huazhong university of science and technology. restrictions apply to the availability of these data, which were used under licence for this study. key: cord-301983-aks5z29t authors: vakili, k.; fathi, m.; sayehmiri, f.; mohamadkhani, a.; hajiesmaeili, m.; rezaei-tavirani, m.; pezeshgi, a. title: critical complications of covid-19: a systematic review and meta-analysis study date: 2020-06-16 journal: nan doi: 10.1101/2020.06.14.20130955 sha: doc_id: 301983 cord_uid: aks5z29t background: coronavirus disease 2019 (covid-19) is a novel coronavirus infection that has spread worldwide in a short period and caused a pandemic. the goal of this meta-analysis is to evaluate the prevalence of most common symptoms and complications of covid-19. methods: all related studies assessing the clinical complications of covid-19 have been identified through web search databases (pubmed and scopus). relevant data were extracted from these studies and analyzed by stata (ver 14) random-effects model. the heterogeneity of studies were assessed by i2 index. the publication bias was examined by funnel plots and eggers test. results: 30 studies were in our meta-analysis including 6 389 infected patients. the prevalence of most common symptoms were: fever 84.30% (95% ci: 77.13-90.37; i2=97.74%), cough 63.01% (95% ci: 57.63-68.23; i2=93.73%), dyspnea 37.16% (95% ci: 27.31-47.57%; i2=98.32%), fatigue 34.22% (95% ci: 26.29-42.62; i2=97.29%) and diarrhea 11.47 %(95% ci: 6.96-16.87; i2=95.58%), respectively. the most prevalent complications were acute respiratory distress syndrome (ards) 33.15% (95% ci: 23.35-43.73; i2=98.56%), acute cardiac injury 13.77% (95% ci: 9.66-18.45; i2=91.36%), arrhythmia 16.64% (95% ci: 9.34-25.5; i2=92.29%), heart failure 11.50% (95% ci: 3.45-22.83; i2=89.48%), and acute kidney injury (aki) 8.40 %(95% ci: 5.15-12.31; i2=95.22%, respectively. according to our analysis, mortality rate of covid-19 patients were 12.29% (95% ci: 6.20-19.99; i2=98.29%). conclusion: we assessed the prevalence of the main clinical complications of covid-19 and found that after respiratory complications, cardiac and renal complications are the most common clinical complications of covid-19. since the first emergence of a cluster of pneumonia cases in wuhan, china on december 2019, the global attraction has been drawn to this disease. the china center for disease control and prevention, on 9 january 2020, stated that the cause of this newly emerged disease is a novel virus from coronavirideae family, which has been further named severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and the disease caused by this virus was called corona virus disease 2019 . unfortunately, this epidemic was not limited to china; the world health organization (who), on 11 march 2020, announced covid-19 outbreak a pandemic (1, 2). according to who, until the time that we are writing this (11 may 2020), more than 4 000 000 individuals were diagnosed with covid-19 and unfortunately about 279 000 of them have died (3) . based on the latest reports, the most common symptoms of covid-19 are fever, dry cough, fatigue, dyspnea and diarrhea (4) . the main clinical complications of covid-19 are related to respiratory system, from a simple pneumonia in mild cases to acute respiratory distress syndrome (ards) and shock in severe patients. the angiotensin-converting enzyme 2 (ace2) is the host cell receptor responsible for the entry of sars-cov-2 and the facilitation of infection. lung, heart, kidney and intestine cells express ace2. according to animal models, ace2 is downregulated in lung injuries (5) ; therefore, severe lung inflammation due to sars-cov-2 infection can lead to dysregulation of the renin-angiotensin system and further development of ards. furthermore, sars-cov-2 is expected to affect all tissues that express ace2. therefore, in addition to respiratory manifestations, cardiovascular and renal complications may occur following covid-19 infection. in practice, growing evidence demonstrates cardiovascular involvement in covid-19 disease and its negative impact on prognosis (6) . there are also many studies which confirm that acute and chronic renal injuries are expected due to the high expression of ace2 in the renal tubular epithelium (7) . since these complications are extremely life-threatening, their prevalence in the clinical outcomes of patients can act as a determining factor in the morbidity and mortality rate of the disease. therefore, this article aims to determine the prevalence of critical complications of patients with covid-19 by systematically reviewing recent literatures and analyzing related data. 2.1.study selection to find eligible cross-sectional and case-control studies published on covid-19 until 1 st may 2020, we conducted a web search with citations in the pubmed. two authors conducted the search process independently. our search queries included: 'ards and covid', '((heart) or cardio-) and covid', '((kidney) or renal) and covid' and, 'complications and covid'. on the basis of paper titles, eligible studies were chosen. in addition, the reference lists of all related reviews (narrative and systematic) were searched to find more related articles. all the studies in which the clinical complications of covid-19 were analyzed were examined. to be included in the final analysis, screened studies must report data on the prevalence of each clinical complication in covid-19 patients, including ards, acute heart damage, arrhythmia, heart failure and aki. only human studies have been included. the exclusion criteria in our search strategy were systematic reviews and meta-analyzes, duplicate publications, non-human studies, lack of sufficient data and non-english publications. since covid-19 is a newly emerged disease and the literature related to this disease is still limited, the quality of the included literatures has not been evaluated. for all studies, related data including the name of the first author, date of publication, location of publication, sample size, sample age, sample gender, prevalence of symptoms (including: fever, cough, dyspnea, fatigue, and diarrhea), critical complications (including: ards, acute cardiac injury, arrhythmia, heart failure, and aki) and clinical outcomes (mortality rate) were extracted. to avoid conflicting results, the authors extracted data from each study separately and then the results were compared. the prevalence of cardiovascular and renal complications was the effect size in this study. using the binomial distribution, its variance was assessed (with 95% confidence interval). average weight was applied to combine the prevalence of different studies. the inverse relationship was existed between the study weight and its variance. q statistics and i 2 index with α significance level of less than 10% were applied to investigate the heterogeneity. meta-analysis (random effects model) were applied, when the studies were heterogeneous. for data analysis, stata software (version 14) was applied. the metaprop (meta-analysis for proportion) command was applied in stata and when p was close to 0 or 1. in order to stabilize the variances, we applied freeman-tukey double arcsine transformation (8) . in metaprop two variables in the format such that p = n/n are required to be declared. this study was carried out under the approval of ethics committee of shahid beheshti university of medical sciences (ir.sbmu.retech.rec.1399.083). for analysis, we used prisma checklist (9) . initially, 137 studies were identified through database searches, and 44 additional studies through other sources. of these 181 studies, 61 of them were excluded due to duplication. after screening the abstracts, other 55 articles were excluded too. therefore, the full-text of 85 remaining were evaluated and 28 other studies were excluded for some reasons (lack of enough information). after careful review of these selected studies, 30 published articles between february 2020 and april 2020 were included for the further analysis ( fig. 1, table 1 ). pooling all extracted data together, the total number of covid-19 positive patients was 6 389 including 1402 patients with ards, 494 patients with acute cardiac injury and 418 patients with aki. selected studies have been conducted primarily in china except 1 in the united states. according to the average calculated from the articles reporting the median age of subjects, the mean age of patients were 57.64 and 45.29%, (95% ci: 42.61% to 47.99%; i 2 =74.56%) of the patients were female. our meta-analysis revealed that the most common symptoms of covid-19 were fever 84.30% (95% ci: 77.13-90.37; i 2 =97.74%), cough 63.01% (95% ci: 57.63-68.23; i 2 =93.73%), dyspnea 37.16% (95% ci: 27.31-47.57%; i 2 =98.32%), fatigue 34.22% (95% ci: 26.29-42.62; i 2 =97.29%) and diarrhea 11.47% (95% ci: 6.96-16.87; i 2 =95.58%), respectively. cardiac and renal complications in these patients were also assessed. these most common respiratory complication was ards 33.15% (95% ci: 23.35-43.73; i 2 =98.56%). the prevalence of arrhythmia, acute cardiac injury and heart failure were 16.64% (95% ci: 9.34-25.5; i 2 =92.29%), 15.68% (95% ci: 11.1-20.97; i 2 =92.45%), and 11.50% (95% ci: 3.45-22.83; i 2 =89.48%), respectively. unfortunately, few related articles were available for analyzing the prevalence of arrhythmia and heart failure. furthermore, the primary analysis of aki showed a prevalence of 9.87% (95% ci: 6.18-14.25; i 2 =95.64%) ( table 2) . based on the primary analysis, the mortality rate was 21.70% (95% ci: 12.39-32.70; i 2 =98.81%), but after omitting 3 of our included studies conducted only on deceased patients, the total mortality rate was calculated 12.29% (95% ci: 6.20-19.99; i 2 =98.29%). we also conducted a subgroup analysis to determine the mortality rate by location. as stated above, our articles were mainly from china with a mortality rate of 11.20 (95% ci: 5.36-18.75; i 2 =98.34%) and one of these was from the usa with a mortality rate of 52.38 (95% ci: 29.78-74.29). 3.6.sensitivity analysis according to the primary analysis, the prevalence of acute cardiac injury was 15.68% (95% ci: 11.1-20.97; i 2 =92.45%), but after omitting a part of the data from the wen-jun tu study and conducting sensitivity analysis (omitting outlier data) the prevalence was 13.77% (95% ci: 9.66-18.45; i 2 =91.36%) ( figure 2) . apparently, the primary analysis of aki showed a prevalence of 9.87% (95% ci: 6.18-14.25; i 2 =95.64%), and after omitting a part of the data from wen-jun tu study and conducting sensitivity analysis (removed outlier data) the prevalence was 8.40% (95% ci: 5.15-12.31; i 2 =95.22%) (figure 3 ), respectively. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 16, 2020. . figure 4 shows the beggs funnel plot of studies related to cardiac and renal injury in covid-19 patients. the interpretation of this plot showed no sign of publication bias in these studies (p=0.08); this result implies that reports have been published with both positive and negative results ( figure 4 ). from last days of 2019, a novel coronavirus outbreak has emerged, which has been further named coronavirus disease 2019 (covid19) , and has been spreading around the world since then (10) . the city of wuhan in china was the first infected area and the starting point of this pandemic (11) . covid-19 is highly transmittable and has a great ability to cause to the cluster of cases (12, 13) . to date, no definite treatment has been discovered for covid-19. current recommendations regarding this disease include preventive measures to reduce the risk of infection (14, 15) . unfortunately, in severe cases of covid-19, the disease can lead to acute respiratory distress syndrome (ards), which is one of the deadliest complications of covid-19 and can contribute to death. according to tian et al (16) , the prevalence of severe and mild outcomes were 18% of severe cases, while other 82% were common cases (including: including mild cases (73.3%), nonpneumonia cases (4.2%) and asymptomatic cases (5.0%), respectively). our meta-analysis is conducted on data extracted from 30 published studies. these studies collected data from laboratory-confirmed covid-19 patients and were mainly conducted in chinese hospitals. according to previous reports during sars-cov and mers-cov outbreaks, these corona viruses have been seen to affect males more than females (17, 18) . and also regarding covid-19, yang et al revealed that males are at greater risk than females (19) . our results also confirm these literatures; sars-cov-2 has a higher risk in men (54.72% (95% ci: 52.04-57.39; i 2 =74.33%)) compared to women (45.29% (95% ci: 42.61-47.99; i 2 =74.56%)). this difference could be the result of stronger innate immune responses in women (20) , more harmful lifestyle habits (such as smoking) in men (21) and also greater exposure to occupational hazards in men (e.g. hunan wet market in china) (22) . according to the age-based analysis, the mean age of subjects were 57.64, which is close to the number reported in previous studies (23) . elderly patients have indeed been shown to be at greater risk of more serious complications and further death, which may be related to higher prevalence of comorbidities between elderlies (24) or their weakened immune system (21) . we also extracted data about most frequent symptoms of covid-19. according to our analysis, fever 84.30% (95% ci: 77.13-90.37; i 2 =97.74%), cough 63.01% (95% ci: 57.63-68.23; i 2 =93.73%), dyspnea 37.16% (95% ci: 27.31-47.57%; i 2 =98.32%), fatigue 34.22% (95% ci: 26.29-42.62; i 2 =97.29%) and diarrhea 11.47% (95% ci: 6.96-16.87; i 2 =95.58%) are the most prevalent symptoms of covid-19, respectively. these result are almost similar to previous reports (19, 23) . as we looked at the included studies, we realized that the most reported complication was ards; that its prevalence was 33.15% (95% ci: 23.35-43.73; i 2 =98.56%). ards occurs as a result of the accumulation of fluids in alveoli, and this fluid prevents the lungs from receiving enough air. the cause of this phenomenon is the leakage of fluid from capillaries into alveoli, due to damage of their walls (25). this high prevalence of ards is justifiable due to the large pneumonia caused by this virus. from other non-respiratory outcomes, acute cardiac injury and aki have been the most reported. acute myocardial injury and its complications were observed in 9.5% of all terminally ill covid-19 patients in italy (until 13 april 2020) (26) . according to our analyses, the prevalence of acute cardiac injury was 13.77% (95% ci: 9.66% to 18.45%; i 2 =91.36%). this complication has signs and symptoms similar to covid-19 respiratory complications and may develop at any stage of this disease. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 16, 2020. . acute myocardial injuries in patients with covid-19 include arrhythmias, heart failure, cardiac arrest, acute coronary syndromes, cardiomyopathy, myocarditis, cardiogenic shock, pericarditis and pericardial effusion (27). in our analysis, the prevalence of arrhythmia 16.64% (95% ci: 9.34-25.5; i 2 =92.29%) and heart failure 11.50% (95% ci: 3.45-22.83; i 2 =89.48%) were assessed as well, but due to insufficiency of number of articles and lack of enough data, they actually may overestimate the real numbers. symptoms related to acute cardiac injury are dyspnea, severe fatigue, chest pain and palpitation. markers that can help diagnose an acute myocardial injury are high sensitivity troponin i (hs-ctni) or t (hs-ctnt) and nt-probnp. performing an electrocardiogram (ecg) can also be helpful (ecg changes show myocardial ischaemia). troponin level also has diagnostic value, as inflammatory responses of heart to severe illness can lead to elevated troponin levels (27). the prevalence of aki was 8.40% (95% ci: 5.15-12.31; i 2 =95.22%). aki is described as a sudden failure in kidney function, which includes both structural damage (injury) and loss of function (failure). markers that can help diagnose aki are serum creatinine (scr) and/or urine output (uo) (28) . as stated before, the main focus of this study is to determine the most frequent respiratory and non-respiratory complications in covid-19 patients, which can help find the causes of worst outcomes and death in these patients. on march 3, 2020, the mortality rate of covid-19 was reported by 3.4% by world health organization (who) (29) . while according to our analysis, the mortality rate was 12.29% (95% ci: 6.20-19.99; i 2 =98.29%) (this number was calculated after omitting the studies that included only deceased patients). it should be noted that most of our included articles were conducted on severe cases, so this higher mortality rate is reasonable. we also performed a subgroup analysis to determine the mortality rate based on the location, which the results was 11.20% (95% ci: 5.36-18.75; i 2 =98.34%) in china and 52.38% (95% ci: 29.78-74.29) in the usa. these results have also overestimated the mortality rate of patients with covid-19, both due to the inclusion of predominantly severe cases and the lack of sufficient studies with useful data. since no systematic review and meta-analysis on the non-respiratory outcomes of covid-19 have yet been published, we look forward this article having useful results for the medical society. covid-19 infection has a high morbidity rate especially in elderly patients. these severe patients require supportive medical care, which can place a huge burden on nations. there are several complications that can put patients in critical conditions. the most frequent clinical outcome of covid-19 is respiratory complications, in particular ards. there are also some non-respiratory outcomes in covid-19 patients. although these outcomes are less common than respiratory outcomes, they can have fatal effects on patients. two of the most non-respiratory complications in covid-19 patients are acute cardiac injury and aki. knowing this information gives clinicians a brighter insight to what they are fighting against. since these data are updating day by day, further evaluation of these clinical outcomes is recommended. the authors are grateful to shahid beheshti university of medical sciences, tehran, ir iran for their collaborative efforts. none. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 16, 2020. . all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 16, 2020. . (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 16, 2020. . (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 16, 2020. . https://doi.org/10.1101/2020.06.14.20130955 doi: medrxiv preprint who. who announces covid-19 outbreak a pandemic 2020 hypertension, the renin-angiotensin system, and the risk of lower respiratory tract infections and lung injury: implications for covid-19european society of hypertension covid-19 task force review of evidence who. coronavirus disease (covid-19) situation report -112 2020 clinical characteristics of coronavirus disease 2019 in china angiotensin-converting enzyme 2 protects from severe acute lung failure association of cardiac injury with mortality in hospitalized patients with covid-19 in wuhan, china covid-19, ace2 and the cardiovascular consequences transformations related to the angular and the square root the prisma statement for reporting systematic reviews 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with covid-19: evidence from front-line clinical observation in wuhan in-hospital cardiac arrest outcomes among patients with covid-19 pneumonia in wuhan, china. resuscitation clinicolaboratory study of 25 fatal cases of covid-19 in wuhan analysis of 92 deceased patients with covid-19 retrospective study of risk factors for severe sars-cov-2 infections in hospitalized adult patients. polish archives of internal medicine key: cord-295386-voeptwrw authors: liu, j.; huang, t.; xiong, h.; huang, j.; zhou, j.; jiang, h.; yang, g.; wang, h.; dou, d. title: analysis of collective response reveals that covid-19-related activities start from the end of 2019 in mainland china date: 2020-10-16 journal: nan doi: 10.1101/2020.10.14.20202531 sha: doc_id: 295386 cord_uid: voeptwrw while the covid-19 outbreak is making an impact at a global scale, the collective response to the pandemic becomes the key to analyzing past situations, evaluating current measures, and formulating future predictions. in this paper, we analyze the public reactions to the pandemic using search engine data and mobility data from baidu search and baidu maps respectively, where we particularly pay attentions to the early stage of pandemics and find early signals from the collective response to covid-19. first, we correlate the number of confirmed cases per day to daily search queries of a large number of keywords through dynamic time warping (dtw) and detrended cross-correlation analysis (dcca), where the keywords top in the most critical days are believed the most relevant to the pandemic. we then categorize the ranking lists of keywords according to the specific regions of the search, such as wuhan, mainland china, the usa, and the whole world. through the analysis on search, we succeed in identifying covid-19 related collective response would not be earlier than the end of 2019 in mainland china. finally, we confirm this observation again using human mobility data, where we specifically compare the massive mobility traces, including the real-time population densities inside key hospitals and inter-city travels departing from/arriving in wuhan, from 2018 to 2020. no significant changes have been witnessed before december, 2019. as reported by the world health organization (who), a global pandemic, covid-19, has rapidly spread all over the world since december, 2019, e.g., within china (1), the united states (2), european countries (3), etc. the covid-19 pandemic is considered as the greatest challenge for humankind since world war ii (4) . the outbreak of covid-19 has been closely monitored by governments, researchers, and digital tracing applications (5, 6) . as early as january 2, 2020 research (7) has confirmed huanan seafood market in wuhan was epidemiologically associated with most (27 of 44) of the patients from mainland china, the starting point of the collective response to the covid-19 pandemic however remains unclear (8) . to analyze the collective response to covid-19, digital information turns out to be critical, efficient, and effective (6) . for example, mobile phone applications (apps) can be easily used to conduct contact tracing and notification upon case confirmation (6) . with data collected from the mobile phone apps, statistical analysis has been carried out for covid-19-related studies (9) (10) (11) , e.g., baidu migration (12) . further, search engines, e.g., baidu (13) , has been used to understand social responses to the pandemic from the keywords of massive search queries while making users well-informed during the outbreak of covid-19. in addition, mobility data from baidu maps also demonstrates the collective response from the perspective of mobility (14, 15) , where we can compare the massive mobility traces under the pandemic with the regular patterns 2 of determining the starting moment of covid-19, (9) (10) (11) infer the possible origin dates of covid-19 using dynamical systems and the numbers of cases confirmed over time. compared to these studies, our work revisits the early stage of the pandemic from the perspective collective response, using search data and mobility data collected from massive mobile users in a participatory fashion. to uncover the latent factors of epidemiological dynamics, (7, (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) fit parameterized models with the numbers of cases confirmed over time, and interpret the models through the physical and epidemiological meaning of every parameter. compared to these studies, our work does not make any assumptions on the epidemiological dynamics while providing a model-free analysis on the search and mobility data. instead, we simply track the collective response through ranking the frequent search keywords and detecting the changes in population inflow/outflow between chinese cities, in a data-driven fashion. finally, this work incorporates direct evidences through multi-modal data fusion, while existing studies (33) rely on inferences and predictions based on indirect measurements. for example, (33) estimated and compared the volumes of visits to hospitals in wuhan in 2018 and 2019 using remote sensing data from satellites, then claimed abnormalities detected. we directly sample the volumes of visits to hospitals in wuhan from 2018 to 2020 through tracking the massive mobility traces collected from baidu maps , and confirm that there was no abnormality of hospital visit volumes before december, 2019 in wuhan. using search index data, we analyze correlations between the frequent search keywords, related to respiratory diseases, per day and the trends of confirmed cases using dtw and dcca. as both search index data and the number of confirmed cases are time-series data, i.e., each data item associated with a time stamp, we use dtw and dcca as analytical tools. dtw is introduced to adjust the time stamps and to match sequences that are similar but out of phase (35) . dcca is based on detrended covariance to investigate power-law cross-correlations between different simultaneously recorded time-series (30) . both dtw and dcca can analyze the time-series data. for every keyword, we estimate the correlation using dtw and dcca between the everyday search index of the keyword and the number of confirmed cases per day during the pandemic, where we believe the top keywords with highest correlations refer to the most relevant evidences and the correlations estimated by dtw and dcca confirm each other. we rank the keywords in four regions, i.e., wuhan, mainland china, the us, and the world, separately, where the common top five keywords are: • "covid," "epidemic situation," "mask," "pneumonia," and "sterilization" (based on dtw); • "covid," "epidemic situation," "mask," "sterilization," and 'nucleic acid" (based on dcca). in addition, we find that covid-19 relative symptoms (33), such as "diarrhea" (16 th ) and 5 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint "cough" (20 th ), are included within the top keywords to analyze the early stage of the covid-19 epidemic, we study the correlation of the search index of the high-ranked keywords between any two of the four regions (wuhan, china, the us, and the world), using dcca for each year between 2014 and 2020. we take "mask," as an example, as "mask" is high-ranked in all the four regions. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint the correlations between wuhan and the world, wuhan and the us, the world and china, and the us and china have significantly changed and have dropped to negative in 2020, while the overall trends of search index dramatically increased in the same time, compared with other years. it demonstrates the happening of massive events (i.e., which changes the common trends of search at global scale. interestingly, prior to covid-19, we found a short term in 2015 with negative correlations between wuhan and the world, wuhan and the us, the world and china, and the us and china. in that year, an outbreak of middle east respiratory syndrome (mers) was found in korea (36) and influenced several asian countries. similar patterns repeat in the status quo of 2020. from search volumes shown in figure 1b , we find that the search volumes in wuhan or china before november, 2019 were still relatively lower than those in the us or the world. this result indicates that there was no special mask-related epidemic in wuhan or china before november, 2019. in addition, we also find that the search volume of "mask" increased from december, 2019 and reached its peak in january, 2020 in wuhan and china. after great efforts were put into inhibiting the spread of covid-19, the pandemic was mostly under control in china after may, 2020. however, on june 11th, the first case related to xinfadi market in beijing was found, which led to a second wave of pandemic in beijing. this second wave of epidemic persisted for more than a month, and was contained around the end of july. with previous experience in tackling covid-19, this second wave was met with a swift response, not only in news reportage but also in measure implementation. we investigate how the public reacted to this resurgence of covid-19 throughout this entire period by searching frequencies of keywords, and find that beijing's case is consistent with the previous national scenario. from the analysis, we can see that the general public in beijing exhibited a high level of attention to the overall event as the search volume of a majority of keywords, e.g., "nucleic acid," "epidemic," "mask," "sore throat," and "fever," surges significantly following the outbreak on june 11th, where the search index of "nucleic acid" shown in figure 2 is an example. however, a few words, e.g., "stuffy nose," "respiratory failure," and "respiratory distress," which are mostly related to critically ill patients, did not show a noticeable change in search, which is in accordance with the fact that although the outbreak aroused concerns at first, quick containment actions prevented the outbreak from resulting in a huge number of significantly ill patients. until july, the search trends fell back into the previous levels as normalized in earlier months, since the epidemic was fully under control after mid-july. in this section, we try to find abnormal population mobility trends from june, 2018 to march, 2020, exploring the starting point of the collective response to covid-19. we exploit the 8 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint mobility data from baidu maps, which consists of the inflow and outflow to/from wuhan, and the population densities of multiple hospitals in wuhan, from june, 2018 to march, 2020. representing inflow refers to the number of people who entered into the city on that specific date, and correspondingly, each outflow data point refers to the number of people who left the city on that date. we separate inflow and outflow into distinct diagrams in order to demonstrate a sharper focus on time scale comparison. in addition, all absolute values of the mobility data 9 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . figure 4 : the population outflow from wuhan (2018 -2020). the inflow of 2019 is between january 1st and december 31st. the inflow of 2018 is between june 1st and december 31st, which is aligned with that of 2019 using the solar calendar. the inflow of 2020 is between december 22nd, 2019 to march 31st, 2020, which is aligned with that of 2019 using the lunar calendar. 10 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint were standardized to shed light on a more structured inference on an equal baseline across different times. for a few dates with missing data, we utilize the data from a previous date as an estimation. as shown in figure 3 , we find that the collective mobility related response to the pandemic has happened around january 24th (spring festival), 2020. for inflow data shown in figure 3 , we align inflow traces from january 1st, 2018 to december 31st, 2018 along with january yet, the overall trend is steady, without significant stumbling. the line representing inflow of 2020 contains the inflows from december 22nd, 2019 to march, 2020. note that in figure 3 , we align the yearly traces according to the lunar calendar for better comparison. we can see both peaks happened around spring festival due to the national holidays. it is after spring festival that we witness a significant decline in inflow approaching a standardized score of -2, as the pandemic began and china announced travel restrictions. from the population inflow traces, we conclude that there is no obvious abnormal trend before spring festival in wuhan compared to previous year's data, which implies our finding. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint as shown in figure 4 , with the analysis of outflow, we also find that the collective mobility related response to the pandemic has happened around spring festival. in figure 4 , two lines of 2018 and 2019 exhibit a high level of superposition, with peaks around national holidays similar to scenarios in inflow diagrams. zooming in for the latter part of 2019, the outflows from october to december maintain a paralleling trend, indicating no aberrant leaving or public panic. the increasing slopes of the outflow are similar in 2019 and 2020, as wuhan is a city with abundant migrant workers. yet, we can see some abnormal humps in the outflow at january 11th, 2020, where outflow is obviously above the previous year's level, probably suggesting an onset of covid-19 and more people leaving the city to avoid it. it is after spring festival that we witness a significant decline in outflow, approaching a standardized score approximating -2, implying that the start of the collective response to the pandemic is likely to have happened around spring festival. finally, the combination of the analysis of inflow and outflow further confirms that the collective mobility related response to the pandemic have happened three days before spring festival, i.e., january 21st, 2020. for speculating a point as a start of the collective response to the pandemic, we need to find abnormal trends with high outflow and low inflow. if people were aware of abnormal events, people within the city would want to leave and people outside of city would not want to enter. yet, we do not note any significant declining trend in inflow nor rising trend in outflow during the second half of the year in 2019. we find an abnormal peak of outflow around january 11th, 2020, and a higher increase in outflow than the previous year, peaking around january 21st, 2020. reflected within the data, we also see a highly efficient government measure implementation, as both inflow and outflow tumbled after travel restrictions (from/to wuhan) announced on january 23rd, 2020, hitting an unprecedented level of almost -2, and this low level persisted afterwards. 12 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint as well, the analysis of the population in the hospitals of wuhan suggests that the collective response did not start before the end of 2019. by concentrating on the figures of hospitals, 13 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint we align the data based on years. it was suspected that covid-19 infections had begun at the second half of the year (33), so we mainly focus on the latter part of this timeline. the two lines of 2018 and 2019 were matched in similar trends. generally, we see a nearly parallel shape from june to mid-september. it is after mid-september that we see a discernable climbing trend of population visiting hospitals, and the higher level persists as a plateau shape until the end of search index is an important indicator for monitoring the outbreak of a pandemic. in this work, we analyzed the correlation of search index corresponding to covid-19-related keywords. we first ranked the keywords based on the correlation of the search index and the number of confirmed cases of covid-19. we found that "mask," "cough," and "diarrhea" are within the 28 highly ranked keywords but not within the top rankings among all. then, we analyzed the correlation between any two regions among the four regions (wuhan, mainland china, the us, and the world). we found that the correlations and the search index did not change much (because of covid-19) before december, 2019, in wuhan or in mainland china. we thus argue that the collective activities start from december, 2019 in mainland china. 14 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint furthermore, we analyzed the mobility data of wuhan and the population in 26 hospitals of wuhan to confirm our claim. by comparing the trends in the second half of 2019 with that of 2018, we did not find abnormal deviations from the previous year, indicating that the start of the collective response to the pandemic occurred after december, 2019. additionally, the increasing outflow and decreasing inflow, which signaled the pandemic, was not observed in the data of baidu migration in wuhan in the second half of 2019, further supporting the claim. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint in this section, we present the details on data normalization, correlation analysis of other keywords, and some other details. to visualize the search index data of keywords in different regions in a single figure, we plotted figures using normalized data. in figures 1, s1 , s2, s3, s4, s5, s6,s7, s8, s9, s10, s11, s14 and s15, we visualized the search index data of different keywords in four regions, i.e., wuhan, china, the us, and the world. given the search index of a keyword in a region from january, 2014 to june, 2020, we normalized the data using z-score standardization. given the overall volumes of the search volume in a region from january, 2014 to june, 2020, we first calculated the mean value and the standard derivation value of the search index as µ and σ respectively. then we normalized the search index in each region as in this way, the search index of each keyword in the study is normalized to almost the same scale, which fits into the same figure. similarly, data normalization was also applied when we calculated the inflow, outflow and the population in the hospitals of wuhan from june, 2018 to march, 2020. in this section, we present the detailed ranking results using dtw and dcca. table s1 represents the ranking of the top 28 keywords in wuhan using dtw and dcca. from the table, we can see that the common highly (top 10) ranked keywords are "covid," "epidemic situation," "nucleic acid," "pneumonia," "sterilization," and "infection" based on dtw and dcca. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint in addition, "mask" is highly ranked (4 th ) using dtw. table s2 represents the ranking of the top 28 keywords in china using dtw and dcca. the common highly ranked keywords are "covid," "nucleic acid," "runny nose," "sterilization," and "hypoxemia" based on dtw and dcca. in addition, "mask" is also highly ranked using dtw (8 th ) and dcca (12 th ). table s3 demonstrates the ranking of the top 28 keywords in the us using dtw and dcca. the common highly ranked keywords are "covid," "mask," "sterilization," "body temperature," and "epidemic" based on dtw and dcca. "mask" is also highly ranked using both dtw (2 nd ) and dcca (1 st ). table s4 demonstrates the ranking of the top 28 keywords all over the world, using dtw and dcca. the common highly ranked keywords are "covid," "mask," "sterilization," "body temperature," "epidemic situation," "respiratory distress," and "respiratory failure" based on dtw and dcca. "mask" is highly ranked using both dtw (2 nd ) and dcca (2 nd ). in this section, we present the correlation analysis on "mask," "cough," and "diarrhea". "cough" and "diarrhea" are considered as key symptoms for covid-19 in (33) . the search volumes of "mask" in four regions are shown in figures s1 and s2 . similar to "mask," as shown in figure s3 , we can see that the correlations were positive and did not change much between 2014 and 2019. in 2015, the correlations became less significant, which may also have been caused by the outbreak of middle east respiratory syndrome (mers), as "cough" is one of the most important symptoms (36) . however, the correlations have changed to be negative in 2020. in addition, the search index also significantly increased in 20 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint compared with the us and the world. this is due to the fact that early confirmed cases were found in december, 2019 (3, 37). all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. figure s4 : comparison of the search volume of "cough" between two regions in 2019 with normalized data. the correlation analysis of "diarrhea" is shown in figure s6 , to analyze the decrease of the correlation from 2019, we zoom in on 2019 and 2020. figure s7 shows that the search volumes actually decreased in wuhan or china from june, 2019 to november, 2019. this result indicates that there was no evidence to support the outbreak of diarrhea-related epidemic in wuhan or china before december, 2019. in addition, figure s8 shows that the search volume of "diarrhea" increased from december, 2019 and reached its peak 23 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. figure s7 : comparison of the search volume of "diarrhea" between two regions in 2019 with normalized data. in january, 2020 in wuhan and in february, 2020 in china. similar to the "cough," the search volumes of "diarrhea" spiked in wuhan and china in december, 2019 compared to the us and the world. this is also due to the fact that early confirmed cases were found in december, 2019 (3, 37) . in figures s9, s10 , and s11, we visualize correlations using (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint 27 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint we examined the correlations of search trends between every pairs of the four geographical regions, i.e., china, wuhan, the us, and the world, using spearman's rank correlation (38) . with the correlation coefficients, we apply the hypothesis test of the "significance of the correlation coefficient" to decide whether the correlation between two search trends is significant or not. we use the significant level of 0.05, which is α = 0.05. thus, we consider the correlation with p-value less than 0.05 as "significantly correlated"; otherwise, the correlation is considered "insignificant." by summing up the number of queries with significant correlated trends, an indicator for overall correlation of epidemic-relation search queries between two regions can be drawn. to clearly identify the changing trends from 2014 to 2020, we separate the data into 7 subsets according to the corresponding year. figure s12 shows the yearly trends for the number of significant queries between two of the four examined regions. except for 2020, during which the number of queries with significant correlated trends between world and usa decreases to (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint wuhan are significantly correlated. this concurs with the fact that national attention has been highly focused on covid-19 during the first five months of 2020. the analysis results indicate that the collective response to the covid-19 pandemic exists in 2020. for over 30 search queries related to the covid-19 pandemic, we analyze the daily search index trend in beijing from march 1st, 2020 to july 20th, 2020 for each keyword, as beijing was in the center of the epidemic. from the analysis, we are able to categorize them into two 29 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. main categories, one group that has an abnormal rise in accordance with the pandemic shown in figure s14 , and another that has a relatively mild reaction shown in figure s15 . some representative queries that belong to the first category include "nucleic acid," "epidemic," "mask," "sore throat," "fever," "fatigue," "pneumonia," "diarrhea," "coronavirus," "xinguan (stands for covid)," "patient," and "body temperature." these words are mostly in high rankings in our previous correlation analysis, indicating consistency and effectiveness of analytical tools above. let us take the word "epidemic" as an example. the searching trend of this word underwent stable declination throughout the period until the start of june, with the highest point between (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint engaged in testing and containment measures in relevant locations in beijing. the entire set of abnormal trends fits perfectly with the developing situation of the second wave of the pandemic, indicating the close-knit relationship between search trends and epidemic circumstances and the effectiveness of using search volume data as tools for exploring public reactions. other search queries, such as "fever" and "nucleic acid," show very similar patterns, with either parallel trend or decreasing trend over the past few months, and an obvious, exceptional, sudden rise starting at around june 10th or june 11th. one intriguing factor is that the keyword "diarrhea" is also in category one, with a significant high peak from june 10th to june 19th. however, "diarrhea" ranked relatively low in previous dcca and dtw rankings, meaning that it's not considered very pertinent to the virus by the general public. yet, its search trend's acute rise in the second wave of the epidemic differs from previous search trend changes in the first national wave. one reason may be that the epidemic center of beijing is in xinfadi, one of the most important food markets in that region, so people in beijing may have become more concerned with food safety and food-related searches. similar patterns of abnormal increase also applied to other common symptom words such as "fatigue" and "fever," with their tremendous pump-ups in search volumes matching exactly with the period of the second wave of the pandemic in a range of approximately 15 days after the first announcement of the news, on june 11th, 2020. furthermore, there are certain words that do not show abnormal patterns as discussed above, with no significantly abrupt increase in their overall trend from march to july 2020. for instance, the keyword "stuffy nose" has a searching trend with a peak in around the second half of march, following by a parallel trend throughout the period with normal daily fluctuations in a stable range. although the peak at the week of june 11th, signaling the start of the second wave of the pandemic, was mildly wider than other fluctuations, it only showed a slightly higher search volume and a quick fall back to normal levels. it is hard to perceive significant traces of the second wave of the epidemic from the diagram directly. in similar fashion, search queries 33 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint such as "respiratory failure" and "respiratory distress" display no significant deviation from the general trend since march, with no especially peculiar shape of fluctuations. although these words are considered relevant to covid-19, these symptoms are more related to severely ill patients. consequently, it is reasonable to see no significant change in these keywords, since beijing has had only a few critically ill patients, compared to the first national wave of the pandemic, resulting in many fewer people searching for these symptoms of serious illness. other keywords, including "respiratory symptom," "dehydration," and "affection" also show no obvious change in search volume trend during this second epidemic in beijing. one crucial search query, "cough," also displays less significant change in trend compared to other keywords. upon closer examination, there is a hump from early june to the end of june, with the highest peak on june 11th. yet most peaks around the period from june 11th to july 20th are still at equivalent levels, compared to the high points in april and may, and thus the second wave of beijing epidemic outbreak did not cause a tremendous increase in search volume for "cough." among keywords, "cough" is also abnormal. it varies from other search trend changes. in the first national wave of the epidemic, its ranking is very high by dcca and dtw rankings; but in the second wave, the public did not show a strong reaction by searching significantly more frequently for "cough." comprehensive reasons are still under investigation, but it may be due to the fact that the confirmed case number is not very high, due to the efficient measures to contain the spread. another possibility to consider is that public education had already covered early on that coughs could be a symptom, while the knowledge that other symptoms, such as diarrhea, could derive from the new novel coronavirus emerged later. in fact, our techniques lend credence to the notion that looking proactively at what diagnostic terms are being searched for could potentially help identify symptoms that are not already known to be part of the pandemic. notwithstanding this word, most other words show strong consistency with our previous analysis, as search queries with ranking higher than the 15 th place are mostly in category one. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint in this section, we present the figures of population data in shelter (fangcang) hospitals (39) and huanan seafood market. we calculate the total population of shelter hospitals and the population of huanan seafood market. as shown in figure s16 , the figure of shelter hospitals exhibits highly similar patterns with the figure of hospitals described in the section, analysis of population densities in hospitals of wuhan. after areas were used to build shelter hospitals, steps to close off and manage ingress and egress were implemented, meaning that strict restrictions on people entering and leaving were enacted; thus, the population data fell off enormously. there is no significantly aberrant deviation of trend in population data of late 2019 in reference to data of late 2018. this conclusion also applies to patterns of population densities in huanan seafood market as shown in figure s17 , as there is no abnormal deviation from paths in the previous year. consequently, the latter part of 2019 did not witness any aberrant signal that could link to the collective response to the covid-19 pandemic. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint figure s16 : population data of shelter hospitals in wuhan. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . asthenia ncov 40 all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint figure s17 : population data of seafood markets in wuhan. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted october 16, 2020. . https://doi.org/10.1101/2020.10.14.20202531 doi: medrxiv preprint greatest test since world war two, says un chief acm sigkdd international conference on knowledge discovery & data mining acm sigkdd international conference on knowledge discovery and data mining covid-19 statistics encyclopedia of biostatistics key: cord-283048-hyjzofps authors: steele, edward j.; qu, jiangwen; gorczynski, reginald m.; lindley, robyn a.; tokoro, gensuke; temple, robert; wickramasinghe, n. chandra title: origin of new emergent coronavirus and candida fungal diseases—terrestrial or cosmic? date: 2020-07-14 journal: adv genet doi: 10.1016/bs.adgen.2020.04.002 sha: doc_id: 283048 cord_uid: hyjzofps the origins and global spread of two recent, yet quite different, pandemic diseases is discussed and reviewed in depth: candida auris, a eukaryotic fungal disease, and covid-19 (sars-cov-2), a positive strand rna viral respiratory disease. both these diseases display highly distinctive patterns of sudden emergence and global spread, which are not easy to understand by conventional epidemiological analysis based on simple infection-driven humanto-human spread of an infectious disease (assumed to jump suddenly and thus genetically, from an animal reservoir). both these enigmatic diseases make sense however under a panspermia in-fall model and the evidence consistent with such a model is critically reviewed. in the past 40 years there have been a number of suddenly emerging epidemic viral diseases. many were self-limiting and "went away" or "disappeared" almost as quickly as they appeared (sars, mers, zikav). the origins in all cases were a mystery, and very controversial. others such as the far more deadly hiv retrovirus has finally succumbed to highly effective antiretroviral therapy (haart) making life bearable for infected hiv+ people. however it has integrated into the human germline in many cases and is likely to be a permanent "endogenized retroviral signature" in the human germline, joining the many thousands of other hervs, human endogenous retrovirus sequences that litter the human genome as fragments or potentially active retroviruses (wickramasinghe, 2012; wickramasinghe & steele, 2016) . however the great exemplar of the emergence of a new pandemic disease of considerable virulence and pathogenicity was the spanish flu pandemic 1918-1919. that pandemic has been analyzed in great detail by hoyle and wickramasinghe (1979) , and the astute and engaged reader of all that evidence is left with only one conclusion-the spanish flu disease came from space on a massive scale, and killed tens of millions before the advent of air travel. we do not intend here to discuss these earlier epidemics and pandemicswhich have been covered in previous papers (some cited here). we focus our analysis on the actual origins of two recently emergent epidemics: a fungal disease caused by candida auris and the current coronavirus "common coldtype" epidemic caused by the covid-19 virus. these two epidemics display distinctive features and clear evidence that they may have come from a space in-fall of infectious viruses and micro-organisms in cometary dust or meteorite-derived dust particles. candida species are well-known yeasts that can cause a variety of cutaneous and invasive infections; however, they had never been considered a serious global health threat until the recent emergence of candida auris. this was first reported in the ear canal of a patient in japan in 2009. since then, cases have been recorded on all continents except antarctica (rhodes & fisher, 2019) . it can cause a variety of invasive infections with a mortality rate of up to 60%, typically infecting susceptible hosts, namely those with long hospitalizations, many illnesses and impaired immunity (bradley, 2019) . in addition, it can be resistant to multiple antifungals and has the capacity to cause outbreaks within healthcare facilities (chow et al., 2018) . its ability to colonize and persist for a long time on human skin, tolerate some disinfectants that are commonly used in healthcare settings, and to survive on inanimate surfaces for many weeks, all contribute to its effectiveness as an outbreak agent ( jackson et al., 2019) . even more remarkable though is its emergence. an analysis of whole genomic sequencing from 54 isolates of c. auris from four regions around the world revealed four major clades or genetically distinct populations. this finding supports the hypothesis of the nearly simultaneous and independent emergence of these clades in geographically separate human populations the sentry antifungal surveillance program is a global system that has continued for 20 years (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005) (2006) (2007) (2008) (2009) (2010) (2011) (2012) (2013) (2014) (2015) (2016) . it collects consecutive invasive candida isolates from medical centers located in four regions during each calendar year, namely: north america, europe, latin america, and the asia-pacific (pfaller, diekema, turnidge, castanheira, & jones, 2019) . despite going back to 1997, the sentry data did not identify c. auris until 2009 ( jackson et al., 2019) . in fact, the earliest c. auris isolates were found in south korea in 1996 and japan in 1997 . although it is a candida species, c. auris is quite distinct from its candidal relatives. the genus consists of > 500 species, many of which greatly differ from each other. c. auris comes from the clavispora clade of the metschnikowiaceae family. it has not been identified from any natural environments ( jackson et al., 2019) . it is relatively thermotolerant in that it can grow at temperatures as high as 42°c. such thermotolerance could potentially allow it to infect avian hosts (chatterjee et al., 2015) . thus, infections caused by the fungus candida spp. have been recognized for many years. however, of interest here is the abrupt emergence of a new strain candida auris which presents a profound puzzle (lockhart et al., 2017) . this new strain which is multi-drug resistant has emerged as a major cause of mortality and is posing a serious challenge for health officials the world over (chowdhary, sharma, & meis, 2017; cortegiani et al., 2018; jeffery-smith et al., 2018; lockhart et al., 2017) . while candida auris was reported for the first time in japan in 2009 it appears to have been isolated more or less simultaneously in many widely separated locations across the world. phylogenetic analysis by lockhart et al. (2017) has identified four distinct clades separated by tens of thousands of single nucleotide polymorphisms (snps) each of which is geographically localized. a large number of snps have been discovered in isolates that were recovered from four widely separated locations (south asia, east asia, south america, and south africa). whole genome sequencing of these isolates has revealed an exceedingly low genetic diversity within individual regions even across the largest clade involving some 36 isolates from as wide a field as india and pakistan. the conclusion by lockhart et al. (2017) is that c. auris must have arisen almost simultaneously in multiple four different global locations. further, from isolates of candida from four continents lockhart et al. (2017) did not find c. auris before 2009 confirming that this pathogen was not simply misidentified previously. while there have been claims that earlier isolates of candida species may also have been candida auris which were incorrectly identified, these assertions have not been confirmed. thus, it seems reasonable to conclude that a 2009 date for the origin candida auris is fairly secure (cortegiani et al., 2018) . since global cross-infection over a short timescale (<1 year) appears very unlikely one possibility is of independent multiple origins of candida auris from some widely present candida ancestor. a fungicide driver model has been advanced to explain the phenomenon. however this vague model does not fit the available data. we thus argue here that a panspermic in-fall model should be considered as a plausible and better alternative. thus, in our explanation (from all the available data) it could be concluded that c. auris first arose in 2009 from several environmentally-induced hypermutation events that occurred after in-fall from cosmic (cometary) dust clouds through which the earth had traversed sometime during or before 2009. thus this new c. auris would appear simultaneously in many widely separated places on the earth. alternatively, a genetic hybridization event may have taken place at this time involving a globally distributed set of comet-borne gene segments that were themselves genetically diverse. how could this have occurred? we critically evaluate the data from a genetic point of view. the data demands that there are at least four preexisting clades (!10,000 snp differences) in an external non-terrestrial source (cometary dust tails) and these came down separately in separate regions and thereafter spread clonally (lockhart et al., 2017) . the other alternative is to consider the existence of a single "mother" or "parent" c. auris clade in the cometary dust source, which upon landing and infection of susceptible hosts is induced into a hypermutation-adaptation sequence via a fast, essentially lamarckian, adaptive mutation strategy (rosenberg, 2001; chapter "the efficient lamarckian spread of life in the cosmos" by steele et al.) thereby generating in excess of 10,000 new snp differences from the parent orbiting cosmic strain. the final step that can be envisaged is the dispersal of a successful adaptive variant in a particular region to other hospitals in that region. thus on the basis of a panspermic model there are two possible explanations for the strange and striking c. auris patterns of genome diversity. the lamarckian hypermutation strategy at each separate in-fall location (susceptible hospital patients) from a pure line "mother" strain is, on parsimony grounds, preferred. we have previously argued that a sudden emergence of new pathogenic variants of circulating viruses could be linked to cosmic events related to the well-known 11-year sunspot cycle wickramasinghe et al., 2017 wickramasinghe et al., , 2019 . the earth's magnetosphere, and the interplanetary magnetic field in its vicinity, are both modulated by the solar wind that controls the flow of charged particles onto the earth. during times of sunspot minima, a general weakening of magnetic field occurs and this would be accompanied by an increase in the flux of galactic cosmic rays (gcr's) and also of charged interstellar and interplanetary dust particles. evidence for such periodic increases linked to solar activity is evident in the high frequency of noctilucent clouds (as at present, in 2019-2020) and also in the increase of particulate deposits in polar ice cores. since the latter could, in our view, include biological entities such as bacteria, viruses and other eukaryotic microorganisms like c. auris, an increase in their incidence on the earth will therefore be expected at such times. it is interesting to note that in 2008-2009 (the solar minimum under discussion) the interplanetary magnetic field was the lowest on record since the beginning of the space age. we would therefore expect a significantly enhanced flux of both cosmic rays as well as electrically charged biological entities at this time, so the arrival of a new clade of c. auris from a space source should not be ignored. a crucial fact relating to the first appearance of candia auris in 2009 is that this time marks not merely a solar minimum but the lowest minimum of the sunspot cycle in 100 years (see figs. 1 and 2). this particular minimum was all the more remarkable because the sun was spotless (devoid of spots) for more than 70% of the time. the opportunity of the transference of both galactic cosmic rays (gcr's) and charged molecular structures (e.g., c. auris) thus remained continuously optimal over extended periods. at the present time (february 2020) as we approach a new sunspot minimum the sun continues to be exceedingly "quiet" and the expectations are that we are heading for an even deeper minimum than before. the case for epidemiological vigilance for new microbial and viral pathogens cannot be greater than at the present time. we now turn to our critical analysis of the origin of the covid-19 epidemic underway as we draft this chapter. the global extent of the emotion around this epidemic in the mainstream popular media, and even the scientific press (science magazine) is disturbing. it is without parallel in our experience in this social media internet age. however, it does approach the justified hysteria around the far more serious, and initially more lethal, hiv epidemic/pandemic that suddenly emerged 40 years ago. the actual covid-19 viral disease itself causes respiratory "common cold-like" illness in most people diagnosed with symptoms (but many potential carriers of the disease are asymptomatic). the infection can progress to severe pneumonia in elderly and already medically-compromised patients with other conditions (diabetes, coronary disease, etc.). about 2% of all covd-19 cases have died due to the pneumonia (fig. 4 ). vaccine and antivirals will not help the latter group, but standard well trusted medical care will-to help patients through the respiratory crisis of the lifethreatening pneumonia and dangerous inflammatory bronchitis symptoms. such care will allow recovery of most patients. the fact that "recoveries" far exceed "deaths" (fig. 4) indicates that timely medical care for this otherwise "common cold" respiratory illness must be the medical priority in the epicenter of the infection in wuhan and nearby regions in china. we believe this medical care is being implemented throughout china. but it is the origin of this new emergent virus disease which has raised the most angst. it is literally explosively centred on wuhan, which appears to be the epicenter. and it appeared suddenly without warning. the theory that it jumped from bats via snakes to humans is implausible (below). the same angst over viral origins was also evident when hiv, sars, mers, ebola, and zikav suddenly appeared on the scene. we will not deal with these earlier diseases as their origins, in our considered opinion, are far less clear cut than covid-19. however sorting out what is true from what is untrue is a challenge. the current distribution and case numbers as february 14, 2020 are shown in figs. 3 and 4. the epidemic is centred on the city of wuhan, in the central hubei province of china (for an update on our analyses since drafting of this chapter, see appendix c). kong. an update on the total toll of the pandemic, now approaching a global total of 9 million confirmed cases as june 22, 2020 is in appendix c. from about mid-january the chinese government ordered the complete quarantine and lock-down of wuhan and wider region around the city in hubei province, affecting 50-100 million people. abc news in australia estimates coronavirus (covid-19) has affected 500 million people in china under lock-down (updated february 15, 2020, 1:29 a.m.). a problem with all these reports is the lack of detailed information that led officials to such an extraordinary quarantine decision. we speculate later on this. at the time of writing, the case incidence of this newly discovered coronavirus is passing through 60,000 and >99.99% of all cases, almost exclusively, are chinese. from reports of cases that exited wuhan by aircraft in late january to other countries, say to australia, the disease does not spread in a sustained way easily person-to-person. but there are clearly apparent cases of person-to-person spread elsewhere (say in united kingdom and europe, box 1). but there is no doubt this disease is centred on china. the johns hopkins university covid-19 case density maps are extremely informative. these are in figs. 5-7. to put one interpretation on the striking case patterns in figs. 5-7, particularly the symmetrical pattern in fig. 7 it actually looks like a huge viral bomb explosion took place near or over wuhan and then the radial fall-out of the disease causing viral particles to land on the millions of people either laterally or from above-some of those infected would be susceptible and who then have succumbed to the respiratory illness (in appendix a, in relation to the expected fall of viruses through the stratosphere is an analysis by way of quantitative analogy, of the expectation of radioactive fall-out patterns from an atmospheric nuclear test in 1958). moreover, and paradoxically, asymptomatic patients can be efficient "spreaders" of the disease. this is contrary to normal expectations as usually the infected potential spreader would display overt and full blown disease (and the coughed-up aerosols from such a patient would be dense with viral particles). indeed, there are wide reports in the media that incubation times can range from 1 to 28 days. but once a potentially infective virus successfully navigates the innate immune response (see table 1, chapter "the efficient lamarckian spread of life in the cosmos" by steele et al.) it would be expected to rapidly multiply within cells and spread peaking in virion numbers 5-7 days later. the actual size of the infective dose is also an important variable. so these wide-range estimates of incubation time reflect, in our view, the variable depth and extent of the actual physical viral contamination in the immediate environment of a susceptible subject viz. potentially all objects in the family home environment as well as cars, bicycles, and on their bodies-hair, clothes-and other personal effects, clothes, money, keys, etc. indeed, the external box 1 summary of united kingdom cases (n.c. wickramasinghe email report to edward j. steele). • january 21, 2020 cdc confirms 1 case of transmission between person who returned from wuhan, and a person who shared accommodation in the united states. via a ski resort in the french alpine town of les contamines-montjoie, near switzerland, late last month, • january 28, 2020 a cluster linked to an alpine chalet a british man (mr. walsh) from brighton, was found to have the virus when he returned to the uk (london gatwick airport) from geneva on january 28 on an easyjet flight. a total of six people in britain, including mr. walsh, and britons in france who have the virus have been staying in two apartments in a ski chalet in the alpine resort area near mont blanc when they were visited by mr. walsh on january 24 who had attended a business conference at the grand hyatt hotel singapore, where he is believed to have contracted the virus. mr. walsh is thought to have passed the virus onto eleven confirmed cases while he was at the ski resort. but he is thought to have come into contact with scores of people after leaving singapore and no others have yet succumbed. all the supposed transmissions of the virus from mr. walsh to the others were while they occupied the chalets in france. four are from brighton and hove. they are dr. greenwood and three men, one of whom is a healthcare worker. he also passed it to one other person in the united kingdom, one person who is now in mallorca and five united kingdom nationals in france-one of which is dr. greenwood's husband bob saynor and another their 9-year-old son. none are said to be in a serious condition. so far, the places in brighton and hove being quarantined are: • county oak medical centre, where dr. catriona greenwood worked one admin day last week, and its branch surgery at deneway. • grenadier pub in hangleton, which was visited by steve walsh on february 1. • cornerstone community centre, where a yoga teacher came into contact with steve walsh on february 3. no other people have been advised to self-isolate. • easyjet flight ezs8481 to gatwick from geneva on january 28, which is believed to be the flight mr. walsh took back to the united kingdom. • bevendean primary school, where a staff member has been in close contact with someone who has been advised to self-isolate (but is not themselves diagnosed). • portslade academy, which told parents on friday one of its pupils has been advised to self-isolate for a fortnight after coming into contact with the hove father. it's believed pupils at other schools have been given the same advice. • patcham nursing home, which has closed its doors to all visitors after being visited by one of the medics now confirmed as having the virus. the cluster associated with mr. walsh could have been coinfected from a common source, with mr. walsh showing symptoms first. surface of the face mask may be the main carrier of the physical contamination. we explore the extent of viral environmental contamination further below. we now analyze all reliable genetic, epidemiological and geophysical and astrophysical data. this leads to the alternate hypothesis that covid-19 arrived via a meteorite, a presumed relatively fragile and loose carbonaceous meteorite, that struck north east china on october 11, 2019. this is at odds with the main stream expert "infectious disease" opinion of traditional person-to-person spread of an infectious endemic disease such as, for example, cholera (vibrio cholerae). we then assume the viral debris and particles then made land fall in the wuhan and related regions about a month to 6 weeks later resulting in first cases of the viral pneumonia caused by covid-19 emerging in wuhan regions late november 2019-early december 2019 (cohen, 2020; huang et al., 2020) . such an hypothesis is indeed consistent with the striking patterns shown in fig. 7 . and it makes, therefore, an extraordinary set of predictions, that we will explore at some length in our conclusions. it suggests, first, massive region-wide physical contamination with potentially trillions of infective covid-19 viral particles in central china-contaminating buildings, roadways, cars and factory equipment, vegetation, surface water pools, people (and their clothes, body parts such as hair, skin, personal affects, mobile phone, keys, wallets, etc.) as well as wild and domestic animals, etc. this would explain the actions of the chinese government who are acting to appear to be in receipt of such presumed knowledge (or information) from region-wide sampling to detect covid-19 rna sequences in swabs from physical objects, people and animals (via real time pcr). the recent paper by huang et al. (2020) and the extremely important news commentary by cohen in science (cohen, 2020) highlights many unusual aspects of the outbreak of covid-19. the evidence demonstrates that many cases of disease (about 30% of case reports) arose in locations unconnected with the wuhan seafood and meat market, and the total tally continues to increase. phylogenetic analyses of covid-19 (previously named ncov-2019) sequences show little by way of sequence variation thus indicating low mutation rates thus approximating closely to what would be expected for a pure culture, of a single infecting and replicating sequence affecting disease cases (andersen, 2020; lu et al., 2020) . these facts are now combined with the global epidemiological data, that points in the main to little or no really sustained human-to-human transmission thus far (e.g., latest reports by the australian department of health). we are aware there are apparent exceptions, e.g., the "super-spreader" from singapore, via the french alps, and then to a united kingdom gp surgery reporting mild symptoms, resulting in the gps also getting the disease (box 1). we interpret that spread by viral contamination of physical objects in the main rather than direct "cough in your face" human to human spread. in any case, current data suggest that the human-to-human spread rate is unusually low, and may be dependent on proximity and dose of virus delivered at very close quarters. the "lethality" or "death rate" from this or any other epidemic disease increases in older patients with pre-existing conditions so wider global estimates yield a death rate at 2% of infected (fig. 4) . all these basic facts now appear agreed. the initial traditional explanation of the new epidemic of covid-19 is that it jumped from bats (possibly via snakes) to humans and then spread by human-to-human infection contact mutating at a high rate. this explanation is at odds with the data at present. indeed jon cohen the respected science magazine journalist reports that the head of the huang et al. (2020) study when interviewed said: bin cao of capital medical university, the corresponding author of the lancet article and a pulmonary specialist, wrote in an email to scienceinsider that he and his co-authors "appreciate the criticism" from lucey (daniel lucey, an infectious disease specialist at georgetown university confirmed the epidemic could not possibly be caused by visits to the wuham seafood and meat market). "now it seems clear that [the] seafood market is not the only origin of the virus," he wrote. "but to be honest, we still do not know where the virus came from now." (our italics) indeed dr. bin cao speaks for all mainstream medical and epidemiological professionals around the world-no formal traditional explanation can be provided for the origins of covid-19. thus andrew rambaut, professor of molecular evolution at the university of edinburgh tweeted: "don't think any epidemiologist is still thinking that a non-human animal reservoir has had anything to do with the ncov-2019 epidemic since december. certainly the genome data doesn't support that." (reported in heidi han and kieran gair, associated press, the australian newspaper january 27, 2020.) thus, when we combine all the available facts we cannot rule out a viral in-fall event targeting the wuhan province and the wider region around it as an explanation as a first cause of the epidemic. this would fit with the admittedly heterodox view of viral pandemics first proposed by hoyle and wickramasinghe as far back as 1978 (hoyle & wickramasinghe, 1979 , 1990 wickramasinghe et al., 2019; wickramasinghe, wainwright, & narlikar, 2003) . this concept accords with the theory of cosmic biology for which growing evidence have recently been presented in the chapters of this book and in recent peer-reviewed papers where all the main extant evidence has been reviewed and is consistent with the hoyle-wickramsinghe thesis (steele et al., 2018; steele, al-mufti, et al., 2019; steele, gorczynski, et al., 2019) . our theory thus posits a sporadic input of cosmic bacteria, viruses and other micro-organisms that has the potential to interact with evolving terrestrial life forms, causing terrestrial diseases and further adaptive evolution on earth. east china, october 11, 2020 in the case of the current coronavirus epidemic in china it is interesting to note that an exceptionally bright fireball event was seen on october 11, 2019 over sonjyan city in the jilin province of ne china (see fig. 8 ). it is tempting to speculate that this event (although it happened hundreds of kilometers distant from hubei) had a crucial role to play in what is now unfolding in and throughout china. indeed, the match with the johns hopkins university case incidence patterns is so striking it is difficult to easily dismiss this as a chance correspondence of patterns, in both time and place (e.g., fig. 7) . if a fragment of a fragile and loosely held carbonaceous meteorite carrying a cargo of trillions of viruses/bacteria and other primary source cells (for the cosmic replication of the covid-19 virus), may have entered the mesosphere and stratosphere at high speed $30 km/s, its outer, loosely-held envelope carrying a biological cargo may have got dispersed in the mesosphere stratosphere and troposphere. indeed, a much larger original meteoroid could easily have been fragmenting and dispersing its contents before the ignition of the fireball event. a reasonable assumption is that the fireball which struck 2000 km n of wuhan may have been part of a wide tube of debris the bulk of which was deposited in the stratosphere to fall over wuhan. the fall time through the atmosphere of 1-10 μm-sized solid particles could range from a few months to well over a year on the basis of straightforward calculations (e.g., in the appendix of hoyle & wickramasinghe, 1979 "diseases from space"). because dispersal at ground level depends on the vagaries of meteorology and precipitation the deposition of virus at ground level is expected to be patchy in regard to both time and place. this is certainly consistent (thus far) with what has happened in relation to the new covid-19 coronavirus epidemic between november 2019 and the present day (february 15, 2020). following the initial deposition of infective particles in a small localized region (e.g., wuhan, hubei province, china) particles that have already become dispersed over a wider area in the troposphere will fall to ground in a higgledy-piggledy manner, and this process could be extended over a typical timescale of 1-2 years until an initial inoculant of the infective agent would be drained. this accords well with many new strains of viruses including influenza that have appeared in recent years (wickramasinghe et al., 2019) . the possible link of sunspots with pandemics has been discussed over many years wickramasinghe et al., 2017 wickramasinghe et al., , 2019 and is worthy of brief further discussion. the present cycle (interface between cycles 24 and 25, fig. 2 ) has seen the lowest minimum for well over a century with many sunspot free days recorded in the last months of 2019. sunspot minima are associated with a weakening of the interplanetary magnetic field near the earth, which in turn allows easy ingress of galactic cosmic rays (gcrs) and electrically charged bacteria and viruses to the earth. the mutagenic role of gcrs can cause genetic changes in already circulating viruses, but it is primarily to an enhanced flux of new infective particles released by the exploding meteoroid that we turn. indeed a perfect storm over china is paying out before our eyes, a meteorite delivering covid-19 particles corresponding with a very significant sunspot minimum cycle. it raises the important issue: how would other densely populated countries have reacted to, and handled, this event involving covid-19? it was only the vagaries of chance that it exploded over china. we conclude by noting some predictions and expectations: • we expect the pattern of further spread of the new coronavirus (covid-19) to be dictated mostly by primary in-fall until a high level of person-to-person infectivity might possibly be achieved and the virus then acquires the status of an endemic virus. • viral contamination of the "environment" in the most general sense explains most of the apparent contagion, e.g., news reports like in box 1. • thus, the possibility cannot be ruled out that the diamond princess cruise ship (and the more recent westerdam cruiseship) in the south china sea was contaminated by a fragment of the main covid-19 dust cloud. similar inexplicable events appeared to happen for ships at sea during the 1918-1919 spanish flu pandemic (hoyle & wickramasinghe, 1979) . • and, further to this, other drifting covid-19 smaller dust clouds that have not as yet made land fall may target remote island and other communities, as was also the case during the 1918-1919 spanish flu pandemic (hoyle & wickramasinghe, 1979 ). • given the low mutation rate, the very wide apparent in-fall infectivity pattern (fig. 7) the expectation is this pure viral culture has inoculated millions of chinese citizens (as well as potentially millions of wild and domestic animals in china) inducing protective adaptive immune responses (acquired herd immunity) on a very large scale. • thus, development of a so called "covid-19 vaccine" which is much in the news at the time of writing would be a waste of public tax-payer funds if mounted on the scale envisaged by governments and national centers for disease control. • we thus expect the decline of the epidemic (peaking and declining at time of writing) to be driven by this mass natural vaccination process now underway in china. so, the suddenly emerging covid-19 epidemic, like many similar suddenly emerging human epidemics in the past (sars, mers, zikav), is expected to rapidly end by the self-limiting processes of wide spread herd immunity (a pattern likely to be repeated in other countries, appendix c). • we thus expect that the incidence of serum antibodies specific for covid-19 to be wide-spread in the chinese population in the coming months. so, millions will be potentially immunized for life against future infections with covid-19. • how long will covid-19 remain potentially infective in the physical environment? clearly for some time-given that over the space of a month or so many cases appeared rapidly, spread by environmental contamination in our view, and not by traditional person-to-person generated aerosols at the height of the donor's infection. this is consistent with those news reports out of china "as the death toll rose to 80, china said, increasing concerns about the potential the virus was infectious even before symptoms were visible rapidity of its spread." (heidi han and kieran gair, associated press, the australian newspaper january 27, 2020.) as this chapter was submitted to the publisher an authoritative news despatch from japan reports sporadic outbreaks across the country with no direct link with china (appendix b). further, in early february we tried to alert the world on our interpretation of the origins of covid-19 with many of the same arguments and analyses listed in this chapter. one succinct letter was sent to the lancet, and the other was a more general article for a wider lay readership, to the australian newspaper-both articles were rejected by the editors. the archived pdfs of both articles can be found at the vixra. org site under accession numbers urls http: //vixra.org/abs/2002.0039? ref¼11076818, and https://vixra.org/abs/2002.0118 . however an expanded comments on the origin and spread of the 2019 coronavirus has now been published in wickramasinghe et al. (2020a wickramasinghe et al. ( , 2020b wickramasinghe et al. ( , 2020c , and see steele and lindley (2020) also in discussion in appendix c. we thank professor sanjaya senanayake for bringing the candida auris data to our attention and for discussions. the defining feature of infectious diseases which are caused by biological entities that arrive from space relates to the manner in which they come to be distributed over the earth's surface. if such microbial agents are introduced via the agency of cometary bolides that survive frictional heating in the mesosphere, their fragmentation and dispersal as clouds of particles in the stratosphere will determine the way in which they finally arrive at the surface of the earth. the falling speed of spherical particles of various sizes (with a notional density 1 g cm à3 ) through the atmosphere can be calculated as a function of height (y-axis) was calculated from formulae and data given by kasten (1968) . the results are shown in fig. a1 . we note from the extreme right curve of fig. a1 that a particle of radius 10 μm falls through the lowest 10 km of the stratosphere at a speed of $1 cm/s and so takes only a few days to cover what for smaller particles is the slowest part of their downward journey. all such particles fall comparatively rapidly through the mesosphere (z ¼ 80-50 km), and then more and more slowly down through the stratosphere below z ¼ 50 km. a particle with the size of a typical bacterium $1 μm, falls through the lowest 10 km of the stratosphere at a speed of about 2 â 10 à2 cm/s and thus falls to ground in a time-scale of $5 â 10 7 s, that is about 2 years. because there is more of the stratosphere through which such a particle must fall at high latitudes than in the tropics (the troposphere being higher in the tropics) the slow part of the journey is more extended the higher the latitude. a bacterium falling in $1 year in the tropics would fall in $2 years in temperate latitudes and in 2-3 years towards the poles. if a particle of the size of a typical virus, a particle say with a diameter of $0.03 μm, fell under gravity through still air the timescale for the slowest part of the journey through the bottom 10 km of the stratosphere (z ¼ 20-10 km) will be $10 9 s, that is about 30 years (see fig. a1 ). this is so slow that other means of descent involving large-scale air movements in the stratosphere have to be considered. further, the possibility of large clumps of viruses encased in cosmic dust particles will also change the relative effective sizes of infective particles and consequently their speeds of entry. we say this because … "the sophistication of viral infectivity and their modus operandi of cell-cell spreading does not end here … viral genomes … can be propagated almost indefinitely (combe, garijo, geller, cuevas, & sanjuan, 2015) as 'virion clusters' of mixtures of infective and crippled genomes with significant numbers of newly minted virus particles enwrapped in protective membrane vesicles-a type of multiunit nanoparticle. this then constitutes the actual infective dose (or unit) rather than just a single exported virion entering a nearby target cell to cause a productive infection as is commonly believed (chen et al., 2015; combe et al., 2015) ." text and references from steele et al. (2018) . thus, although in general vertical mass movements of air are feeble compared to those in the troposphere, some vertical stratospheric movement takes place despite the inhibiting effect of an inverted temperature gradient. the physical mechanism for mass stratospheric movements is the equatorto-pole temperature difference which acts as a heat engine across parallels of latitude, a heat engine that operates more strongly the larger the temperature difference-i.e., much more strongly in winter than in the summer. a similar mechanism applies also to the troposphere, where an engine crossing parallels of latitude transfers heat from tropical regions towards the poles, again more in winter than in the summer. ozone measurements can be used to trace the mass movements of air in the stratosphere. such measurements show a winter downdraft that is strongest over the latitude range 40-60 degrees. taking advantage of this annual downdraft, individual virus particles (or dust-encased clumps) incident on the atmosphere from space would therefore reach ground-level generally in temperate latitudes, which therefore emerge from these considerations as the regions of the earth where upper respiratory infections are likely to be most prevalent. this is true on the supposition that the earth is smooth, which of course it is not. the exceptionally high mountains of the himalayas on the north india-china boundary rearing up through most of the height range to the stratosphere, introduce a large perturbation to the smooth condition, which may be expected to affect adversely this particular region of the earth, particularly china. in effect the himalayan peaks, higher than 8 km, could act as a drain plug for most of the viruses incident on the atmosphere at latitude about 30 degrees n. the vast 1.4 billion population of china will thus be inundated by this drainage effect making china the quickest and worst affected region of the planet for cosmic pathogen-particle in-falls. as a consequence other parts of the earth at about 30 degrees n could fortunately be largely free of incoming viral particles, unless it happens that such particles are incident as components within larger particles. a direct proof that the winter downdraft effect in the stratosphere occurs overwhelmingly over the latitude range 40-60 degrees was demonstrated by kalkstein (1961) . in the last of the series of nuclear bombs that were tested in the atmosphere, a radioactive tracer element rh-102 was introduced into the atmosphere at a height above 100 km and the fall out of the tracer was measured month by month through airplane and balloon sampling at altitudes of $20 km. the radioactive tracer rh-102 took more than a decade to clear itself through repeated seasonal downdrafts of the kind we have described. the fall out was found to be much greater at temperate latitudes than elsewhere with the period january to march being the dominant months for the northern hemisphere. this is exactly similar to the pattern of incidence of influenza and other seasonal respiratory viral diseases in northern temperate latitudes, a situation that is well-known to every medical practitioner and health authority. in the southern hemisphere the situation is similar but 6 months displaced. this is clearly evident in fig. b1 . note that in a tropical location such as sri lanka no discernible seasonal effect can be detected in the data between 1968 and 1974. • these cases raise new challenges for health officials, who until now had been trying to contain the virus by closely monitoring people with the possibility of contracting the disease. if more people with no direct links to china become sick, determining infection routes will become impossible. instead of containment, treating seriously sick people may have to become the priority. set of key variant putative riboswitch sites (ranging from 2 to 5 on average across the length of the 29,903 nt rna genome) which define a given haplotype. thus, there is much haplotype homogeneity in china, but considerable haplotype diversity in new york city. the virus appears to adapt to new host genetic backgrounds by switching putative haplotype presumably allowing superior rna replication in that cellular environment. the only factor we cannot explain then is why the super explosions of the viral epidemics in certain locations and not others. one likely factor would be the infective dose of the virus which we predict was far greater at these epicentre locations because it came in as a high dose in-fall in meteorite dust from the upper atmosphere. clock and tmrca based on 27 genomes novel candida auris infection draft genome of a commonly misdiagnosed multidrug resistant pathogen candida auris phosphatidylserine vesicles enable efficient en bloc transmission of enteroviruses multiple introductions and subsequent transmission of multidrug-resistant candida auris in the usa: a molecular epidemiological survey candida auris: a rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally wuhan seafood market may not be source of novel virus spreading globally single-cell analysis of rna virus infection identifies multiple genetically diverse viral genomes within single infectious units epidemiology, clinical characteristics, resistance, and treatment of infections by candida auris candida auris: the recent emergence of a multidrug-resistant fungal pathogen diseases from space influenza-evidence against contagion: discussion paper clinical features of patients infected with 2019 novel coronavirus in wuhan, china. the lancet on the origins of a species: what might explain the rise of candida auris candida auris: a review of the literature simultaneous emergence of multidrug-resistant candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. the lancet twenty years of the sentry antifungal surveillance program: results for candida species from 1997-2016 sars, mers and the sunspot cycle weakened magnetic field, cosmic rays and the zikavirus outbreak global epidemiology of emerging candida auris evolving responsively: adaptive mutation cause of cambrian explosion-terrestrial or cosmic? cause of cambrian explosion-terrestrial or cosmic?-reply to commentary by r duggleby lamarck and panspermia-on the efficient spread of living systems throughout the cosmos analysis of apobec and adar deaminase-driven riboswitch haplotypes in covid-19 rna strain variants and the implications for vaccine design. accepted for publication in research reports dna sequencing and predictions of the cosmic theory of life dangers of adhering to an obsolete paradigm: could zika virus lead to a reversal of human evolution comments on the origin and spread of the 2019 coronavirus growing evidence against global infection-driven by person-to-person transfer of covid-19 predicting the future trajectory of covid-19 sunspot cycle minima and pandemics: the case for vigilance sars-a clue to its origins? the lancet space weather and pandemic warnings? an update on published and submitted work by the group as june 22, 2020the covid-19 pandemic has now engulfed almost all parts of the globe inhabited by human beings. confirmed cases are approaching 9 million and confirmed global deaths as june 22 are 468,589. we have updated our analysis here as the pandemic further unfolded. these analyses are now in several papers which have been published (or under-submission) since this paper was drafted. the most important developments are covered in the new citations in the reference list (and below), particularly our discussion on the progress of the major explosive outbreaks following the original epidemic in wuhan through december-january 2020. initially, in february, this appeared to go from china across the pacific to the us west coast (wickramasinghe et al., 2020b) , but it then became apparent the putative viral-laden meteorite dust clouds moved along the north 40°l atitude band heading in a westerly direction from china towards europe (wickramasinghe et al., 2020c) . we speculate this transportation took place mainly in the stratosphere and upper troposphere, and this helps explain in part the major explosive outbreaks of covid-19 in the temporal order, tehran/qom, italy/lombardy, spain then new york city all on the north 40°latitude band. the genetic sequence of the virus has been analyzed where available in each of the major explosive locations, particularly wuhan and new york city (steele & lindley, 2020) . contrary to a widely held perception that the covid-19 is a hypermutating contagious virus it is still the case, at the time of writing, that the most vulnerable at risk of death through respiratory complications are the co-morbid elderly. further, the virus does not hypermutate, it appears to a use a riboswitch-mediated haplotype variation strategy which could be associated with the ethnicgenetic background of the subjects infected. thus the genetic sequence of the virus in wuhan/china, west coast usa (february, 2020), spain and new york city is essentially !99.98% identical apart from a small key: cord-320930-9yiu0080 authors: liu, zeming; li, jinpeng; huang, jianglong; guo, liang; gao, rongfen; luo, kuan; zeng, guang; zhang, tingbao; yi, meilin; huang, yihui; chen, jincao; yang, yibin; wu, xiaohui title: association between diabetes and covid-19: a retrospective observational study with a large sample of 1,880 cases in leishenshan hospital, wuhan date: 2020-07-14 journal: front endocrinol (lausanne) doi: 10.3389/fendo.2020.00478 sha: doc_id: 320930 cord_uid: 9yiu0080 aims: this study aimed to investigate the clinical courses and outcomes of diabetes mellitus patients with coronavirus disease 2019 (covid-19) in wuhan. methods: this study enrolled 1,880 consecutive patients with confirmed covid-19 in leishenshan hospital. we collected and analyzed their data, including demographic data, history of comorbidity, clinical symptoms, laboratory tests, chest computed tomography (ct) images, treatment options, and survival. results: the percentages of patients with diabetes among the severe and critical covid-19 cases were higher than those among the mild or general cases (89.2%, 10.8 vs. 0%, p = 0.001). however, patients with and without diabetes showed no difference in the follow-up period (p = 0.993). the mortality rate in patients with or without diabetes was 2.9% (n = 4) and 1.1% (n = 9), respectively (p = 0.114). univariate and multivariate cox regression analyses and the kaplan-meier curves did not show any statistically significant differences between patients with and without diabetes (all p > 0.05). conclusions: our study results suggested that diabetes had no effect on the prognosis of covid-19 patients but had a negative association with their clinical courses. these results may be useful for clinicians in the management of diabetic patients with covid-19. coronavirus disease 2019 (covid-19) cause by severe acute respiratory syndrome-coronavirus 2 (sars-cov-2) was first identified in wuhan, china, and has subsequently and quickly spread to more than 70 countries, including the united states, spain, and italy (1, 2) . sars-cov-2 could cause severe, even lethal pneumonia and lung failure. as of april 25, 2020, more than 2,800,000 confirmed cases and 190,000 deaths of covid19 have been reported worldwide (3) . as an emergency specialty field hospital hosted by the zhongnan hospital, leishenshan hospital was put into use in february to provide treatment for covid-19 patients in wuhan, marking a milestone in china's battle against covid19 . in leishenshan hospital, 1,880 patients were diagnosed with covid-19 between february 8, 2020 and april 15, 2020. among those patients, 139 cases had a previous diagnosis of diabetes mellitus. diabetes mellitus (dm) is a common endocrine disease (4) and widely known as a chronic, low-grade inflammatory disease caused by long-term immune system imbalance, metabolic syndrome, or nutrient excess (5, 6) . since the outbreak of covid-19, several studies have been conducted to examine the relationship between diabetes and covid-19 (1, 7, 8) . however, their sample sizes were relatively small, and they did not clarify whether diabetes was a predictor of poor clinical outcomes and higher mortality of covid-19. in this study, we investigated the association between diabetes as a comorbidity and negative clinical courses and outcomes of covid-19 in a large sample of patients from a single hospital in wuhan, china. the findings are expected to inform follow-up clinical treatment for patients with both diseases and covid-19. this single-center retrospective observational study was conducted on 1,880 patients diagnosed with covid-19 at leishenshan hospital. after excluding cases without information about the history of diabetes, the final sample included 934 patients. data were collected on admission or during hospitalization by attending physicians and documented in the form of electronic medical records. this study was approved by the ethics commission of the zhongnan hospital of wuhan university (approval number: 2020074) and carried out in accordance with the principles of the declaration of helsinki revised in 2008. the need for informed consent from patients was waived due to the time constraints during the covid-19 emergency. we collected data of 1,880 patients from their medical records. these data included age, sex, comorbidities, levels of illness severity (mild, moderate, severe, and critical), signs and symptoms, treatment options (i.e., antiviral therapy, antibiotic therapy, traditional chinese medicine therapy, anticoagulation therapy, and administration of corticosteroid and vitamin c), laboratory findings, and computed tomography (ct) images. all the data were reviewed and analyzed by two senior physicians. the primary outcomes of this study included the survival of patients (alive vs. dead) and their highest level of illness severity. another important primary outcome was the patients' ct score-a semi-quantitative scoring system-generated according to the features of ct images. each of the ct image features, namely ground-glass opacities, reticulation or cords change, consolidation, and pleural effusions, was assigned 1 point. score 1 was the sum of points, and score 2 ranged from 0 to 4 points based on the area of lung involvement: no involvement, 0; <25% involvement, 1; 26-50% involvement, 2; 51-75% involvement, 3; and 76-100% involvement, 4. the total score was the sum of score 1 and score 2. normally distributed continuous variables are expressed as means ± standard deviations, and non-normally distributed continuous variables as medians and interquartile ranges. meanwhile, categorical variables are described as frequencies and percentages. the independent t-test or mann-whitney u-test was conducted to compare continuous variables between the group of patients with diabetes (group 2) and that of patients without diabetes (group 1). meanwhile, the χ²-test or fisher's exact test was used to analyze the associations between categorical variables. cox regression analysis and the kaplan-meier survival curves were performed to explore the prognosis of patients with and without diabetes. besides, curve fitting analysis was conducted to further evaluate the association between the ct score and the duration from symptom onset (in days) in both groups. two-sided p < 0·05 were considered as statistically significant, and all statistical analyses were performed using spss (version 23.0 for windows). table 1 shows that group 2 consisted of 139 patients whereas group 1 had 795 patients. the two groups showed no differences in gender distribution (p = 0.076), means of age (p = 0.773), and the number of patients with malignancy, nervous system disease, and digestive system disease (all p > 0.05). however, they showed a significant difference in the number of patients with cardiovascular or pulmonary disease (both p < 0.05). the percentages of patients with diabetes among the severe and critical covid-19 cases were higher than among the mild or general cases (89.2%, 10.8 vs. 0%, p = 0.001). however, no difference was observed in the follow-up period between patients with and without diabetes (p = 0.993). the mortality rate was 2.9% (n = 4) in group 2 and 1.1% (n = 9) in group 1 (p = 0.114). as shown in table 2 , the positive rate of igg against sars-cov-2 among patients with diabetes was lower than that among those without diabetes (82.5 vs. 91.8%, p = 0.029). survival analysis figure 1 presents the distribution of the number of deaths by the level of illness severity in both groups. there were six critical covid-19 cases in group 2, and three cases in group 1. besides, no deaths were observed among the severe cases in group 2 while there were six deaths in group 1. as shown in table 3 , the difference between the prognosis of group 2 and that of group 1 was demonstrated using either the univariate cox regression analysis (p = 0.124) or the multivariate analysis (p = 0.256, table 3 ). similarly, the kaplan-meier curves showed no difference between the two groups (p = 0.111, in supplemental figure 1 ). score 1 for all patients and that for patients without diabetes present the same tendency, i.e., rising and then descending (figures 2a-c for all patients vs. figures 2d-f for patients without diabetes). similarly, score 1 for patients with diabetes sharply increased and significantly decreased after peaking at 2.70 points on day 23 ( figure 2g) . however, score 2 for patients with diabetes showed an inverse tendency (figure 2h) , reaching its nadir of 2.30 points on day 35. this inconsistent tendency might be because the largest area of lung involvement for patients with diabetes appeared earlier than that for all patients or those without diabetes. in patients with diabetes, the total score peaked at 5.30 points after 19 days (figure 2i) , exceeding the peak of 4.95 points on day 20 in all patients ( figure 2c) and that of 4.95 points on day 19 in patients without diabetes (figure 2f) . curve fitting equation for figure 2 and coefficients of each curve are shown in supplemental table 1 . the prevalence of diabetes mellitus is anticipated to increase substantially during the next decades worldwide and considered to be main cause of human deaths (9) . people with diabetes are more susceptible to certain infectious diseases, such as staphylococcus aureus and mycobacterium tuberculosis, possibly because of their dysregulated immune system (10, 11) . during the outbreak of sars in 2003 in guangzhou, yang et al. reported that plasma glucose levels and diabetes were independent predictors for mortality and morbidity, and metabolic control might improve the prognosis in patients with sars (12) . recently, covid-19 has been a focal topic of research, and several investigations have focused on diabetes as a predictor of clinical course and prognosis of covid-19 cases (13) (14) (15) (16) . certain studies found that diabetes negatively affected medical complications, including mortality, in covid-19 cases (13, 17, 18) . in our study, we collected data with a large sample from leishenshan hospital. we found that covid-19 patients with dm were older and the proportion of patients with cardiovascular disease were higher among covid-19 patients with dm than covid-19 patients without dm. however, the latter had a higher proportion of pulmonary disease as comorbidities than the former. furthermore, aspartate aminotransferase (ast) and platelet counts were lower in covid-19 patients with diabetes than those without disease. in addition, non-diabetes-related comorbidities did not ameliorate the severity of illness on admission or improve survival outcomes, compared to diabetes-related ones. however, severe or critical covid-19 cases were more prevalent among patients with diabetes than those did not suffer from this disease. a systematic review by huang et al. revealed that diabetes was associated with mortality, severity, acute respiratory distress syndrome, and disease progression in patients with covid-19 (19) . the results of our present study differ from those of previous ones possibly because leishenshan hospital is a designated hospital for covid-19, and the standard of care for patients with diabetes has become better. further researches are needed in the future to generate more precise results. having assessed the association between diabetes with the severity of covid-19, wu et al. found out the proportion of diabetes as a comorbidity among severe covid-19 cases was significantly higher than that among mild cases (14) . similarly, our data supported that the proportion of severe or critical covid-19 cases among patients with diabetes was higher than that among those without diabetes. this means the clinical course of covid-19 in patients with diabetes may be more severe than that in those without diabetes. currently, the mechanisms behind this phenomenon remain unknown; however, high glucose levels may play a certain role in the impaired antibacterial neutrophil function and complications caused by chronic diabetes (9) . in addition, the comorbidity with cardiovascular diseases, such as ischemic heart disease and heart failure, was reported to have an association with higher mortality due to covid-19 (20) . in our study population, 64.0% of patients with diabetes suffered from cardiovascular diseases, higher than that of those without diabetes. this may partly explain that the group of patients with diabetes had a higher proportion of covid-19 cases in severe or critical conditions than the group of those without diabetes. in our present study, biochemical laboratory test results showed that the increased ast level, an indicator of liver injury, was not observed in the blood of all patients, regardless of their status of diabetes. furthermore, the two groups showed no difference in the levels of albumin and hemoglobin, suggesting that both groups had similar nutritional status. having analyzed 138 covid-19 patients, wang et al. found that cytokine storms, sustained inflammatory response, and acute kidney injury might be associated with the mortality of covid-19 patients (21) . cytokine storms also proved to be the main cause of eventual deaths among many patients with ebola virus infections (13) . in our study, however, patients with diabetes shared similar lymphocyte and neutrophil counts than patients without diabetes, the inflammation-related biomarkers (e.g., il-6). these results indicate that the inflammatory response of patients with diabetes was not different from that of those without diabetes, resulting in similar rates of mortality due to covid-19. the use of angiotensin-converting enzyme 2 (ace2) inhibitors and angiotensin ii receptor antagonists (arbs) for covid-19 patients has been of great controversy. ace2 is the surface receptor for sars-cov-2 that directly interacts with the spike glycoprotein (22) . wrapp et al. has recently suggested that the affinity between ace2 and the receptor binding domain of sars-cov-2 is much higher than that between ace2 and the rbc of sars-cov (23) . the expression of ace2 in various organs, including the cardiovascular system, lungs, kidneys, and brain might explain why some covid-19 patients died of multiple organ failure (24, 25) . ace inhibitors and arbs may play a protective role in the treatment of covid-19 cases (26) . however, cure et al. demonstrated that sars-cov-2 could enter cells by attaching to ace2 enzymes and then cause infection. furthermore, ace inhibitors enhanced the sympathetic activity via the central stimulation and then increased pulmonary capillary leaking, possibly resulting in the development of ards. the authors suggested that the morbidity and mortality of covid-19 among patients with diabetes would be higher if they used ace inhibitors and arbs (27) . our primary findings showed that as a comorbidity, diabetes did not increase the risk of mortality but negatively regulated the clinical course of covid-19. therefore, the treatment for covid-19 patients should be appropriately adjusted. our study has serval limitations that need to be addressed. first, the retrospective, non-randomized nature led to sample heterogeneity. second, we were not able to collect and analyze the characteristic data of patients with diabetes, such as the type of diabetes, glucose level, hba1c and treatment options for diabetes due to the time limitation; hence, we could not analyze the data on anti-dm treatment although they could affect the clinical course and treatment outcome of covid-19. third, we did not examine the relative mechanism behind the effect of diabetes on covid-19 in this study. finally, the difference in disease progress and prognosis between the covid-19 patients with or without diabetes may change with a longer follow-up period. our findings which were contradictory to those of previous studies with large sample sizes, suggested that diabetes did not significantly impact the prognosis of covid-19 patients but negatively affect their clinical course. this may be helpful for clinicians in managing covid-19 patients with diabetes. however, future prospective studies with larger sample sizes should focus on examining whether patients with diabetes are more at risk of covid-19. the raw data supporting the conclusions of this article will be made available by the authors, without undue reservation, to any qualified researcher. the studies involving human participants were reviewed and approved by ethics commission of the zhongnan hospital of wuhan university zhongnan hospital of wuhan university. the ethics committee waived the requirement of written informed consent for participation. zl: conceptualization, writing-review, and editing. jh: formal analysis and writing-original draft preparation. jl, lg, and rg: investigation and data curation. kl and gz: methodology and software. tz, my, and yh: software, visualization, and validation. jc, yy, and xw: supervision and project administration. all authors: contributed to the article and approved the submitted version. risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in wuhan, china clinical characteristics of laboratory confirmed positive cases of sars-cov-2 infection in wuhan, china: a retrospective single center analysis epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study increase in the incidence of diabetes and its implications cells of innate and adaptive immunity in type 2 diabetes and obesity the immune system's involvement in obesity-driven type 2 diabetes covid-19 in critically ill patients in the seattle region -case series diabetic patients with covid-19 infection are at higher risk of icu admission and poor short-term outcome diabetes and infection: is there a link?-a mini-review increased risk of common infections in patients with type 1 and type 2 diabetes mellitus immunological mechanisms contributing to the double burden of diabetes and intracellular bacterial infections plasma glucose levels and diabetes are independent predictors for mortality and morbidity in patients with sars diabetes is a risk factor for the progression and prognosis of covid-19 early antiviral treatment contributes to alleviate the severity and improve the prognosis of patients with novel coronavirus disease (covid-19) what is the role of angiotensin-converting enzyme 2 (ace2) in covid-19 infection in hypertensive patients with diabetes? covid-19 infection in italian people with diabetes: lessons learned for our future (an experience to be used) commentary: covid-19 in patients with diabetes covid-19 in patients with diabetes: risk factors that increase morbidity diabetes mellitus is associated with increased mortality and severity of disease in covid-19 pneumonia -a systematic review, meta-analysis, and meta-regression clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan a crucial role of angiotensin converting enzyme 2 (ace2) in sars coronavirus-induced lung injury cryo-em structure of the 2019-ncov spike in the prefusion conformation role of the ace2/angiotensin 1-7 axis of the renin-angiotensin system in heart failure a human homolog of angiotensin-converting enzyme. cloning and functional expression as a captopril-insensitive carboxypeptidase sars-cov2: should inhibitors of the renin-angiotensin system be withdrawn in patients with covid-19? angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may be harmful in patients with diabetes during covid-19 pandemic the supplementary material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fendo. 2020.00478/full#supplementary-material conflict of interest: the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright © 2020 liu, li, huang, guo, gao, luo, zeng, zhang, yi, huang, chen, yang and wu. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord-337809-bxvgr6qg authors: xiong, yong; song, shihui; ye, guangming; wang, xinghuan title: family cluster of three recovered cases of pneumonia due to severe acute respiratory syndrome coronavirus 2 infection date: 2020-05-04 journal: bmj case rep doi: 10.1136/bcr-2020-235302 sha: doc_id: 337809 cord_uid: bxvgr6qg the coronavirus disease (covid-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was first reported in wuhan, china, in late 2019 and has affected more than 1 270 000 people worldwide. the numbers of reported cases continue to rise and threaten global health. transmissions among family members are frequently observed, although the route of transmission is partially known. here we report three cases of sars-cov-2 infection within one family. sequencing of the s gene of the viral genome showed 100% identity among samples, suggesting that the same strain caused the infection. following treatment with oseltamivir and short-term methylprednisolone combined with symptomatic management, all three patients recovered within 3 weeks, as evidenced by the disappearance of their symptoms, clearance of pulmonary infiltrates and consecutive negative molecular diagnostic test findings. our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/moderate pneumonia in covid-19 cases. the coronavirus disease (covid-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was first reported in wuhan, china, in late 2019 and has affected more than 1 270 000 people worldwide. the numbers of reported cases continue to rise and threaten global health. transmissions among family members are frequently observed, although the route of transmission is partially known. here we report three cases of sars-cov-2 infection within one family. sequencing of the s gene of the viral genome showed 100% identity among samples, suggesting that the same strain caused the infection. following treatment with oseltamivir and short-term methylprednisolone combined with symptomatic management, all three patients recovered within 3 weeks, as evidenced by the disappearance of their symptoms, clearance of pulmonary infiltrates and consecutive negative molecular diagnostic test findings. our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in covid-19 cases. severe acute respiratory syndrome coronavirus 2 (sars-cov-2) is the pathogen responsible for the ongoing outbreak of pneumonia in wuhan, china. since the first cluster of atypical pneumonia cases was reported on 31 december 2019, 1 the disease has spread with surprising speed. while much attention has been focused on viral transmission dynamics and the spectrum of clinical illness, these aspects are not yet completely understood. [2] [3] [4] [5] [6] [7] [8] this report describes the epidemiological and clinical features of coronavirus disease (covid-19) among three members of a family following sars-cov-2 infection. owing to the unavailability of effective vaccines for the prevention of sars-cov-2, most preventive measures aim to reduce the risk of infection. 9 despite several recommended drugs, including the combination of lopinavir/ritonavir, nelfinavir and interferon-beta-1b, effective treatment options are scarce. 2 hence, prevention of infection is of utmost importance. we provide evidence to support the increasing concerns regarding person-to-person transmission of sars-cov-2. on 10 and 11 january 2020, a family of three, comprising the father (65 years), the mother (61 years) and the son (38 years), were admitted to the department of infectious disease at the zhongnan hospital of wuhan university with symptoms of cough and fever. on 21 december 2019, the mother had started coughing with expectoration. five days later, the father also developed a cough; he developed fever 7 days prior to admission. he had a history of hypertension and coronary heart disease, for which he had received a stent. both had symptoms of restricted breathing. on 3 january 2020 (12 days after the mother's illness), the son developed a cough. prior to admission, all three patients experienced fatigue and intermittent fever (37.9℃-39.1℃) for at least 1 day (figure 1). they had no shortness of breath or chest pain. physical examination revealed some degree of tonsil enlargement in the father and the son. lung auscultation revealed rhonchi in the father and the mother. other examination findings were generally unremarkable. none of the patients had visited the huanan seafood wholesale market in wuhan or the surrounding area in the previous 2 weeks. they denied any contact with diagnosed patients with similar symptoms. on admission, haemograms revealed lymphocyte counts reduced by nearly 50% in the mother and near-to-low-normal in the father and the son. other parameters such as white cell count, neutrophil and blood platelet counts were near-to-low-normal, suggesting not only lymphopaenia but also a haematological regeneration abnormality following infection. moreover, all of these parameters doubled on discharge of the patients from the hospital. none of the patients had abnormal haemoglobin values. oxygen saturation values were normal. additional laboratory investigations in these three patients showed no abnormalities except for increased c reactive protein levels (table 1) . pneumonia was diagnosed based on chest ct scans. the mother's lung showed a peripheral lesion with increased intensity and bilateral patchy shadows in the outer zone of the lungs. numerous patchy or segmental ground-glass opacities were observed in both lungs of the father and the son. 10 the lung opacities started to clear after 10 days of hospitalisation (figure 2). rapid nucleic acid amplification tests for respiratory syncytial virus, adenovirus, influenza virus a new disease figure 1 body temperature (blue) and heart rate (red) values after hospitalisation. the temperature of all three patients decreased within 3-5 days. the mother experienced only occasional febrile episodes, while the son had moderate-to-high fever for 4 days after admission. (table 2) . the treatment during hospitalisation was largely supportive. the patients intermittently received supplemental oxygen through a nasal cannula at a rate of 2 l per minute. owing to the difficulties in early diagnosis, all three patients were initially treated for suspected influenza with 75 mg oseltamivir phosphate capsules two times per day for the first 5 days of hospitalisation. the patients received 80 mg of methylprednisolone sodium succinate per day for the first 3 days, followed by 40 mg per day during the following 3 days, and 20 mg per day for another 3 days before being discontinued. the father received methylprednisolone at a dose of 40 mg per day for 5 days and 20 mg per day for another 5 days. considering the possibility of bacterial coinfection, the mother and the father were administered amoxicillin sodiumflucloxacillin sodium (6 g, intravenous infusion every 12 hours) for 2 weeks. the son received ceftriaxone-tazobactam (2 g, intravenous infusion, every 12 hours) for 3 days, followed by biapenem (0.3 g, intravenous infusion every 8 hours) for another 9 days. additionally, the mother and the son were administered levofloxacin (0.4 g, intravenous infusion, daily) starting on admission day 6 until day 14. the father received moxifloxacin (0.4 g, intravenous infusion, daily) for 2 weeks starting on admission day 1. the fever disappeared in all three patients approximately 5-7 days following admission and their clinical conditions further improved thereafter. after approximately 3 weeks of hospitalisation, lung inflammation had largely resolved, as indicated by ct scans, and two consecutive throat swab samples tested negative for sars-cov-2 with the rt-pcr test performed for each new disease figure 2 chest ct scans of the three patients. the mother's lung shows a peripheral lesion with increased intensity and bilateral patchy shadows in the outer zones. multiple patchy or segmental ground-glass opacities were observed in both lungs of the father and the son. due to the initial shortage of testing kits for sars-cov-2, the cases were not diagnosed until 20 january 2020. throat swabs obtained from all three patients on admission day 9 tested positive. subsequently, throat swabs obtained from them on admission days 18 and 20 tested negative for sars-cov-2 (figure 1). the genetic sequences of the viral s gene from samples collected from each family member were identical (data not shown) to each other and also were 100% identical to the reported viral strain (whu01) currently spreading in wuhan. our results not only support human-to-human transmission but also suggest that close contact within families is a high-risk factor. effective intervention measures for the prevention of family transmission need to be adopted. ► severe acute respiratory syndrome coronavirus 2 transmission among family members was confirmed. ► the patients recovered after treatment with oseltamivir and methylprednisolone. ► prevention of family transmission is important. ► the current integrated treatment for mild/moderate pneumonia is effective in covid-19. world health organization. pneumonia of unknown cause china potential of large "first generation" human-to-human transmission of 2019-ncov epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster importation and human-to-human transmission of a novel coronavirus in vietnam transmission of 2019-ncov infection from an asymptomatic contact in germany early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a novel coronavirus from patients with pneumonia in china potential inhibitors against 2019-ncov coronavirus m protease from clinically approved medicines clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china acknowledgements we thank all the doctors and nurses who cared for these three patients. the case report was written by yx and ss and edited by gy and xw.funding this study was funded by the medical science advancement program (clinical medicine) of wuhan university (grant number tflc2018002). patient consent for publication obtained. copyright 2020 bmj publishing group. all rights reserved. for permission to reuse any of this content visit https://www.bmj.com/company/products-services/rights-and-licensing/permissions/ bmj case report fellows may re-use this article for personal use and teaching without any further permission.become a fellow of bmj case reports today and you can: ► submit as many cases as you like ► enjoy fast sympathetic peer review and rapid publication of accepted articles ► access all the published articles ► re-use any of the published material for personal use and teaching without further permission if you have any further queries about your subscription, please contact our customer services team on +44 (0) 207111 1105 or via email at support@bmj.com.visit casereports.bmj.com for more articles like this and to become a fellow key: cord-306373-61snvddh authors: xu, xiao-wei; wu, xiao-xin; jiang, xian-gao; xu, kai-jin; ying, ling-jun; ma, chun-lian; li, shi-bo; wang, hua-ying; zhang, sheng; gao, hai-nv; sheng, ji-fang; cai, hong-liu; qiu, yun-qing; li, lan-juan title: clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series date: 2020-02-19 journal: bmj doi: 10.1136/bmj.m606 sha: doc_id: 306373 cord_uid: 61snvddh objective: to study the clinical characteristics of patients in zhejiang province, china, infected with the 2019 severe acute respiratory syndrome coronavirus 2 (sars-cov-2) responsible for coronavirus disease 2019 (covid-2019). design: retrospective case series. setting: seven hospitals in zhejiang province, china. participants: 62 patients admitted to hospital with laboratory confirmed sars-cov-2 infection. data were collected from 10 january 2020 to 26 january 2020. main outcome measures: clinical data, collected using a standardised case report form, such as temperature, history of exposure, incubation period. if information was not clear, the working group in hangzhou contacted the doctor responsible for treating the patient for clarification. results: of the 62 patients studied (median age 41 years), only one was admitted to an intensive care unit, and no patients died during the study. according to research, none of the infected patients in zhejiang province were ever exposed to the huanan seafood market, the original source of the virus; all studied cases were infected by human to human transmission. the most common symptoms at onset of illness were fever in 48 (77%) patients, cough in 50 (81%), expectoration in 35 (56%), headache in 21 (34%), myalgia or fatigue in 32 (52%), diarrhoea in 3 (8%), and haemoptysis in 2 (3%). only two patients (3%) developed shortness of breath on admission. the median time from exposure to onset of illness was 4 days (interquartile range 3-5 days), and from onset of symptoms to first hospital admission was 2 (1-4) days. conclusion: as of early february 2020, compared with patients initially infected with sars-cov-2 in wuhan, the symptoms of patients in zhejiang province are relatively mild. in december 2019 a group of patients with pneumonia of unknown cause were confirmed to be infected with a novel coronavirus, known as 2019-ncov, in wuhan, hubei province, china, which had previously not been detected in humans or animals. 1 epidemiological evidence suggested that most of these patients had visited a local seafood market in wuhan 2 and that the gene sequence of the virus obtained from these patients was highly similar to that identified in bats. 3 the virus was subsequently renamed sars-cov-2 as it is similar to the coronavirus responsible for severe acute respiratory syndrome (sars-cov), a member of the subgenus sarbecovirus (beta-cov lineage b), with which it shares more than 79% of its sequence, but it is more distant to the coronavirus responsible for middle east respiratory syndrome (mers-cov), a member of the merbecovirus subgenus (only 50% homology with sars-cov-2). all these viruses are categorised within the same genus of the subfamily orthocoronavirinae within the family coronaviridae. [4] [5] [6] [7] some researchers have found that sars-cov-2 has strong affinity to human respiratory receptors, 8 suggesting a potential threat to global public health. initially, the first confirmed cases were nearly all related to the huanan seafood market (closed on 1 january 2020) and were concentrated in wuhan. 9 coronavirus disease 2019 (covid-19) soon drew global attention because of the rapidly increasing numbers of new cases. 2 the new type of coronavirus infection was believed to have been transmitted from animals, and by january 2020 it was suspected that the initially doi: 10 .1136/bmj.m606 | bmj 2020;368:m606 | the bmj affected patients had been infected with the virus through human to human transmission. 10 since january 2020 the spread of covid-19 has escalated and the virus has extended rapidly to most parts of china as well as to other countries. as of 8 february 2020 a confirmed 37 589 people have been infected with sars-cov-2 globally, including 302 people across 24 other countries. 11 these figures are updated daily and are expected to increase further. despite the increasing number of confirmed cases, the clinical investigation of patients was insufficient. a previous study reported the clinical characteristics of the first 41 infected patients in the greater wuhan area, contributing to an understanding of the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of those patients. 9 a second study found a familial cluster of sars-cov-2, clearly suggesting human to human transmission in family homes and hospitals and showing that spread of the virus between cities is possible. 10 in late january 2020 large numbers of people across china were returning to their home towns after visiting wuhan for the chinese lunar new year. this weeklong holiday accounts for the largest mass movement of people worldwide each year. consequently, over time more patients are expected to emerge across china and perhaps the world. we found that the characteristics of patients outside of wuhan differed from those initially reported in patients in wuhan. 10 we describe the clinical characteristics and laboratory findings of patients in zhejiang province infected with sars-cov-2 to provide an insight into the prevention and treatment of covid-19 across china and elsewhere. we conducted a retrospective study focusing on the clinical characteristics of confirmed cases of covid-19 in zhejiang province from 10 january 2020 to 26 january 2020. since the outbreak of covid-19, strict precautionary measures have been implemented in zhejiang province, including the creation of fever clinics that exclusively receive patients with suspected sars-cov-2 infection, defined as presenting with a fever or any respiratory symptoms, including dry cough, and especially in those with a history of travel to wuhan or exposure to infected people within two weeks before the onset of illness since january 2020. case definitions of confirmed human infection with sars-cov-2 are in accordance with the interim guidance from the world health organization. 1 only patients with a laboratory confirmed infection were enrolled in this study. we collected data on 62 patients admitted to hospital with laboratory confirmed sars-cov-2 infection in seven designated tertiary hospitals in zhejiang province (see supplementary file for further details). information was collected on dates of illness onset, visits to clinical facilities, and hospital admissions. epidemiological data were collected through brief interviews with each patient. several investigators interviewed each patient to collect exposure histories during the two weeks before illness onset, including the dates and times of close contact (gathering, living, or working together) with individuals from wuhan with confirmed or suspected sars-cov-2 infection. the incubation period was defined as the time from exposure to the onset of illness, which was estimated among patients who could provide the exact date of close contact with individuals from wuhan with confirmed or suspected sars-cov-2 infection. we also investigated the possibility of familial clusters-that is, index patients who travelled to wuhan and then infected others in their families. we extracted the medical records of patients and sent these to the data collection centre in hangzhou. a team of doctors who had been treating patients with covid-19 collected and reviewed the data. because of the urgent need to collect data on this emerging pathogen, the requirement for informed consent was waived. we used a standardised case report form to collect clinical data. if information was not clear, the working group in hangzhou contacted the doctor responsible for the treatment of the patient for clarification. sputum and throat swab specimens collected from all patients at admission were tested by real time polymerase chain reaction for sars-cov-2 rna within three hours. laboratory confirmation of the virus was performed using real time reverse transcription polymerase chain reaction. 9 virus detection was repeated twice every 24 hours. laboratory tests were conducted at admission, including a complete blood count, serum biochemistry, and identification of other respiratory pathogens such as influenza a virus (h1n1, h3n2, h7n9), influenza b virus, respiratory syncytial virus, parainfluenza virus, and adenovirus. most patients received antiviral treatment with interferon alpha inhalation (50 μg twice daily), lopinavir and ritonavir (400 mg twice daily and 100 mg twice daily, respectively), and arbidol (200 mg three times daily). patients received treatment with corticosteroid (40-80 mg/day) and gamma globulin (15-20 g/day) for 3-5 days when their resting respiratory rate was more than 30 per minute, or oxygen saturation was below 93% without oxygen, or multiple pulmonary lobes showed more than 50% progression of disease in 48 hours on imaging. patients also received treatment with probiotics in most cases. quinolones and second generation beta lactams (oral and intravenous) were administered if fever lasted for more than seven days or c reactive protein levels were 30 mg/l or more (normal range 0-8 mg/l). patients suspected of being infected with sars-cov-2 were discharged from hospital once the results of two real time reverse transcription polymerase chain reaction tests taken 24 hours apart were negative for sars-cov-2 antigens. as a previous study 9 has shown that patients' condition worsens on the 10th day after illness onset, we divided the cohort into patients with symptoms for more than 10 days and those with symptoms for less than 10 days. we summarised continuous variables as either means and standard deviations or medians with interquartile ranges. for categorical variables, we calculated the percentages of patients in each category. all analyses were done with spss software, version 22.0. this was a retrospective case series study and no patients were involved in the study design, setting the research questions, or the outcome measures directly. no patients were asked to advise on interpretation or writing up of results. by 26 january 2020, clinical data were collected on 62 patients in zhejiang province with laboratory confirmed sars-cov-2 infection. twenty five (40%) of the patients were aged 19-40 years, 33 (53%) were aged 41-65 years, 2 (3%) were aged 10 and 11 years, and 2 (3%) were aged 65 years and older. the median age was 41 years (interquartile range 32-52 years; table 1). as of 26 january 2020, more than half of the 62 patients (35, 56%) were men. no patients had a history of exposure to the huanan seafood market and all 62 patients had been exposed to individuals with confirmed sars-cov-2 infection. among the 62 patients, 23 (37%) resided in wuhan and the remaining 39 (63%) had made short term trips to wuhan before illness onset. fifty six (90%) patients could provide the exact date of close contact with someone with confirmed or suspected sars-cov-2 infection. of the 33 patients with symptoms for more than 10 days after illness onset, 10 (30%) were aged 19-40 years, 22 (67%) were aged 41-65 years, and 1 (3%) was older than 65 years. the median age of patients was 45 years (interquartile range 37-54 years; table 1). twenty of the 62 patients (32%) had underlying diseases-seven (11%) had liver disease, five (8%) of the 33 patients with symptoms for more than 10 days after illness onset, 13 (39%) had underlying diseases: four (12%) patients had liver disease, four (12%) had hypertension, and one each had chronic obstructive pulmonary disease (3%), diabetes (3%), and cerebrovascular disease (3%). among 56 patients who could provide the exact date of close contact with someone with confirmed or suspected sars-cov-2 infection, the median incubation period from exposure to symptoms was 4 days (interquartile range 3-5 days). the median time from onset of symptoms to first hospital admission was 2.0 (1.0-4.3) days. the most common symptoms at illness onset were fever (48, 77%), cough (50, 81%), expectoration (35, 56%), headache (21, 34%), myalgia or fatigue (32, 52%), diarrhoea (3, 8%), and haemoptysis (2, 3%). only two (3%) patients developed shortness of breath. among the 33 patients who had symptoms for more than 10 days after illness onset, the median incubation period from exposure to symptoms was 3 days (interquartile range 3-4 days). the median time from onset of symptoms to first hospital admission was 6.5 (5.0-9.0) days. the most common symptoms at onset of illness were cough (27, 82%), fever (24, 73%), expectoration (19, 58%), myalgia or fatigue (19, 58%), headache (15, 45%), diarrhoea (3, 9%), and haemoptysis (2, 6%). only one (3%) patient developed shortness of breath. on admission, the blood counts of 19 of the 62 (31%) patients showed leucopenia (white blood cell count <4×10 9 /l) and 26 (42%) showed lymphopenia (lymphocyte count <1.0×10 9 /l; table 2). the d-dimer levels were within normal range (median 0.2 mg/l (interquartile range 0.2-0.5 mg/l). levels of aspartate aminotransferase increased in 10 (16%) patients. 1) . only one patient did not have pneumonia. of the 62 patients, only one was transferred to an intensive care unit for acute respiratory distress syndrome and received mechanical ventilation (table 3) . fifty five (89%) patients received antiviral treatment, 28 (45%) were given empirical antibiotic treatment, and 16 (26%) were given systematic corticosteroid and gamma globulin treatment. at this point, one (2%) patient had been discharged and no patients had died. fitness for discharge was based on abatement of fever for at least three days, with improved evidence on chest radiography and viral clearance in samples from the lower respiratory tract. as of 8 february 2020, more than 30 000 laboratory confirmed cases of infection with the novel coronavirus (sars-cov-19) were reported in china. 12 the number of infections is increasing rapidly. it is possible that an even greater number of infected patients exist without a diagnosis because their symptoms were less severe and because of the incubation period. thousands of patients with suspected sars-cov-2 infection could eventually receive a diagnosis. the clinical features of early cases of covid-19 in wuhan were not the same as those in other areas of china. according to our data, none of the infected patients in zhejiang province had been exposed to the huanan seafood market, and as the number of familial clusters in infected patients in our study is large, this might suggest human to human transmission. this finding is also consistent with a published article. 10 further detailed investigations should aim to ascertain the exact mode of transmission. most of the infected individuals in zhejiang province were male patients, but the age range of patients is large as sars-cov-2 also infected children and those older than 65 years. 9 13 no major differences were found between the initial clinical symptoms of patients in zhejiang province and those in wuhan. most of the patients in zhejiang province, however, had mild to moderate symptoms, and only a small portion of them had dyspnoea. only one patient developed acute respiratory distress syndrome and was admitted to an intensive care unit. the laboratory test results showed that the patients also experienced mild illness. there were fewer patients with abnormal renal function and lactate dehydrogenase and procalcitonin levels. through media and national advocacy, patients with fever, cough, expectoration, and other upper respiratory tract symptoms were asked to go to hospital at an early stage. even those who had contact with other patients, or patients with suspected infection were asked to go to hospital. we also analysed patients with symptoms for more than 10 days after illness onset. we found that the clinical features of patients with symptoms for longer than 10 days in zhejiang province were less severe than those of the primary infected patients from wuhan. 9 13 this phenomenon was also apparent during the transmission of mers-cov. the global case mortality of mers-cov was about 40%, whereas the mortality from second generation mers-cov was about 20%. 14 15 patients in the two cohorts received antiviral treatment, but the types of drugs used varied between patients. treatment with lopinavir and ritonavir were reported to have the potential to treat sars infections, 16 and we suppose this treatment might be a beneficial part of the treatment for covid-19. the rate of antibiotic and corticosteroid use was different. less than half the patients in zhejiang province received antibiotics. whether the use of antivirals, antibiotics, or steroids affects the prognosis of patients remains unknown. given that most infections in zhejiang province were in patients who had no direct contact with the original site of outbreak, our findings provide valuable information in the understanding of the clinical features of covid-19, as the number of people with confirmed disease continues to increase rapidly. our study population might represent most of the clinical characteristics of infected patients since january 2020. further containment proposals should be implemented by the chinese government, such as preventing people from wuhan having contact with those elsewhere, banning gatherings of more than 100 people, conducting daily public-wide educational campaigns on precautionary measures against exposure to sars-cov-2, encouraging people to cancel traditional family gatherings such as during the chinese lunar new year, and extending the chinese lunar new year holiday to prevent large scale spread. our study has several limitations. firstly, only 62 patients were included. a large number of patients were continually being admitted to hospital as data were being collected, and thus we obtained data on most but not all of the patients with laboratory confirmed infection in zhejiang province during the study period. secondly, as the patients were only from zhejiang province, it might be that more clinical features related to covid-19 will be identified. thirdly, at the time of study submission, most patients had not been discharged, so we are unable to estimate either the case fatality rate or the predictors of fatality. moreover, the time since illness onset in some of our patients might be shorter than the observation period of 10 days, which could result in biases of clinical observation characteristics. compared with the symptoms of the initial patients with sars-cov-2 infection in wuhan, those of patients from zhejiang province in our study were relatively mild. currently, no effective drug treatment or vaccine exists. it is necessary for monitoring of the virus to be strengthened and drugs and vaccines to be developed against sars-cov-2 infection as soon as possible. 1 we thank song-jia tang for assisting with english translation. contributors: x-wx and x-xw contributed equally to this article. xwx and ljl conceptualised the paper. xxw analysed the data, with input from jfs, kjx, xgj, ljy, clm, sbl, hyw, sz, hng, hlc, and yqq. xwx and xxw wrote the initial draft with all authors providing critical feedback and edits to subsequent revisions. all authors approved the final draft of the manuscript. l-lj is the guarantor. the corresponding author attests that all listed authors meet authorship criteria and that no others meeting the criteria have been omitted. funding: no funding. competing interests: all authors have completed the icmje uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organisation for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work. ethical approval: this study was approved by the ethics committee of the first affiliated hospital, zhejiang university school of medicine (2020iit a0001). patient consent: obtained. data sharing: no additional data available. transparency: the lead authors and manuscript's guarantor affirm that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that any discrepancies from the study as planned have been explained. dissemination to participants and related patient and public communities: no study participants were involved in the preparation of this article. the results of the article will be summarised in media see rights and reprints this is an open access article distributed in accordance with the creative commons attribution non commercial (cc by-nc 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is noncommercial clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human middle east respiratory syndrome coronavirus (mers-cov): announcement of the coronavirus study group isolation of a novel coronavirus from a man with pneumonia in saudi arabia genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding who. middle east respiratory syndrome coronavirus evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission clinical features of patients infected with 2019 novel coronavirus in wuhan, china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating personto-person transmission: a study of a family cluster novel coronavirus (2019-ncov) epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study middle east respiratory syndrome coronavirus (mers-cov) outbreak in south korea, 2015: epidemiology, characteristics and public health implications role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings supplementary information: description of clinical centres and cases enrolled in this study, and case report form key: cord-296182-hhswage4 authors: meng, lingzhong; qiu, haibo; wan, li; ai, yuhang; xue, zhanggang; guo, qulian; deshpande, ranjit; zhang, lina; meng, jie; tong, chuanyao; liu, hong; xiong, lize title: intubation and ventilation amid the covid-19 outbreak: wuhan’s experience date: 2020-04-08 journal: anesthesiology doi: 10.1097/aln.0000000000003296 sha: doc_id: 296182 cord_uid: hhswage4 the covid-19 outbreak has led to 80,409 diagnosed cases and 3,012 deaths in mainland china based on the data released on march 4, 2020. approximately 3.2% of patients with covid-19 required intubation and invasive ventilation at some point in the disease course. providing best practices regarding intubation and ventilation for an overwhelming number of patients with covid-19 amid an enhanced risk of cross-infection is a daunting undertaking. the authors presented the experience of caring for the critically ill patients with covid-19 in wuhan. it is extremely important to follow strict self-protection precautions. timely, but not premature, intubation is crucial to counter a progressively enlarging oxygen debt despite high-flow oxygen therapy and bilevel positive airway pressure ventilation. thorough preparation, satisfactory preoxygenation, modified rapid sequence induction, and rapid intubation using a video laryngoscope are widely used intubation strategies in wuhan. lung-protective ventilation, prone position ventilation, and adequate sedation and analgesia are essential components of ventilation management. t he outbreak of the "coronavirus disease 2019" started in december 2019 and quickly became a sweeping and unprecedented challenge to different stakeholders in mainland china. 1 although the epidemic of covid19 is not yet over, it has already outpaced the previous severe acute respiratory syndrome (sars) in 2003 and middle east respiratory syndrome (mers) in 2012 in nearly every respect, except for the mortality rate (table 1). as of march 4, 2019, a total of 80,409 patients were diagnosed with covid-19, and a total of 3,012 patients among those confirmed cases died, corresponding to a mortality rate of 3.7% (http://www.nhc.gov.cn/; accessed march 5, 2020) . at the writing of this article on march 5, 2020, it appears that the momentum of the epidemic in mainland china, especially that in the epicenter of wuhan, hubei province, china, has slowed down. however, the disease is gaining momentum outside of china, and it could ultimately become very severe (https://www.who. int/emergencies/diseases/novel-coronavirus-2019/eventsas-they-happen; accessed march 5, 2020). the concern is whether the covid-19 epidemic could become a oncein-a-century pandemic. 2 it did not take more than a few days before the healthcare system and providers in the epicenter of wuhan were stunned by the covid-19 outbreak's scale, speed, severity, and serious threat to healthcare providers themselves. many patients developed serious symptoms, with some of them becoming critically ill. 1 the hospitals were quickly overwhelmed, forcing the administration to lock down the city of wuhan, reactivate the workforce a few days ahead of the most popular holiday in china, lunar new year, reorganize the case flow, convert noninfectious floors and hospitals into infectious ones, build two new hospitals from ground zero, and open 16 fang cang hospitals using the big sport, conference, exhibition, and performance buildings ( fig. 1 ; http://wjw.wuhan.gov.cn/; accessed march 1, 2020). the most common and severe complication in patients with covid-19 is acute hypoxemic respiratory failure or acute respiratory distress syndrome (ards), requiring oxygen and ventilation therapies. 3 some of these critically ill patients required intubation and invasive ventilation. 3, 4 moreover, although elective surgeries were largely cancelled, emergency surgeries for patients with confirmed or suspected covid-19 were permitted to proceed. some of these surgeries were performed under general anesthesia with endotracheal intubation. intubating and ventilating special section: patients with covid-19 who are critically ill or require emergent surgical procedures present some unique challenges to providers. the healthcare system and providers need to be prepared in and outside of china for the covid-19 outbreak now and for any outbreaks in the future. preparedness is a pressing issue considering that many places and countries in the world are under-resourced, and at the time of writing this article, covid-19 is quickly unfolding and evolving outside of mainland china. healthcare providers, who are tasked with taking care of critically ill patients, need to perform the best practices of intubation and ventilation tailored explicitly to the victims of this sweeping covid-19 outbreak and, at the same time, adhere to strict self-protection precautions. wuhan's experience needs to be highlighted and quickly communicated throughout the world. in february 2020, we conducted four webinars specifically discussing the issues related to preparedness, airway management, lung-protective ventilation, the goal of oxygenation, and extracorporeal membrane oxygenation ( fig. 2 ). we summarize the results of these discussions, which were based on firsthand experience with treating critically ill patients in wuhan. covid-19 has a wide spectrum of clinical severity, ranging from asymptomatic to critically ill, and ultimately death. 1,5,6 a common and prominent complication of advanced covid-19 is acute hypoxemic respiratory insufficiency or failure requiring oxygen and ventilation therapies ( fig. 3 ). 3, 4 a recent report showed that 14% of patients developed dyspnea, tachypnea with a respiratory rate greater than or equal to 30 per minute, desaturation with peripheral oxygen saturation (spo 2 ) less than or equal to 93%, poor oxygenation with a ratio of partial pressure of arterial oxygen (pao 2 ) to fraction of inspired oxygen (fio 2 ) less than 300 mmhg, or lung infiltrates greater than 50% within 48 h. 1 ards occurred in 20% of the 138 patients hospitalized and in 61% of the 36 patients admitted to the intensive care unit (icu) in zhongnan hospital in wuhan. 4 organ dysfunction, injury, or failure, excluding the lungs, is common. cardiac injury occurred in 23%, liver injury in 29%, and acute kidney injury in 29% of critically ill patients. 3 neurocognitive impairments occurred in more than one third of patients with advanced covid-19. 7 invasive ventilation via an endotracheal tube is common amid this outbreak. it was performed in 2.3% of the 1,099 patients with confirmed covid-19 based on the patient cohort from 552 hospitals in 30 provinces, autonomous regions, and municipalities in mainland china, 1 in 47% of the 36 patients admitted to the icu in zhongnan hospital in wuhan, 4 and in 42% of the 52 patients admitted to the icu in jin yin tan hospital in wuhan. 3 although elective surgeries were cancelled in the epicenter of wuhan, emergent surgeries were permitted amid this outbreak. as of february 29, 2020, a total of 105 emergent surgical procedures, including 90 cesarean sections (classified as emergent surgery amid this outbreak; fig. 4 ), were performed in patients with confirmed or suspected covid-19 in tongji hospital in wuhan (data from dr. wan). some of these procedures were performed under general anesthesia with endotracheal intubation. the anesthesiologists from the department of anesthesiology at tongji hospital in wuhan performed approximately 200 nonoperating room intubations in patients with confirmed covid-19 as of february 29, 2020. this is just a snapshot of the anesthetic practice in the epicenter of wuhan amid this outbreak. currently, we do not have data detailing the total number of patients with covid-19 who received intubation and invasive ventilation or details about the outcomes associated with and after these invasive interventions. nonetheless, we can attempt to estimate this based on the available data. as of february 29, 2020, a total of 2,870 patients with confirmed covid-19 have died (http://www.nhc.gov.cn/; accessed march 1, 2020). it is assumed that all of these patients died in icus, as most, if not all, of them should have been admitted to the icu before their death. we estimate that, if using a mortality rate of 50% among patients who were admitted to the icu, a total of 5,740 patients would have been admitted to the icu (2,870 × 2 = 5,740) as of february 29, 2020. one recent report showed a mortality rate of 61.5% in patients who were admitted to the icu. 3 the other report showed a mortality rate of 49% among critically ill patients. 8 we used a mortality rate of 50% in our estimate. based on the data reporting an invasive ventilation rate of approximately 45% in patients who were admitted to the icu, 3,4 we estimate the decision to intubate can be obvious and require little deliberation, as for patients with cardiopulmonary arrest or a lost or jeopardized airway. it can also be a decision that lacks quality evidence for guidance and, thus, is a decision made at the discretion of the treating physician. in patients with acute hypoxemic respiratory failure due to covid-19, it can be challenging when deciding whether to proceed with intubation and invasive ventilation. the chinese society of anesthesiology task force on airway management released a fast-track publication with the recommendation to proceed with endotracheal intubation for patients showing no improvement in respiratory distress, tachypnea (respiratory rate greater than 30 per minute), and poor oxygenation (pao 2 to fio 2 ratio less than 150 mmhg) after 2-h highflow oxygen therapy or noninvasive ventilation. 9 these criteria should be regarded as empirical as there is no robust supporting evidence. the frontline physicians taking care of critically ill patients in wuhan suggest that intubation and invasive ventilation may have been adversely delayed in some patients. they are concerned that, amid this particular outbreak, intubation is more often used as a salvage therapy than a proactive means of supporting patients whose oxygenation is progressively declining and oxygen debt keeps increasing. the most recent report showed that, among the 22 icu patients who were intubated, 19 (86%) of them died. 3 although most frontline physicians believe the decision of intubation in some critically ill patients with covid-19 had been adversely delayed, we do not know at this time if early intubation could save more lives. we do know, based on the work performed 30 yr ago by shoemaker et al., that there is a close association between the oxygen debt accumulated over 48 h and the chance of survival in patients undergoing high-risk surgery and icu admission afterward. 10 shoemaker et al.'s work highlights the importance of timely stopping an enlarging oxygen debt using effective oxygenation and ventilation therapies. the decision-making process for nonoperating room intubation used in wuhan is summarized in figure 5 . timely, not premature, intubation is the keyword in decision-making. we added liberal criteria, including spo 2 less than 93% in room air and a pao 2 to fio 2 ratio less than 300 mmhg, to facilitate preparedness for intubation based on the experience of taking care of critically ill patients in wuhan. this proposal is justified as unprepared emergent intubation carries more risks, including cross-infection. it is also justified by the observation that some patients are relatively asymptomatic although they have a good degree of hypoxemia for inexplicable reasons (referred to as "silent hypoxemia" in wuhan). 11 silent hypoxemia may be responsible for the quick deterioration in some patients because it gives a false sense of well-being when the oxygen debt has been actually and asymptomatically increasing. this algorithm emphasizes vigilance by asking two questions for patients with respiratory distress or hypoxemia. one is whether the condition has been progressively deteriorating or if it is expected to get worse; if the answer is yes, the next question is whether 2-h high-flow oxygen therapy or noninvasive ventilation is effective. both patients and healthcare workers have to endure enhanced, but distinctive, risks during intubation and ventilation management amid the covid-19 outbreak. the enhanced risks to patients will be discussed in the coming sections of this article. the enhanced risk to healthcare workers is cross-infection. copyright © 2020, the american society of anesthesiologists, inc. unauthorized reproduction of this article is prohibited. of the 138 hospitalized patients with confirmed covid-19 in zhongnan hospital in wuhan, 40 (29%) patients were healthcare workers with hospital-associated transmission suspected as the mechanism of infection. 4 five anesthesia providers working in tongji hospital in wuhan were diagnosed with covid-19. two providers likely contracted the infection when taking care of patients with covid-19 in december 2019 when the self-protection mandate had not yet been established. the other three providers likely contracted the infection from family members. all five providers have recovered. since the establishment of the self-protection mandate in january 2020, no anesthesia providers in tongji hospital have contracted the infection. dr. shanglong yao, a well-known anesthesiologist and former vice president of the union hospital in wuhan, was diagnosed with covid-19, with the infection likely transmitted from his daughter. dr. yao was hospitalized for a prolonged 4 weeks for close observation of the new-onset atrial fibrillation and poorly controlled hypertension. he eventually recovered and was discharged home ( fig. 6 ). these are just some examples of the situations related to the healthcare providers who were infected. it was estimated that, as of february 11, 2020, a total of 1,716 health workers had confirmed covid-19 and five had died (0.3%) in mainland china. 12 the total number of cases of healthcare worker infections could be much more than this estimate. it was an observation that most of these infections occurred at the early stage of this outbreak when the self-protection mandate had not been established and reinforced. the mechanisms of transmission responsible for these infections are unknown; some cases may be nosocomial infections while the remainder may not be work related. we also do not know how many nosocomial infections are attributable to the intubation process or ventilation management. the lesson we learned from the 2003 sars outbreak is that, compared with healthcare workers who do not perform intubation or ventilation management, those who perform these tasks have a higher risk of contracting the infection. a systematic review showed that compared with healthcare workers who did not perform aerosol-generating procedures, those who performed tracheal intubation had an increased risk of contracting the 2003 sars (odds ratio, 6.6), as were those who performed noninvasive ventilation (odds ratio, 3.1), tracheotomy (odds ratio, 4.2), and manual ventilation before intubation (odds ratio, 2.8). 13 a separate study found that the protection guidelines failed to thoroughly prevent the transmission of 2003 sars to healthcare workers and that 9% of the interviewed healthcare workers who had intubated patients contracted sars. 14 however, the cause-effect relationship between infection and intubation in these healthcare workers who contracted sars was unknown. 14 despite the enhanced risk to healthcare workers, the potential harm of withholding intubation may outweigh the potential risk of cross-infection in patients who would benefit from invasive ventilation support. 15 whenever intubation and invasive ventilation are needed, they should be timely and effectively provided. the healthcare workers who are involved in caring for patients with known or suspected covid-19 should strictly adhere to the self-protection mandate (table 2) . the self-protection mandate for healthcare workers was quickly established and reinforced throughout different hospitals in wuhan after the recognition of humanto-human transmission of covid-19 toward the end of january 2020. extensive and efficient education and training were provided to all healthcare workers. at the same time, personal protective equipment that was most needed was delivered to wuhan and the rest of the country where the epidemic was quickly evolving. the contact and airborne precautions, with components of personal protective equipment, are presented in table 2. the different levels of precautions were scaled per the settings of patient care in wuhan and the rest of china (table 3) . full precaution (level iii) is mandatory for any care that involves direct patient contact, including intubation and ventilation management. in china, it is mandatory to strictly follow the personal protective equipment donning process for high-risk exposure in the following order: disposable hair cover, fittested n95 respirator or equivalent, fluid-resistant gown, two layers of gloves, goggle and face shield, and fluid-resistant shoe covers. 9 before entering an isolation area, an experienced nurse or assistant is responsible for checking the donning process ( fig. 7) . it is crucial to make sure the personal protective equipment is donned in the manner that will not interfere with procedures. it is also mandatory to strictly follow the personal protective equipment doffing process after high-risk exposure in the following order: hand hygiene, face shield and goggle removal, fluid-resistant gown removal, outer glove removal, shoe cover removal, inner glove removal, hand hygiene, n95 respirator or equivalent removal, and hair cover removal. 9 the doffing process should also be supervised, but not facilitated, to reduce the chance of contamination. it is mandatory to report any inadvertent contamination of the skin or mucosa to the hospital infection control office to assess the need for quarantine. a shower and the use of oral, nasal, and external auditory canal disinfectants are recommended after the removal of personal protective equipment. patients with confirmed or suspected covid-19 should be regarded as having an augmented risk of presenting potentially difficult and complicated intubation for the following reasons. first, when a patient requires intubation for acute hypoxemic respiratory failure, they have minimal to no respiratory reserve, and their compensatory mechanisms have already been exhausted. it is common to see a patient who starts with a dangerously low spo 2 quickly decline after loss of spontaneous breathing, followed by a slow recovery with manual facemask ventilation. second, due to strict infection control and the urgency of intubation, a careful airway evaluation is frequently not possible. third, the personal protective equipment mandated by the level iii scaled precaution makes the performance of the procedure clumsy, which may easily compromise the intubation process. fourth, strict infection and traffic control restrict backup supplies and helpers from being readily available when they are needed. fifth, the psychological pressure related to concerns of cross-infection challenges the providers, which may make an otherwise easy intubation complicated. preparedness minimizes the chance of cross-infection and improves the chance of smooth intubation. the proposed approach to prepare for intubation for patients with confirmed or suspected covid-19 is summarized in table 4. we recommend using the acronym oh-ms. maid-oxygen, helper, monitor, suction, machine, airway supplies, intravenous access, and drugs-to facilitate the preparation process for intubation. in wuhan, all portable supplies, needed or potentially needed, are packed in one package. one-time use disposable supplies are preferred. equipment that has to be reused is dedicated for patients with confirmed or suspected covid-19. no glitch or imperfection is minor when there is an associated risk. preparedness is even more crucial amid the covid-19 outbreak, as the chance of contamination may be readily enhanced during the process of a complicated intubation when all attention is devoted to saving a patient's life. an experienced practitioner, instead of students or junior personnel, should be assigned to this job. a careful and efficient airway evaluation, whenever possible, should be performed ahead of intubation. equipment that is used for more than one patient should be cleaned and disinfected before and after each use. the mixture of ethanol and chlorhexidine is recommended as the disinfecting solution for the breathing circuit in china. two single-use filters (pall bb50t breathing circuit filter, pall corp., usa), placed in the inhalation and exhalation breathing circuits, are used for infection control in wuhan. this breathing circuit filter appears capable of preventing the spread of influenza a (h1n1) virus from intubated patients, 16 and thus is implicated to be equally capable of preventing the spread of the 2019 novel coronavirus. in wuhan, most of the patients were on either high-flow oxygen therapy or bilevel positive airway pressure ventilation when the intubation was called. if the patient is on high-flow oxygen therapy, consider using a bag valve mask or a tightly fitting facemask connected to the already prepared ventilator for preoxygenation. if the patient is on a bilevel positive airway pressure machine, continue bilevel positive airway pressure ventilation for preoxygenation (supplemental digital content, http://links.lww.com/aln/c348). increase oxygen flow and use 100% fio 2 to maximize oxygenation. make sure the airway is patent. it is well advised to apply an oral or nasal airway at the first sign of difficult masking. consider manual positive pressure ventilation using a bag valve mask if preoxygenation fails to improve oxygenation. it was shown that noninvasive ventilation applied for 3 min before tracheal intubation resulted in better oxygenation than a nonrebreather bag valve mask. 17 however, a multicenter randomized trial based on the evaluation of 100% fio 2 administered with noninvasive ventilation versus that with a facemask for 3 min before tracheal intubation failed to demonstrate any benefits of using noninvasive ventilation as a preoxygenation method to reduce organ dysfunction in hypoxemic, critically ill patients. 18 clearly, there is a gap between improved oxygenation and unchanged outcomes. although the aerosol-generating potential of noninvasive ventilation is a potential concern to some providers, 19 the bilevel positive airway pressure machine is widely used amid this outbreak for patients with acute hypoxemic respiratory failure in wuhan and the rest of china. we would not recommend using bilevel positive airway pressure for preoxygenation in patients who are not on bilevel positive airway pressure ventilation; however, bilevel positive airway pressure ventilation should be continued if it is already in use. after satisfactory preoxygenation, modified rapid sequence induction is the recommended technique for anesthesia induction. 9 midazolam 1 to 2 mg may be considered for extremely anxious patients. intravenous lidocaine, 1.5 mg/kg or more, is effective in suppressing coughing during endotracheal intubation. 20 use a small dose of etomidate (0.2 to 0.3 mg/kg) for patients with hemodynamic instability or propofol (1 to 1.5 mg/kg) for patients with stable hemodynamics for induction. 9 some providers may opt to avoid etomidate due to concerns of adrenal suppression. rocuronium 1 mg/kg or succinylcholine 1 mg/ kg is administered immediately after loss of consciousness. fentanyl 50 to 100 mcg, sufentanil 10 to 20 mcg, or remifentanil 2.5 mcg/kg 21 may be used to suppress laryngeal reflexes and optimize the intubation condition. because opioids have the potential to cause coughing, 22 some providers prefer to give opioids after the accomplishment of satisfactory muscle relaxation. the choice and dose of anesthetics should be determined on a case-by-case basis, with the patient's hemodynamic stability, severity of illness, and mental status taken into consideration. vasoactive drugs should be readily available to treat extreme cardiovascular reactions. ventilation through a patent airway and using a small tidal volume should be continued throughout the induction process until the patient is intubated. the goal copyright © 2020, the american society of anesthesiologists, inc. unauthorized reproduction of this article is prohibited. is to have the patient intubated within 60 s after administration of muscle relaxants. 9 the rationale behind modified rapid sequence induction in china is to shorten the period of potentially ineffective ventilation, from the moment of losing consciousness to the moment of successful endotracheal intubation, in critically ill patients with minimal to no oxygen reserve due to covid-19. the approach of using modified rapid sequence induction in this patient population may be criticized, as some providers may prefer to proceed with slow and controlled induction if there is no immediate aspiration risk. they may argue that maximizing oxygen reserve, immediately after anesthetic induction but before endotracheal intubation, is warranted in patients with acute hypoxemic respiratory failure. they may also argue that immediately administering muscle relaxants after anesthesia induction, without testing the effectiveness of bag valve mask ventilation, is not well advised. we recognize this potential difference in approaches and leave it open for further discussion. patient coughing during intubation can generate aerosols and should be avoided. gentle airway manipulation is warranted. it is prudent to use video laryngoscopy rather than direct laryngoscopy for intubation because the former increases the distance between the healthcare worker's face and the patient's face, which may minimize the risk of contamination ( fig. 8 ). videoscopes also allow assistants to visualize the airway so that they can better facilitate the procedure. in wuhan, chest auscultation after intubation is not recommended, unless absolutely needed, due to concerns of contamination. capnography, fogging inside of the endotracheal tube, chest movement, spo 2 , the color of the patient's skin and mucous membrane, and vigilance are used to differentiate between a failed and successful intubation. the same precautions should be considered during extubation. measures to prevent patient agitation, coughing, and bucking should be applied. appropriate levels of sedation, such as dexmedetomidine (0.4 mcg · kg -1 · h -1 ) 23 or remifentanil (1 to 4 ng/ml target organ concentration) 24 infusion, should be considered. intravenous lidocaine (1 to 1.5 mg/kg) is effective for cough reduction. 25, 26 alfentanil (15 mcg/kg) is also effective in decreasing coughing and agitation during anesthesia emergence. 27 mechanical ventilation, though vital in supporting respiratory function in patients with acute hypoxemic respiratory failure or ards, may promote lung damage, a phenomenon known as ventilator-induced lung injury. 28 currently, we lack any guidelines or evidence to help us manage invasive mechanical ventilation in critically ill patients with covid-19. it is well advised to adopt the guidelines established for patients with ards, 29, 30 with appropriate modifications based on the firsthand patient care experience in wuhan (table 5) . this is justified as 67% of the icu patients developed ards based on the recent report. 3 the ards lung-protective ventilation guidelines emphasize: (1) a tidal volume less than or equal to 6 ml/ kg predicted body weight; (2) a respiratory rate less than or equal to 35 breaths/min; (3) a plateau airway pressure less than or equal to 30 cm h 2 o; and (4) a positive end-expiratory pressure (peep) greater than or equal to 5 cm h 2 o. 31, 32 the tidal volume can be started at 8 ml/kg and then lowered with an ultimate goal of 6 ml/kg. some clinicians believe that, as long as the plateau pressure can be maintained at less than or equal to 30 cm h 2 o, it may be safe to ventilate the patient with tidal volumes greater than 6 ml/kg predicted body weight. 33 the precise tidal volume for an individual patient should be adjusted according to the patient's plateau pressure, selected peep, thoracoabdominal compliance, and breathing effort. 29 it is advantageous to have a driving pressure (plateau pressure minus peep) below 12 to 15 cm h 2 o via tidal volume and peep adjustments in patients who are not spontaneously breathing. 34 in wuhan, patients with acute hypoxemic respiratory failure due to covid-19 have a poor tolerance to high peep, likely as the result of the direct and severe lung damage by the virus and inflammatory reactions. the plateau pressure reaches 40 to 50 cm h 2 o when the peep is set at 18 cm h 2 o, fio 2 at 100%, and the tidal volume at 6 ml/kg according to the fio 2 and peep table. 32 the widely used practice in wuhan, after lung recruitment maneuvers, is to set peep at 20 cm h 2 o and titrate down in a decrement of 2 to 3 cm h 2 o each time until the goals of oxygenation, plateau pressure, and compliance are all achieved. the commonly used peep in this patient population is less than 10 cm h 2 o. no mode of ventilation has been suggested to be superior to others. 35 there is literature suggesting that high-frequency oscillatory ventilation may be an option for viral-induced lung injury. 36 however, it may be best to avoid high-frequency oscillatory ventilation in patients with covid-19 due to concerns of aerosol generation. 19, 37, 38 high-frequency oscillatory ventilation has not been used amid this outbreak in wuhan. pressure-regulated volume control ventilation, although increasingly popular in the perioperative arena, has not gained momentum in icus due to the lack of evidence for its outcome benefits. in patients with acute lung injury or ards, the tidal volume can markedly exceed the lung-protective ventilation target during pressure-regulated volume control ventilation, 39 which is not desirable. pressure-regulated volume control is not the preferred mode of ventilation in wuhan. ventilation in the prone position improves lung mechanics and gas exchange and is currently recommended by the guidelines. 29, 30 the prone position, if planned, should not be a desperate final attempt but should be considered in the early stages of the disease, 40 as the evidence suggests that the early application of prolonged ventilation in the prone position decreases 28-and 90-day mortality in patients with severe ards. 41 prone position ventilation is currently widely used for critically ill patients in wuhan ( fig. 9 ). lung recruitment maneuvers, via transient elevations in airway pressure applied during mechanical ventilation, can open collapsed alveoli and thus increase the number of alveoli available for gas exchange. lung recruitment maneuvers do not significantly reduce mortality but may improve oxygenation and shorten the length of hospital stay in ards patients. 42 overall, recruitment maneuvers are not supported by high-quality evidence, 43 and caution should be exercised when using it because it can be irritating, incite coughing, and generate aerosols. adjunct therapies can be considered. many patients with acute hypoxemic respiratory failure due to covid-19 have breathing overdrive. appropriate sedation and analgesia, such as dexmedetomidine, propofol and remifentanil infusion, are warranted. the outcome evidence related to the use of muscle relaxants has been controversial. 44, 45 a recent meta-analysis concluded that muscle relaxants improve oxygenation after 48 h, but do not reduce mortality in moderate and severe ards patients. 46 nonetheless, muscle relaxation should be considered in cases of breathing overdrive, patient-ventilator dyssynchrony, and inability to achieve the targeted tidal volume and plateau pressure. it is appropriate to be conservative with intravenous fluids in patients with severe lung injury if there are no signs of tissue hypoperfusion. 29 conservative fluid therapy is the strategy used in wuhan. it is important to avoid corticosteroid treatment, given that this treatment has been shown to increase mortality and hospital-acquired infections in patients with severe influenza. [47] [48] [49] however, the most recent study suggested that early dexamethasone administration may reduce overall mortality and mechanical ventilation duration in ards patients. 50 corticosteroid treatment is currently used in selected patients with severe inflammatory lung injury in wuhan. disconnecting the patient from the ventilator results in loss of peep and atelectasis, and it should be avoided. in-line catheters for airway suctioning and endotracheal tube clamping are recommended before disconnecting breathing circuits. extracorporeal membrane oxygenation was successfully used in patients with severe influenza 51 and may play an important role in select patients. a recent review concluded that the potential of extracorporeal membrane oxygenation in reducing mortality in patients with ards due to h1n1 infection was apparent and that extracorporeal membrane oxygenation should be used as a salvage option in severely hypoxemic ards patients. 52 the conventional ventilation or ecmo for severe adult respiratory failure (cesar) trial showed that there is a potential role for extracorporeal membrane oxygenation-based management protocols in patients with severe but potentially reversible respiratory failure, and these protocols may improve survival without causing severe disabilities. 53 the ecmo to rescue lung injury in severe ards (eolia) trial showed that extracorporeal membrane oxygenation was not able to significantly reduce 60-day mortality in patients with very severe ards; 54 however, the post hoc bayesian analysis suggested a potential mortality benefit under a broad set of assumptions. 55 extracorporeal membrane oxygenation has been used in some critically ill patients with covid-19 in wuhan. more than 40 extracorporeal membrane oxygenation cases (combined) have been treated in zhongnan hospital, jin yin tan hospital, and lung hospital in wuhan. the outcomes of these patients remain to be analyzed. the covid-19 outbreak is a sweeping and unprecedented challenge in china. its impacts are currently rapidly unfolding outside of china. as of march 4, 2020, covid-19 was confirmed in 80,409 patients and led to 3,012 deaths in mainland china. approximately 3.2% of patients with covid-19 received intubation and invasive ventilation support. how to provide the best practices of intubation and ventilation amid this mass medical emergency is a real but unprecedented question. in this article, we summarize the firsthand experience pertinent to intubation and ventilation management from the physicians who are taking care of the critically ill patients with covid-19 in wuhan. in patients with acute refractory hypoxemic respiratory failure, timely, but not premature, intubation and invasive ventilation support may be superior to high-flow oxygen therapy and bilevel positive airway pressure ventilation in boosting transpulmonary pressure, opening collapsed alveoli, improving oxygenation, decreasing oxygen debt, and offering a better chance for the lungs to heal. the invasive nature of intubation and ventilation exposes patients to an augmented risk of procedure-related mishaps. at the same time, these procedures present healthcare providers with an enhanced risk of cross-infection; thus, strict self-protection precautions are mandatory. tilation and the goal of oxygenation amid the covid-19 outbreak. the authors also thank dr ) for their participation in the fourth webinar held on february 29, 2020, discussing extracorporeal membrane oxygenation amid the covid-19 outbreak. all these four webinars were organized by dr responding to covid-19-a once-in-acentury pandemic? clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in clinical features of patients infected with 2019 novel coronavirus in epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study neurological manifestations of hospitalized patients with covid-19 in wuhan, china: a retrospective case series study characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the chinese center for disease control and prevention chinese society of anesthesiology task force on airway management: expert recommendations for tracheal intubation in critically ill patients with noval coronavirus disease 2019 role of oxygen debt in the development of organ failure sepsis, and death in high-risk surgical patients critical care crisis and some recommendations during the covid-19 epidemic in china novel coronavirus pneumonia emergency response epidemiology team: [the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review intubation of sars patients: infection and perspectives of healthcare workers should noninvasive ventilation be considered a high-risk procedure during an epidemic? can breathing circuit filters help prevent the spread of influenza a (h1n1) virus from intubated patients? noninvasive ventilation improves preoxygenation before intubation of hypoxic patients effect of preoxygenation using non-invasive ventilation before intubation on subsequent organ failures in hypoxaemic patients: a randomised clinical trial critically ill patients with middle east respiratory syndrome coronavirus infection intravenous lidocaine as a suppressant of coughing during tracheal intubation in elderly patients the optimal dose of remifentanil for acceptable intubating conditions during propofol induction without neuromuscular blockade tussive effect of a fentanyl bolus administered through a central venous catheter efficacy of intraoperative dexmedetomidine infusion on emergence agitation and quality of recovery after nasal surgery effects of maintaining a remifentanil infusion on the recovery profiles during emergence from anaesthesia and tracheal extubation bloodpressure and pulse-rate responses to endotracheal extubation with and without prior injection of lidocaine a comparative study between the effects of 4% endotracheal tube cuff lignocaine and 1.5 mg/kg intravenous lignocaine on coughing and hemodynamics during extubation in neurosurgical patients: a randomized controlled double-blind trial alfentanil suppresses coughing and agitation during emergence from isoflurane anesthesia mechanisms of ventilator-induced lung injury european society of intensive care medicine, and society of critical care medicine: an official american thoracic society/european society of intensive care medicine/society of critical care medicine clinical practice guideline: mechanical ventilation in adult patients with acute respiratory distress syndrome lung protective ventilation strategy for the acute respiratory distress syndrome ventilation with lower tidal volumes as compared with traditional tidal volumes for acute lung injury and the acute respiratory distress syndrome ventilatory management of acute respiratory distress syndrome: a consensus of two driving pressure and survival in the acute respiratory distress syndrome pressure-controlled versus volume-controlled ventilation for acute respiratory failure due to acute lung injury (ali) or acute respiratory distress syndrome (ards) ventilator management for hypoxemic respiratory failure attributable to h1n1 novel swine origin influenza virus high-frequency oscillatory ventilation versus conventional ventilation for acute respiratory distress syndrome nursing and infection-control issues during high-frequency oscillatory ventilation work of breathing during lung-protective ventilation in patients with acute lung injury and acute respiratory distress syndrome: a comparison between volume and pressure-regulated breathing modes ventilator management for acute respiratory distress syndrome associated with avian influenza a (h7n9) virus infection: a case series prone positioning in severe acute respiratory distress syndrome lung recruitment maneuvers for ards patients: a systematic review and meta-analysis recruitment manoeuvres for adults with acute respiratory distress syndrome receiving mechanical ventilation acurasys study investigators: neuromuscular blockers in early acute respiratory distress syndrome early neuromuscular blockade in the acute respiratory distress syndrome neuromuscular blockade in acute respiratory distress syndrome: a systematic review and meta-analysis of randomized controlled trials esicm h1n1 registry contributors: use of early corticosteroid therapy on icu admission in patients affected by severe pandemic (h1n1) v influenza a infection corticosteroids as adjunctive therapy in the treatment of influenza corticosteroids as adjunctive therapy in the treatment of influenza: an updated cochrane systematic review and meta-analysis gonzález-martín jm; dexamethasone in ards network: dexamethasone treatment for the acute respiratory distress syndrome: a multicentre, randomised controlled trial extracorporeal membrane oxygenation for 2009 influenza a(h1n1) acute respiratory distress syndrome extracorporeal life support: the next step in moderate to severe ards-a review and meta-analysis of the literature elbourne d; cesar trial collaboration: efficacy and economic assessment of conventional ventilatory support versus extracorporeal membrane oxygenation for severe adult respiratory failure (cesar): a multicentre randomised controlled trial extracorporeal membrane oxygenation for severe acute respiratory distress syndrome extracorporeal membrane oxygenation for severe acute respiratory distress syndrome and posterior probability of mortality benefit in a post hoc bayesian analysis of a randomized clinical trial a novel coronavirus outbreak of global health concern a review of isolation gowns in healthcare: fabric and gown properties prone position for acute respiratory distress syndrome. a systematic review and meta-analysis prone-supine ii study group: prone positioning in patients with moderate and severe acute respiratory distress syndrome: a randomized controlled trial prone position for acute respiratory failure in adults semi-recumbent position versus supine position for the prevention of ventilator-associated pneumonia in adults requiring mechanical ventilation cov study group: clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: a report of nosocomial transmission address correspondence to dr. xiong: department of anesthesiology and perioperative medicine, shanghai fourth people's hospital, tongji university school of medicine, shanghai 200081, china. mzkxlz@126.com. information on purchasing reprints may be found at www. anesthesiology.org or on the masthead page at the beginning of this issue. anesthesiology's articles are made freely accessible to all readers, for personal use only, 6 months from the cover date of the issue. the authors declare no competing interests. key: cord-323481-uz6usokd authors: wang, yixuan; wang, yuyi; chen, yan; qin, qingsong title: unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (covid‐19) implicate special control measures date: 2020-03-29 journal: j med virol doi: 10.1002/jmv.25748 sha: doc_id: 323481 cord_uid: uz6usokd by 27 february 2020, the outbreak of coronavirus disease 2019 (covid‐19) caused 82 623 confirmed cases and 2858 deaths globally, more than severe acute respiratory syndrome (sars) (8273 cases, 775 deaths) and middle east respiratory syndrome (mers) (1139 cases, 431 deaths) caused in 2003 and 2013, respectively. covid‐19 has spread to 46 countries internationally. total fatality rate of covid‐19 is estimated at 3.46% by far based on published data from the chinese center for disease control and prevention (china cdc). average incubation period of covid‐19 is around 6.4 days, ranges from 0 to 24 days. the basic reproductive number (r(0)) of covid‐19 ranges from 2 to 3.5 at the early phase regardless of different prediction models, which is higher than sars and mers. a study from china cdc showed majority of patients (80.9%) were considered asymptomatic or mild pneumonia but released large amounts of viruses at the early phase of infection, which posed enormous challenges for containing the spread of covid‐19. nosocomial transmission was another severe problem. a total of 3019 health workers were infected by 12 february 2020, which accounted for 3.83% of total number of infections, and extremely burdened the health system, especially in wuhan. limited epidemiological and clinical data suggest that the disease spectrum of covid‐19 may differ from sars or mers. we summarize latest literatures on genetic, epidemiological, and clinical features of covid‐19 in comparison to sars and mers and emphasize special measures on diagnosis and potential interventions. this review will improve our understanding of the unique features of covid‐19 and enhance our control measures in the future. and figure 1 , covid-19 has caused 82 623 confirmed cases and 2858 deaths globally. the total case-fatality rate is 3.46% as shown in table 1 . because covid-19 started from wuhan, the capital city of hubei province with a large population of nearly 14 million people, 58.3% cases are in wuhan. a total of 1932 health workers have been infected in wuhan alone, 9 which overwhelmed the local health system and resulted in the highest case-fatality rate (4.42%). excluding hubei province, the rest of china has 13 045 cases, 109 fatalities (0.84%). outside of china, covid-19 has spread to 46 countries and has caused 3664 infections and 67 fatalities (1.83%). overall, the case-fatality rate of covid-19 so far is much lower than either sars (9.6%) or mers (34.5%). 10 here, we summarized common and discrete features of sars-cov-2 in comparison to its two predecessors (sars-cov and mers-cov) in genetics, epidemiology, clinical features, and further discussed challenges for diagnosis and special control measures for covid-19. full-length genome sequences of sars-cov-2 were obtained from early infected individuals related to a wild animal market in wuhan by different research groups through next-generation sequencing. 1, 2, 11 full genomic length of this novel coronavirus ranges from 29 891 to 29 903 nucleotides (nt). 2 1, 2, 11 the close phylogenetic relationship to ratg13 suggests bats are probably natural hosts for sars-cov-2. 2 human sars-cov-2 have a unique rrar motif in the spike protein which is not found in coronaviruses isolated from pangolins, suggesting sars-cov-2 may not come directly from pangolins. 12 an evolutionary study 13 based on 86 genomic sequences from gisaid (https://www.gisaid.org/) showed three deletions were found in isolates from japan, usa, and australia, 93 mutations found over the entire genomes. of note, eight mutations were found in the spike surface glycoprotein, especially three mutations (d 354 , y 364 , and f 367 ) located in the spike surface glycoprotein receptor-binding domain (rbd), which suggested sars-cov-2 may rapidly evolve to evade immune response and adapt to other hosts in the future. sars-cov-2 share 79% nt sequence identity to sars-cov and around 50% to mers-cov. 2 however, the seven conserved replicase domains in orf1ab (used for cov species classification) of sars-cov-2 are 94.6% identical to sars-cov, implying the two belong to same species. 1, 2 the receptor-binding protein spike (s) gene of sars-cov-2 is highly divergent to all previously described sarsr-covs with less than 75% nt sequence identity to except a 93.1% nt identity to ratg13. homology modeling revealed sars-cov-2 had a similar rbd structure to that of sars-cov. 11 further study showed sars-cov-2 uses the same cell entry receptor, ace2, as sars-cov, not cd26 as mers-cov. 2 structural analysis by cryo-electron microscopy revealed sars-covs protein binds ace2 with 10 to 20 folds higher affinity than sars-cov, 14 which suggests that sars-cov-2 may be more infectious to human than sars-cov. transmission of infectious diseases must rely on three conditions: sources of infection, routes of transmission, and susceptible hosts. 21 with enforced implementation of isolation strategies, r 0 was expected to decline in coming days. the mean incubation period was around 6.4 days (ranges from 0 to 24 days). 19, 22 similar to sars and mers, nosocomial transmission was a severe problem to covid-19, and even worse. a recent retrospective study 9 indicated that a total of 1716 health workers were infected, accounting for 3.84% of total cases. nosocomial infections extremely burdened the health system and hindered early infected individuals from getting immediate medical supports, therefore resulting in high case-fatality rate in wuhan as shown in table 1 vertical transmission was sporadically reported in some media but not yet proved. chen et al 28 hospital. 28 it is reasonable to assume that a newborn could be infected, either in utero or perinatally, and, thus, newborns should be placed in isolation to avoid exposure to any source of infection. in terms of susceptible populations, all groups were generally susceptible to covid-19 regardless of age or sex. 9 patients aged from 30 to 79 accounted for 86.6% of all cases. 9 the median age of the patients was 47 years. 30 unlike sars and mers, patients diagnosed as covid-19 have presented with high viral loads even when those have no fever or mild symptoms. 31 high titers of sars-cov-2 were detected in travelers who recently visited wuhan and have no fever or mild symptoms in the united states 31 and germany 32 and other places. 33 a study showed high viral loads were detected in upper respiratory specimens of patients with covid-19, and viral shedding pattern of patients resembles that of patients with influenza. 33 this suggests sars-cov-2 may stay around for some time like influenza viruses. the full spectrum of disease severity as shown in the guidelines for diagnosis and treatments for covid-19 34 36 less common symptoms included muscle ache, confusion, headache, sore throat, rhinorrhoea, chest pain, sputum production, 36 and nausea and vomiting. 35 severe complications included ards, rnaaemia, acute cardiac injury, and multiple organ failure. 36 the median time from first symptom to dyspnea was 5.0 days, to hospital admission was 7.0 days, and to ards was 8.0 days. 23 67 white blood cell count is generally not high. 76 fell in the early course, it was associated with adverse clinical outcome. 88 aptt, elevated d-dimer, and alt. 39 1. similar to sars, common laboratory findings include leukopenia, 79, 80, 84, 89 elevated ldh, ast, thrombocytopenia, and lymphopenia. 79 2. several cases: viral rna in blood, urine, and stool but at much lower viral loads 80,90 compared to sars. 3. elevated liver enzymes, 91 which may be related to liver injury. 1. depressed total lymphocytes, prolonged pt, elevated levels of ldh, 23 ast, alt, 73 blood urea, and creatinine. 23 and erythrocyte sedimentation rate and normal procalcitonin. 34 and peripheral blood lymphocytes progressively decreased. 34 4. critically ill patients: elevated inflammatory factors. 34 nonsurvivors: the neutrophil count, d-dimer, blood urea, and creatinine levels is very high. 23 radiologic features 1. the predominant involvement of lung periphery and the lower zone. absence of pleural effusion. 67 2. ground-glass opacification and lobe thickening. 92 1. bilateral hilar infiltration, unilateral or bilateral patchy densities or infiltrates, ground-glass opacities, and small pleural effusions. 67 lower lobes are affected with more rapid radiographic progression than sars. 67 1. bilateral distribution of patchy shadows and ground-glass opacity was a typical hallmark of ct scan for ncip. 23 a substantial proportion of patients on initial presentation. 73 pleural effusion is rare. 34 abbreviations: alt, alanine aminotransferase; aptt, activated partial thromboplastin time; ards, acute respiratory distress syndrome; ast, aspartate aminotransferase; ck, creatine kinase. crp, c reactive protein; dic, disseminated intravascular coagulation; ldh, lactate dehydrogenase; mers-cov, middle east respiratory syndrome coronavirus; pt, prothrombin time; sars-cov, severe acute respiratory syndrome-coronavirus. cross-contamination of samples, and inconsistence of sample collections and preparations. rt-pcr methods generated false-positive or false-negative results, 42, 44 which caused troubles for isolating sources of infections and determining hospitalization days. according to current guidelines for diagnosis and treatments for covid-19, if one is tested by rt-pcr negative for twice, he/she is considered the cured and should be discharged. however, some of cured and discharged patients later have been tested positive by rt-pcr. 45 presumably, many factors mentioned above could lead to "false negative" in these cases. on the other hand, a proportion of patients with fever or pneumonia were wrongly isolated together with other confirmed patients with covid-19 in general medical wards because rt-pcr could produce false-positive results due to sample contaminations or other reasons. these patients turned out to be infected by influenza or other pneumonia associated pathogens. a recent large diagnostic study 42 57 in addition to the the authors declare that there are no conflict of interests. qq conceived, wrote, and revised the paper. yw, yw, and yc equally contribute to writing. all authors approved the final version of the manuscript before submission. qingsong qin http://orcid.org/0000-0001-6315-5809 a novel coronavirus from 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gaps of middle east respiratory syndrome coronavirus (mers-cov) in humans clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: a report of nosocomial transmission family cluster of middle east respiratory syndrome coronavirus infections national health and family planning commission of people's republicao of china. diagnosis and treatment plan for middle east respiratory syndrome cases (2015 edition) the clinical and virological features of the first imported case causing mers-cov outbreak in south korea world health organization. who mers global summary and assessment of risk haematological manifestations in patients with severe acute respiratory syndrome: retrospective analysis isolation of a novel coronavirus from a man with pneumonia in saudi arabia clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection middle east respiratory syndrome and severe acute respiratory syndrome: current therapeutic options and potential targets for novel therapies sars: clinical presentation, transmission, pathogenesis and treatment options unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (covid-19) implicate special control measures key: cord-304418-k9owyolj authors: le maréchal, m.; morand, p.; epaulard, o.; némoz, b. title: covid-19 in clinical practice: a narrative synthesis date: 2020-09-29 journal: med mal infect doi: 10.1016/j.medmal.2020.09.012 sha: doc_id: 304418 cord_uid: k9owyolj the coronavirus disease 2019 (covid-19) was first reported in the city of wuhan, china. the disease rapidly spread to the rest of china, to southern-east asia, then to europe, america, and on to the rest of the world. covid-19 is associated with a betacoronavirus named sars-cov-2. the virus penetrates the organism through the respiratory tract, conveyed by contaminated droplets. the main cell receptor targeted is the surface-bound ace-2. as of the 26th july 2020, 15,200,000 covid-19 cases and 650,000 deaths were reported worldwide. the mortality rate is estimated between 1.3 and 18.3%. the reproductive rate without any public health intervention is estimated around 4-5.1 in france. most hospitalized patients for covid-19 present respiratory symptoms, which in some cases is associated with fever. up to 86% of admissions to icu are related to acute respiratory failure. to date, no anti-viral therapy has proven its efficacy considering randomized trials. only immunomodulatory treatments such as corticosteroids have shown to cause significant improvement in patient outcome. a study estimated the rt in the city of wuhan, china, between the 1 st january 2020 and the 8 t march 2020 [22] , during five successive time periods (corresponding to different public health interventions). rt peaked at 3.82 on the 24 th january 2020 (with no major public health intervention), and subsequently declined, to below 1.0 on the 6 th february 2020 (after one week of city lockdown, traffic suspension, and home quarantine) and was below 0.3 on the 1 st march 2020 (after 15 days of quarantine) [22] . in south korea, reproduction number rt was estimated at 1.5 (95% confidence interval (ci) 1.4-1.6) [18] . in france, flaxman et al. estimated rt before lockdown between 4-5.1 (95%ci), and around 0.5 during lockdown [23] . the virus penetrates the organism through the respiratory tract, conveyed by contaminated droplets. while the exact viral progression remains elusive, the virus seems to have a favorable tropism for epithelial cells within the airways, leading to viral replication both in the nasal cavities and in distal bronchioles [24] . the main cell receptor targeted by the viral surface glycoprotein (s) is the surfacebound angiotensin-converter enzyme 2 (ace2) [8] , yet it is still unclear if the virus can benefit from a second receptor to achieve gain cell entry. tmprss2 is a cellular serine proteinase whose role has been pointed out to prime sars-cov-2 cellular entry [25] . the viral s protein, also known as spike, is responsible for both cell attachment and membrane fusion. it is formed by three dimers of two non-covalently bound domains s1 and s2. both subunits are synthetized as a protomer resulting from the expression of the s gene. s1 and s2 are efficiently cleaved by a cellular furin [26] thanks to a polybasic motif (prra) specific of sars-cov-2 [27] . because of its specificity and key role in viral cycle, the s protein constitutes the main target for vaccine candidates [28] . diagnosis of covid-19 requires laboratory confirmation, usually performed by detection of viral rna by a reverse-transcription polymerase chain reaction (rt-pcr). while the first laboratory confirmed cases in wuhan early in january 2020 relied on deep sequencing techniques [29] , highly scalable assays have since been developed after the viral sequence was published. the first rt-pcr protocol was published by drosten and colleagues [30] from charité university in berlin, and since then adopted by the who. this approach relies on the amplification and detection of the following sequences among the sars-cov-2 genetic sequence: the e gene encoding the envelope protein is used as a screening assay targeting all members of the betacoronavirus genera, and both the rdrp gene or the n gene are used as confirmatory assays due to their specific sequence in the sars-cov-2 species. this protocol has been widely adopted in commercially available test kits and is now used in most facilities. the paris institut pasteur has developed its own assay [31] , based on the detection of two sequences in the rdrp gene spanning nucleotides 12621-12727 and 14010-14116. this protocol has been widely used in french laboratories to manage early covid-19 suspicions and cases [32] . such assays can be performed on several samples, and the choice of sampling site has been a debated issue considering the consequences of false negative results. nasal swabs, oropharyngeal swabs, saliva, sputum and bronchoalveolar lavage fluid (bal) were mostly reported. nasal swabs have proven to be effective and provided adequate sensitivity (80%) [33, 34] , if performed properly. oropharyngeal swabs tend to be less sensitive (32%) [35] . saliva collection has been proposed as a viable alternative yielding higher sensitivity (91.7%) [36] , also addressing the availability of swabs issue as worldwide demand surge and laboratories face shortages in stocks. sputum samples, while being more sensitive than upper respiratory tract samples (95.7%) [37, 38] , raise security concerns for the safety of healthcare workers regarding the droplet dissemination nature of the covid-19. bal and other lower respiratory tract samples are widely used in intensive care units and yield very good results (93% sensitivity) [35] . the viral load seemed higher in early stages of the disease [39] , with symptomatic patients exhibiting higher viral titers as assessed by the lower ct numbers [40] . when analyzed by rt-pcr, stools are frequently positive (41%), and high viral loads have been pointed out in such samples in both asymptomatic and symptomatic patients [41] . no relation has been established as of today between enteric viral excretion and clinical outcome and disease severity. in children, the average duration of viral rna shedding in stools are 29 days (+/-12 days). the duration of viral shredding seemed to decrease with age [42] and infectivity of stools is low to non-existent. due to feces positivity, the sampling of wastewater has been proposed to assess viral circulation [43] . plasmatic detection of sars-cov-2 has been reported but only with low viral titers, and mainly in clinically severe cases [44] ; bloodstream infectivity has yet to be demonstrated. urine has remained virus-free except in one study [45] . most genomic testing in asymptomatic patients [46] returned negative after 2-3 weeks, with exceptional long shedding up to 45 days after symptom onset [47, 48] , raising the question of the infectivity of such viral shedding. excretion of infectious virions is thought to span two days before onset of symptoms up to 8 days after onset [49] , viral excretion peaking at day 4 post-infection [50] , supporting the effectiveness of a 14-day quarantine period for case isolation. however, results do not fully correlate with infectivity: viral culture from clinical samples is usually infeasible after 8 days after onset of symptoms [51] . nucleic acid testing (nat) is key to patient management and surveillance of disease propagation. according to several works, incubation period has been estimated between a mean of 4.8 and 6.4 days [52] [53] [54] [55] . lauer et al. estimated that symptom onset will occur within 11.5 days for 97.5% of patients, and that a 14 days quarantine would be sufficient [53] . a large work from zhou et al. described clinical timeline for an 813 patient cohort [56] . the mean time from illness onset to intensive care unit (icu) admission was 9-12 days [21, 56] ; it was 7 days (4-9) to dyspnea [56] , 11-12.5 days to hospital admission [56, 57] , 9 days (7-13) to sepsis, 12 days (8-15) to respiratory failure, and 21-44 days to death, depending on studies [56, 58] . time between onset of symptoms and dyspnea is 5-7 days, to ards 8-12 days [56, 59] . one initially described symptom was fever; however, up to 60% of patients were described as nonfebrile, and up to 52% of patients admitted in icu were non-febrile [52] . coughing was reported in 60-82% of cases, asthenia in 38-70% of cases, myalgia in 11-44% of cases, dyspnea/shortness of breath in 19-55% of cases, and diarrhea in 2-10% of cases [55, [59] [60] [61] . no symptoms are specific of covid-19, but surprisingly, anosmia and ageusia appeared to be strongly linked with covid-19 infection. mechanism for these symptoms is still to be unveiled, as well as for digestive forms in elderly patients presenting with only diarrhea. a study described imaging data among 37 asymptomatic patients [48] . chest ct evidenced in 11 of them (30%) focal ground glass opacities, and in 10/37 (27%) stripe shadows and/or diffuse consolidation; 16/37 (43%) had a normal ct scan. in a 63 asymptomatic chinese cohort, 29/63 patients had abnormal ct scans; few patients (13%) had comorbidities [62] . the most frequent presentation of hospitalized covid-19 is pneumonia (91-100%) with dyspnea and a rarely productive cough [52, 55, 56, 59, 61] . in case of patients diagnosed with clinical pneumonia, chest x-ray and ct-scanner found bilateral ground-glass opacity in 25-100% of cases [56, 59] . when considering all hospitalized covid-19 patients, ct scans evidenced ground-glass opacities in 56-71% of patients and consolidation in 59% of patients [52, 56] . pulmonary injury was bilateral in 52-75% of patients [52, 56] . thromboembolic complications several works have described the high incidence in covid-19 patients of both venous and arterial thromboembolic diseases. in klok's study of 184 patients with proven covid-19 pneumonia admitted to the icu in the netherlands, and who all received at least standard dose thromboprophylaxis, the incidence of thrombotic complication was 31% (95%ci 20-41%) [63] . in an italian study of 362 cases (in icu and on general wards), 28 presented a thromboembolic event (7.7%). the authors estimated that those events were highly underestimated due to the low number of specific imaging tests performed [64] . known risk factors for thromboembolic events that are reported in covid-19 are excessive inflammation and immobilization [65] . however, in a large multicenter international work published by freund et al among 3,253 patients who underwent a computed tomography pulmonary angiogram for a suspected pulmonary embolism, a positive covid-19 status was not associated with pulmonary embolism in multivariate analysis (p=0.40) [66] . cardiac injuries have been described in covid-19 patients. viruses are a common cause of myocarditis [67] ; myocardial injury can be related to direct cell injury caused by the virus, to t lymphocyte mediated cytotoxicity, to hemodynamic damage induced by hypoxia or shock, or related to cytokine storm [67] . arrhythmia has been described as a cause of transfer in icu in 44% of covid-19 patients [59] ; in an covid-19 acute setting, it can result from direct cardiomyocyte injury, to an infection of the pericardium causing massive edema, or to an ischemia due to microcirculation lesions [68] . in a 416 cohort of patients in wuhan, china, 82 patients with elevated levels of cardiac troponin had a higher risk of hospital death [69] . several neurological manifestations of covid-19 have been reported. manifestations are very diverse: -olfactory dysfunction: generally, post-viral olfactory loss account for 11% of acute olfactory dysfunction [70, 71] . several studies reported olfactory dysfunction among covid-19 patients (5-86%) [72] [73] [74] . this may be related to a localized olfactory cleft edema (local inflammation), or a direct neuroinvasion of the olfactory nerve [70, 73] . the loss of flavor perception is also frequently reported; it is considered to be mainly due to a loss of retronasal olfaction rather than a loss of sense of taste itself [70] , -central nervous system manifestations: confusion [72, 75, 76] , acute cognitive disorder, acute myelitis, encephalopathy, encephalitis [77] , intracranial hemorrhage, strokes [72, 75, 76] , seizures, -peripheral nervous system manifestations: guillain-barré syndrome [78] [79] [80] [81] , skeletal muscle damage (hyperckemia, rhabdomyolysis, myopathy [72, 76] ), dysautonomia), -neuropsychiatric symptoms [82] : anxiety, depression, insomnia, and psychosis suggested mechanisms are the hypoxic brain injury on severe pneumonia with peripheral vasodilatation, hypoxia, hypercapnia, and anaerobic metabolism, immune mediated injury related to the cytokine storm, and sars-cov-2 direct neurovirulence, since it has already been described for other coronaviruses [76, 83] . prevalence of reported comorbidities among patients with covid-19 has largely varied according to countries. the largest published cohorts are among chinese and american patients, and main comorbidities are hypertension (17-57%) [19, 84, 85] , obesity (42%) [84] , diabetes (8-34%) [84] , and cardiovascular disease (4%) [19, 85] . being a man was described as the main risk factor for covid-19 [61, 85] . most icu admissions were related with a respiratory failure (54-86%) [56, 86, 87] , that is also the leading cause of mortality (93-100%) [56, 87] . patients with respiratory failure are described to present an acute respiratory distress syndrome (ards), defined as a respiratory failure not fully explained by cardiac failure or fluid overload, bilateral opacities in chest imaging, and oxygenation pao2/fio2 < 300 mmhg [88] . report from critically-ill-patients series suggested that those patients presented a "cytokine storm". biological data showed a higher level of il-6 in critically-ill and non-surviving patients, a higher level of crp and a higher level of ferritin [56, 59, 86, 89] . among severe patients, the lymphocytes count was lower than mid patients or healthy controls (respectively 1,132mol/l, 1,256mol/l, and 2,215mol/l). cd4+ and cd8+ lymphocytes were also lower in the severe-patients group [89] . necropsy of patients who died from covid-19 allowed histological analysis of lung tissue samples. reported patients spent between 1 and 23 days in icu before death. macroscopic examination found lungs which were heavy, congested and edematous with patchy involvement. histological examination found features corresponding to the exudative and early or intermediate proliferative phases of diffuse alveolar damage (capillary congestion, interstitial and intra-alveolar edema, dilated alveolar ducts, collapsed alveoli and loss of pneumocytes). authors also reported interstitial pneumonia (inflammatory lymphomonocytic infiltrate along the slightly thickened interalveolar septa), organizing pneumonia, and acute fibrinous organizing pneumonia [90] . a review article on children presenting covid-19 was published by cui et al. reporting clinical, biological and imaging features on 2.597 children [91] . among all cases 7.6% were asymptomatic, 45 .5% were mild, 41.5% were moderate, 4.4% were severe, 0.9% were critical, and 0.1% (3) led to death. regarding clinical characteristics, authors collected data from 23 articles (452 children): 43% presented with fever, 43% with cough, 20% with sore throat, 17% with tachycardia, 16% with rhinorrhea, 15% with nasal congestion, and 13% with shortness of breath. among 23 critical cases, six had an underlying disease. pulmonary imaging in 294 cases reported 30% of ground glass opacities, 20% of local patchy shadow, 15% of bilateral patchy shadow, and 1% of interstitial lesions. in an international study among 582 children presenting covid-19 infection, reported risk factors for admission to icu or requiring mechanical ventilation were being less than 1-month-old (p<0.001) and having an underlying disease (p<0.001) [92] . observations described a higher risk of kawasaki-like inflammatory syndrome in children infected by sars-cov-2, also called by who the covid-19 associated pediatric multisystem inflammatory syndrome [93] ; e.g., a 497% increase of children admitted for a kawasaki-like syndrome during covid-19 epidemic was described in a small french cohort [94] ; igg antibodies against sars-cov-2 infection were detected among 19/21 of children presenting with a kawasaki-like syndrome during the epidemic in another french cohort [95] . kawasaki disease is described as an acute febrile systemic vasculitis that affects medium and small-sized blood vessels. one suspected mechanism is a post-viral immunological reaction to several viruses (influenza [96] , enterovirus [97] , adenovirus [98] , parvovirus [99] , vzv [100] , ebv [100] , measles [101] , or dengue [102] ). upon infection, humoral antiviral immunity is triggered, owing to the development of specific antibodies. a vast majority of infected patients will generate anti-sars-cov-2 antibodies [103] . antibody titers peak around day 30 post-infection [104] , but from this point forward only decrease.. igm and igg kinetics do not differ significantly [105] , thus making differential isolation of these markers void. seroconversion is witnessed at a median of 14 days after symptom onset [106] . high antibody titers are associated with severe respiratory symptoms, asymptomatic patients having lower titers [105] . this raises the so far unresolved question of covid-19 immune mechanisms and protection. it is not clear whether high antibody titers could promote severe clinical presentations by a mechanism similar to antibody dependent enhancement [107, 108] . on the other hand, pauci-symptomatic forms of covid-19 could trigger a reduced humoral response only that could correlate with a shortened duration of protection [109] . anti-sars-cov-2 antibodies are directed towards both the spike (s) protein and the nucleocapsid (np) [110] . neutralising antibodies are observed in most patients and recognise specifically the spike (s) protein [111] . neutralising activity appears to be correlated with the presence of antibodies binding the receptor-binding domain (rbd) in its closed conformation within the spike protein [112] , and the detection of such antibodies could be a surrogate marker of protection. no cross-reactivity with other human coronavirus (hcov-oc43, hcov-nl63, hcov-229e and hcov-hku1) has been evidenced to date (ref). however, cross-reactivity with sars-cov-1 has been shown at least in vitro [26] . while serological assays allow large epidemiological studies and enable better evaluations of epidemic parameters (rt, for instance), individual benefit is scarce, if existent. accordingly, we believe patient management should focus on molecular based assays. to date, no anti-viral therapy has proven its efficacy and the current management of covid-19 remains supportive care and ventilatory support when needed. remdesivir remdesivir (gs-5734) is a nucleotide analog that targets viral rna polymerases. it has an established in vitro (culture cells) and in vivo (mouse and primate models) efficiency on multiple genetically distinct coronaviruses, and on ebola virus [113, 114] . its in vitro effect on sars-cov-2 has been reported in wang et al.'s work, with a high 90% effective concentration value against infection of vero e6 cells [115] . williamson explored remdesivir's efficiency in 12 rhesus macaques infected with sars-cov-2 infection [116] . one over six macaques in the remdesivir group developed a respiratory disease vs 6/6 in the control group. after euthanasia and lung analysis, no virus was detected in lung tissue samples in the remdesivir group; remdesivir was detected in all six lungs of the treated animals. only 3/36 lobe lungs in the control group were virus-free. there was no difference in viral load in bal between both groups. gilead restricted access to remdesivir since the beginning of covid-19 pandemic to compassionate use and to clinical trials [117] . the first clinical study on remdesivir was published by grein et al. on 53 patients, without any control group. treatment was started 12 days after symptom onset; 68% of treated patients showed an improvement regarding oxygen support, and 13% of patients who completed treatment died [118] . a large international clinical trial compared 541 patients receiving remdesivir with 522 patients treated with placebo. a shorter time to recovery (11 days vs 15 days) was reported in the remdesivir group (p<0.001). adverse events were reported (21% in the remdesivir group and 27% in the placebo group [119] ). goldman et al. compared 5 vs 10 days of remdesivir treatment in a multicentric, international clinical trial among 397 patients and did not observe any difference between the 2 groups at 14 days after treatment onset on primary outcome (clinical efficacy on a 7-points scale) [120] . lopinavir is an antiviral agent developed to target hiv protease; it is generally used in association with ritonavir, a pharmacokinetic "booster" increasing lopinavir plasma concentration. it is widely used in adults living with hiv/aids [121] . lpv/rtv is regarded as a potential anti-sars-cov-2 agent since several trials on sars-cov-1 showed a favorable effect. indeed, in a 2003 study of 1,521 patients with sars, chan et al. reported a 2% death rate in the lpv/rtv group vs 16% in the soc group (p<0.05) if lpv/rtv was used as initial treatment, but with no difference as a rescue treatment [122] . in a 2004 study exploring the efficacy of lpv/rtv in patients with sars regarding a composite primary outcome (severe hypoxemia or death at day 21), chu et al observed that 2% in the lpv/rtv group met the primary outcome, vs 29% in a historic control group (p<0.001) [123] . the first large clinical trial published on lpv/rtv on sars-cov-2 compared 99 patients receiving the antiviral vs 100 receiving soc alone [124] ; there was no difference between the 2 groups regarding the primary end point (time to improvement) (15 vs 16 days, p=0.09). noteworthily, the median time between symptom onset and treatment was 13 days. 48% of patients in the lpv/rtv group vs 50% in the soc group who underwent an adverse event. hydroxychloroquine (hcq) is a widely used molecule in limited forms of lupus, with a low price, and it has an established clinical safety profile [125] in vitro studies showed the effect of chloroquine [115] and hcq in inhibiting sars-cov2 infection [126] . in vitro activity of hcq and chloroquine against sars-cov-2 were not different in liu et. al's work [126] , and hcq was found, in vitro, to reach three times the potent antiviral activity of chloroquine in yao et. al's work [127] . noteworthily, hcq was four times less toxic than chloroquine in animal study [128] . however, a recent in vitro study showed that chloroquine did not block sars-cov-2 infection of the tmprss2-positive lung cell [129] . another in vitro study also found that hcq did not show any antiviral activity in a model of reconstituted human airway epithelium [130] . due to such in vitro results, several trials assessed the efficiency of hcq on viral load in respiratory samples (without clinical considerations [131] [132] [133] [135] . association of hcq and azithromycin was associated with a higher risk of ventricular tachycardia and prolonged qt. hcq alone was responsible for more conduction disorder. however, in patients receiving azithromycin alone compared with hcq alone, there was more prolonged qt and ventricular tachycardia. unchanged before and after hemodialysis [137] . moreover, several observations reported the onset of severe covid-19 in patients who were already receiving hcq as a long-term treatment for an inflammatory disease [138] . one randomized trial evaluated the outcome of hcq whether or not in association with azithromycine on mild to moderate covid-19 [139] . primary endpoint (escalation in icu, mechanical ventilation or death) was reached by 35% of patients in the early corticosteroid group vs 54% in the control group (p=0.005) [141] . recovery was a randomized, controlled trial of the use of 6 mg of dexamethasone vs soc in hospitalized patients with covid-19. at 28 days, 454/2,104 (21.6%) patients had died in the dexamethasone group vs 1,065/4,321 (24.6%) in the soc group (p<0.001) [142] . tocilizumab is a monoclonal antibody against il-6 receptor. it is mainly prescribed in rheumatoid arthritis. an italian team reported the use of tocilizumab to the first 100 patients presenting to the brescia university hospital with a covid-19 ards requiring ventilatory support. at 72h, 58% of patients showed an improvement, and at 10 days after treatment inset, 77% of patients had improved and/or stabilized [143] . anakinra is an antagonist of il-1 receptor. an italian team reported the use of anakinra in 29 patients with moderate to severe covid-19 ards before mechanical ventilation, compared with 16 patients not receiving anakinra. survival rate at 21 days was 90% in the anakinra group vs 56% in the control group (p =0.009). however, there was no difference regarding the mechanical ventilation-free survival (72% in the anakinra group vs 50% in the control group, p=0.150) [144] . a chinese team reported the use in 51 covid-19 patients of convalescent plasma compared with a control group of 50 patients. their primary endpoint was clinical improvement within a 28 day-period (reduction of 2 points on a 6-points disease severity scale). there was no difference between both groups (p = 0.260). in sub-group analysis among patients presenting a severe disease, 91% of patients met the primary endpoint in the plasma therapy group vs 68% in the control group (p = 0.003) [145] . in another study, the outcomes of 1,430 severe or critical patients treated with soc and 138 patients treated with convalescent plasma therapy were compared; 2.2% of patients died in the plasma group vs 4.1% in the soc group (no comparison). 2.4% of patients were admitted to icu in the plasma group vs 5.1% in the soc group (p=0.2) [146] . the effect of ace inhibitor and arb treatment on covid-19 severity and/or mortality has been reported in several studies but seems variable. in zhang et al's work, on 1,128 patients with hypertension and covid-19, multivariate analysis found a lower all-cause mortality in the ace inhibitor/arb group, than in the other group (p = 0.03) [147] . however, li et al did not found any difference in covid-19 severity (p=0.645) or mortality (p=0.340) among 362 patients admitted for hypertension and covid-19 [148] . in chu et al.'s meta-analysis, social distancing was considered as efficient with a -10.2% risk difference (95%ci [-11.5 to -7.5%] of infection in short distance vs further distance [149] . wearing respirators or face masks was associated with a large reduction in risk of infection (risk difference -14.3%, 95%ci [-15.9 to -10.7%]) [149] . eye protection also seemed efficient in infection reduction with a risk difference of -10.6% 95%ci [-12.5 to 7.7%] [149] . however, lockdown had the larger impact on transmission with an 81% [75%-87%] reduction [23] . in france, the number of daily cases of covid-19 was growing by the end of summer 2020, suggesting the debut of a second epidemic wave, as many other countries are facing. the first wave allowed us to develop and strengthen our laboratory tests. since then, french health authorities have implemented a systematic contact tracing (contact-covid) around each patient presenting a positive sars-cov-2 rt-pcr. this highlighted the high number of asymptomatic and mild cases, and made french people massively adapt their daily habits with a systematic face mask protection in all public areas, and restrictions in social events. however, none of the evaluated pharmacological treatments have showna clear efficacy on sars-cov-2. one of the main limitations seem to be the long period between symptom onset and initiation of treatment. an effective vaccine against sars-cov-2 appears to be the only way to end this pandemic. at the end of august 2020, 203 trials were registered on clinicaltrial for a vaccine against covid-19, thus raising hope to end this pandemic in a reasonable amount of time. promed post -promed-mail n diseases is for i. promed post -promed-mail china is consistent with substantial human-to-human transmission who coronavirus disease (covid-19) dashboard | who coronavirus disease who director-general's opening remarks at the media briefing on covid-19 -11 the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 a 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mainly mild to moderate coronavirus disease 2019: open label, randomised controlled trial hydroxychloroquine and azithromycin as a treatment of covid-19: results of an open-label non-randomized clinical trial preliminary evidence from a multicenter prospective observational study of the safety and efficacy of chloroquine for the treatment of covid-19 observational study of hydroxychloroquine in hospitalized patients with covid-19 cardiovascular toxicities associated with hydroxychloroquine and azithromycin: an analysis of the world health organization pharmacovigilance database hydroxychloroquine pharmacokinetic in covid-19 critically ill patients: an observational cohort study covid-19 infection also page 28 of 29 patients taking hydroxychloroquine hydroxychloroquine with or without azithromycin in mild-to-moderate covid-19 successful use of methylprednisolone for treating severe covid-19 early short course corticosteroids in hospitalized patients with covid-19 effect of dexamethasone in hospitalized patients with covid-19: preliminary tocilizumab for the treatment of severe covid-19 pneumonia with hyperinflammatory syndrome and acute respiratory failure: a single center study of 100 patients in brescia interleukin-1 blockade with high-dose anakinra in patients with covid-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study treatment of 5 critically ill patients with covid-19 with convalescent plasma improved clinical symptoms and mortality on severe/critical covid-19 patients utilizing convalescent plasma transfusion association of inpatient use of angiotensin-converting enzyme inhibitors and angiotensin ii receptor blockers with mortality among patients with hypertension hospitalized with covid-19 association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (covid-19) infection in wuhan, china physical distancing, face masks, and eye protection to prevent person-to-person transmission of sars-cov-2 and covid-19: a systematic review and meta-analysis key: cord-315525-u8goc7io authors: backer, jantien a.; klinkenberg, don; wallinga, jacco title: the incubation period of 2019-ncov infections among travellers from wuhan, china date: 2020-01-28 journal: nan doi: 10.1101/2020.01.27.20018986 sha: doc_id: 315525 cord_uid: u8goc7io currently, a novel coronavirus 2019-ncov causes an outbreak of viral pneumonia in wuhan, china. little is known about its epidemiological characteristics. using the travel history and symptom onset of 88 confirmed cases that were detected outside wuhan, we estimate the mean incubation period to be 6.4 (5.6 7.7, 95% ci) days, ranging from 2.1 to 11.1 days (2.5th to 97.5th percentile). these values help to inform case definitions for 2019-ncov and appropriate durations for quarantine. early january 2020, a novel coronavirus 2019-ncov, has been identified as the infectious agent that causes an outbreak of viral pneumonia in wuhan, china, where the first cases had their symptom onset in december 2019 [1] . this newly discovered virus causes a severe acute respiratory disease. the rapid spread in wuhan and throughout china poses a great strain on health care system and disrupts the local societies. the multiple cases showing up outside china cause international concern. the virus is related to the sars coronavirus and mers coronavirus, but is distinct from each of those viruses [2] , such that the epidemiological key parameters have to be identified for this new virus from incoming case reports as the epidemic continues. chief among these key parameters is the incubation period distribution. the range of the values for the incubation period is essential to epidemiological case definitions, and is required to determine the appropriate duration of quarantine. moreover, knowledge of the incubation period helps to assess the effectiveness of entry screening and contact tracing. the distribution of the incubation period is also used in estimating the size of the epidemic [3 -5] and the transmission potential [6, 7] . in absence of data on the 2019-ncov incubation period, the who has worked with a broad range of 0 to 14 days, the cdc has taken a range of 2 to 14 days, and several studies have assumed incubation periods of sars or mers coronaviruses. here we present the distribution of incubation periods estimated for travellers from wuhan with confirmed 2019-ncov infection, using their reported travel histories and symptom onset dates. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. in january 2020 an increasing number of cases were detected outside wuhan, china and confirmed to be infected with 2019-ncov. for 88 cases detected between 20 and 28 january, the travel history (to and) from wuhan is known as well as their symptom onset date. their ages range from 2 to 72 years old (with four missing), 31 of them are women, 57 are men. during this initial stage of the epidemic, it is most likely that these travellers were the data used for this analysis has been translated from chinese sources and made publicly available [8] . we took the data as available on january 29, 2020 (supplementary material s1). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint using the duration of stay in wuhan and the symptom onset date, we obtained a range of possible values for the incubation period of each case. we fitted three parametric forms for the incubation period distribution to these ranges: the weibull distribution, the gamma distribution, and the lognormal distribution. we used a bayesian approach to fitting, that allows for the use of prior knowledge to inform the analysis. we specified strictly positive flat prior probability distributions for the parameter values of the three distributions (supplementary material s2), which ensured our estimates are conservative. because of the high number of observations, the impact of the priors on the outcome was negligible. we used a uniform prior probability distribution over the exposure interval for the moment of infection for each case. we sampled from the posterior distribution using the rstan package [9] in r [10] (supplementary material s3). figure 1 shows the time line for each case, where the cases without a maximum incubation period lack an unexposed (gray) period. however, the estimated infection times for these cases are close to the end of the exposure window, informed by the cases that do have a maximum incubation period. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint 5 fig. 1 time line for each case with travel history from wuhan, sorted by symptom onset date. distinct periods are shown as unexposed (gray), exposed (white), infected but asymptomatic (pink), symptomatic (purple) and reported (blue). the analysis yields the probability of being infected (violet), i.e. the cumulative density function of the estimated infection moments (using the weibull distribution). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint 6 the weibull distribution provided the best fit to the data (tab. 1). the mean incubation period was estimated to be 6.4 (5.6 -7.7, 95% credible interval) days. the incubation period ranges from 2.1 to 11.1 days (2.5 th to 97.5 th percentile) (tab. 2 and fig. 2 ). the results using the gamma distribution provide a slightly poorer description of the data but provide a similar range from 2.4 to 12.5 days. although the lognormal distribution provides the poorest fit to the data, the incubation period ranging from 2.4 to 15.5 days (2.5 th to 97.5 th percentile) may be relevant for a conservative choice of quarantine periods. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. a comparison to the estimated incubation period distribution for mers (tab. 3 and fig. 3) shows that the values are remarkably similar, with mean values differing at most 1 day and 95 th percentiles differing at most 2 days. the estimated mean incubation periods for sars are more variable between studies, including values shorter and longer than presented here for 2019-ncov. these findings imply that findings of previous studies that have assumed incubation period distribution similar to mers or sars will not have to be adapted because of a shorter or longer incubation period. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint we characterized the distribution of incubation periods for chinese travellers infected with 2019-ncov in wuhan, who were reported as cases between 20 and 28 january 2020. the study provides empirical evidence to back reports on a familial cluster where five family members developed symptoms 3 -6 days after exposure [18] and a reported range from 2 to 11 days based on 16 travellers between wuhan and guangdong [19] . it fits within the range from 0 to 14 days that has been assumed by the who. in our analysis we assumed a uniform prior probability of being infected during the period of stay in wuhan. since the epidemic was developing during that time period, it is more likely that travellers were infected toward the end rather than the beginning of their stay. this . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint might produce a slight bias towards longer incubation periods, so the estimated upper limit of 11.1 days could be considered conservative. the travellers in this study represent a selective sample of the reported cases. we found travellers to be more often male and younger than the cases reported. the numbers are too small to detect systematic differences in incubation time with age or sex. because we only have information on confirmed cases, there is likely a bias towards more severe cases in areas with a functioning health care system. as the epidemic continues, it remains important to collect more information on incubation periods of 2019-ncov cases of older ages, of persons with underlying morbidity, of women, and of persons with mild symptoms. there are various choices one can make about the parametric form of the incubation period distribution. the results with the three often-used forms we report here suggest that there is little impact on the mean and dispersion of the incubation periods. of these three, the lognormal distribution assigns higher probabilities to longer incubation periods. although we found that this distribution provided a poorer description of the data than the weibull and the gamma distributions, it is prudent not to dismiss the possibility of incubation periods up to 14 days at this stage of the epidemic. our study helps in choosing an appropriate duration for quarantine. keeping infected persons in quarantine up to 14 days will ensure that they do not develop symptoms after release. we are immensely indebted to the work of dr. kaiyuan sun, ms. jenny chen, dr. cécile viboud and the staff of mobs lab led by prof. alessandro vespignani who traced and translated the information and generously made it available to the wider community. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.01.27.20018986 doi: medrxiv preprint who statement regarding cluster of pneumonia cases in wuhan discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. the biorxiv preprint first posted online report 2: estimating the potential total number of novel coronavirus cases in wuhan city, china nowcasting and forecasting the wuhan 2019-ncov outbreak the extent of transmission of novel coronavirus in wuhan, china, 2020 transmissibility of 2019-ncov lin yang and daihai he (2020) preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak online repository maintained by rstan: the r interface to stan r: a language and environment for statistical computing. r foundation for statistical computing alternative methods of estimating an incubation distribution: examples from severe acute respiratory syndrome a comparative epidemiologic analysis of sars in hong kong, beijing and taiwan incubation periods of acute respiratory viral infections: a systematic review key: cord-311585-h4holhit authors: ling, r.; yu, y.; he, j.; zhang, j.; xu, s.; sun, r.; li, t.; ji, h.; wang, h. title: seroprevalence and epidemiological characteristics of immunoglobulin m and g antibodies against sars-cov-2 in asymptomatic people in wuhan, china date: 2020-06-19 journal: nan doi: 10.1101/2020.06.16.20132423 sha: doc_id: 311585 cord_uid: h4holhit background the seroprevalence of immunoglobulin m (igm) and immunoglobulin g (igg) antibodies against severe acute respiratory syndrome coronavirus 2 (sars-cov-2) may be a more reliable approach to detect true infected population, particularly in asymptomatic persons. few studies focus on the diagnosis of covid-19 patients using serological tests. to detect and assess asymptomatic infections of covid-19 among people in wuhan, the epicenter of the covid-19 pandemic in china, and provide evidence for planning adequate public health measures, we collected and analyzed the clinical data in the wuhan general hospital mandatory for 16to 64-year-old asymptomatic people. this retrospective study estimated the seroprevalence of igm and igg and compared the epidemiological characteristics of asymptomatic sars-cov-2-infected population. methods demographical and radiological data were collected from the wuhan general hospital between march 26 and april 28, 2020. serological tests for igm and igg antibodies against sars-cov-2 were conducted with a colloidal gold method. nucleic acid sequences of viruses were detected with rt-pcr. statistical analyses were carried out using spss 20.0 software. findings between march 26 and april 28, 2020, 18,391 asymptomatic back-to-work participants were enrolled. among them, 89 had positivity for igm (0.48%, 95% confidence interval (ci): 0.38-0.58%); 620 cases had igg positivity (3.37%, 95% ci: 3.11-3.64%), and 650 cases had either igg positivity or igm positivity (3.53%, 95% ci: 3.26-3.80%). after standardizing for the genders and ages in the population of wuhan, the overall standardized seroprevalence of igg was 3.33% (95% ci: 3.07-3.59%) and the standardized seroprevalence of igg was 3.01% (95% ci: 2.69-3.33%) among males and 3.66% (95 % ci: 3.23-4.09%) among females. the standardized seroprevalence of igg was higher in women than in men with a significant difference ({chi}2 = 2,060.3, p < 0.01). by a detection method adjustment, the seroprevalence of igg was 1.57% (95% ci: 1.39-1.75%) in all medical records, of which males were 1.96% (95% ci: 1.64-2.28%), and females were 1.19% (95% ci: 0.99-1.39%). the assay-adjusted seroprevalence of igg was higher in women than in men, and the difference was significant ({chi}2 = 5,871.0, p < 0.01). the differences were significant for the seroprevalence of igg among people who went back to work in different categories of workplace ({chi}2 = 198.44, p < 0.01). the differences in seroprevalence for igg positivity or igm positivity among people who went back to work in different urban and rural areas was also significant ({chi}2 = 45.110, p < 0.01). calculated as igg and/or igm antibody positivity, the number of new infections was reduced by 64.8% from march 26 to april 28, 2020. based on the census population aged 16-64 years in wuhan in 2017, we estimated that 172,340 (95% ci: 157,568-187,112) asymptomatic people aged 16-64 years were infected with sars-cov-2 in wuhan between march 25 and april 28, 2020. this estimate was 3.4-times higher than the officially reported 50,333 infections on april 28. interpretation the seropositivity rate in wuhan indicated that rt-pcr-confirmed patients only represented a small part of the total number of cases. seropositivity progressively decreased in the wuhan population from march 26 to april 28, 2020, comparable to japan and denmark, but well below the level reported in new york, iran, italy, and germany. the prevalence of asymptomatic infection was higher in women than in men among people who went back to work in wuhan. the low seroprevalence suggests that most of the population remains susceptible to covid-19. funding the emergency management project of the national natural science foundation of china (81842035) and advisory research project of the chinese academy of engineering in 2019 (2019-xz-70). the first case of coronavirus disease 2019 (covid19) , which is caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2), was reported on december 8, 2019, in wuhan, hubei province. 1, 2 the chinese public health, clinical, and scientific communities promptly responded in timely recognition of the new virus and shared the viral gene sequence to the world. 3, 4 the world health organization (who) termed the disease covid-19 in january 2020. 2 the pandemic is the third coronavirus outbreak in the last 20 years, with severe acute respiratory syndrome caused by sars-cov and the middle east respiratory syndrome by mers-cov. 5 as of may 17, 2020, covid-19 infections occurred globally at more than 4,657,000 human cases and resulted in more than 312,000 human deaths according to the johns hopkins university. 6 the clinical symptoms of sars-cov-2 infection vary from mild to the onset of severe acute respiratory distress syndrome. many patients can be asymptomatic, greatly increasing the uncertainty of diagnosis. 7 a timely and accurate diagnosis of covid-19 is crucial for limiting further spread of the virus, particularly in people who are asymptomatic or mildly symptomatic, who can be responsible for community transmissions. 8 as wuhan accepted the timely prevention strategies of lockdown and curbing population flow, it controlled the spread of the pandemic effectively. nonetheless, there is still a risk of a second outbreak. therefore, knowing the situation of sars-cov-2 infection in the general population is necessary. this knowledge has a meaning for the control and prevention of covid-19 and epidemiological investigations, the determination of postdisease immunity and the use of future vaccine strategies. quantitative reverse-transcription polymerase chain reaction (rt-qpcr) analysis for sars-cov-2 is the gold standard for covid-19 diagnosis. [9] [10] it is time-consuming and requires special equipment with skilled laboratory technicians and has the weakness that easily leads to false negatives for sars-cov-2. [9] [10] [11] we know sars-cov-2-specific antibodies appear around 3-10 days after infection, with igm appearing first and igg following around 14 days after infection. 12 even after the symptoms of infection disappear, igg can still show seropositivity. 13 therefore, sars-cov-2 serological assays are a good supplementary method for nucleic acid detection. 14 additionally, serological assays allow studying the immune response(s) to sars-cov-2 in a dynamic qualitative and quantitative manner. in addition, serological antibody assays can determine the precise rate of infection in an affected area or a certain population, estimate the cumulative incidence and infection fatality rate, and provide parameters for epidemiological models to assess the possible impact of specific interventions, thus guiding public health decision-making. furthermore, serological assays can be used to elucidate the geographic spread of the virus and identify subgroups of individuals who are more vulnerable to infection. last, the degree of protection of antibodies against sars-cov-2 infection or reinfection can be determined by serological assays. 15,16 therefore, testing for antibodies specific to sars-cov-2 protein could be an alternative method for rapid laboratory diagnosis with high sensitivity. 12 who recommends monitoring changes of seroprevalence over time, which is crucial at the beginning of an epidemic to anticipate and plan an adequate public health response. 9 at present, relatively few domestic and foreign reports exist on the diagnosis of patients with covid-19 using serological tests. thus, we conducted a retrospective study analyzing 18,391 medical all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. hubei province including igm and igg tests for sars-cov-2 antibody, nucleic acid tests from march 26 to april 28, 2020 among people aged 16-64 years who went back to work. current methods for measuring serum igm and igg mainly include enzyme-linked immunosorbent assays, chemiluminescence enzyme immunoassays, lateral flow immunoassays (lfias), and fluorescence immunoassays. lfia specificity can reach about 99% with sensitivity from 80% to 86%. combined igg and igm tests seem to be better choices for sensitivity than measuring either antibody type alone. 17 in our study, the lfia method had a similar sensitivity and specificity for detecting sars-cov-2-specific antibodies. this study provides a reference for estimating the number of asymptomatic examples of covid-19, the transmission patterns of the virus, and pandemic prevention strategies. this was a cross-sectional, retrospective study to investigate seroprevalence in asymptomatic covida total of 17,608 people received nucleic acid tests, with one suspected as nucleic acid-positive, and positive for igg antibodies and negative for igm antibodies. among the 783 people without nucleic acid tests, 10 (1· 28%) were positive by antibody tests and the rest were negative (98· 7%). a total of 18,391 people met the inclusion criteria with a median age of 40·0 years with 11,177 (60· 8%) males with median age 42·0 years and 7,214 (39·2%) females with median age 37·0 years. clinical data were collected from march 26 to april 28, 2020, including serum igg positivity and igm positivity or negative results for sars-cov-2 antibodies, nucleic acid testing, clinical symptoms, previous medical history, and chest ct. sars-cov-2 antibody detection kits (colloidal gold method) were provided by innovita (tangshan, registration certificate for the medical devices of peoples republic of china: 20203400177). 18 all enrolled medical examiners collected 2 ml peripheral venous blood. after centrifugation, serum was taken for sars-cov-2-specific antibody igg and igm detection within 2 hours. nasopharyngeal or oropharyngeal swabs used for sars-cov-2 nucleic acid testing were collected by trained and qualified medical staff for performing nucleic acid tests within 2 hours. the automatic nucleic acid extraction instrument was provided by the hangzhou allsheng instruments co. ltd. (allsheng). the abi-7500 fluorescence pcr instrument was from thermo fisher scientific inc. all operations were carried out according to kit instructions. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. percentile) was used for non-normal distribution data. p < 0.05 was considered statistically significant. to correct for the effects of gender and age structure, the seroprevalence of igm positivity, igg positivity, and igm and/or igg positivity were standardized according to the gender and age-specific population of wuhan in 2017 (attachment 2). 19 to correct for effects from accuracy of the serum antibody test, seroprevalence was corrected according to the sensitivity and specificity of the colloidal gold test in previous studies 13 following the rogan gladen methods. 20 this study was approved by the ethics committee of the hubei provincial hospital of integrated chinese & western medicine. this was a retrospective and observational study and informed consent was obtained. table 1 shows the unadjusted and adjusted seroprevalence for igg and igm against sars-cov-2 in asymptomatic people aged 16 to 64 by gender. the unadjusted seroprevalence of igg in females was higher than in males and was significantly different (x 2 = 6·218, p < 0·05). the unadjusted seroprevalence of igm in females was slightly higher than in males, but was not significantly different (x 2 = 0·207, p > 0·05). when igg and igm positivity were analyzed together, the unadjusted seroprevalence of igg positivity and /or igm positivity in females was higher than in males and was significantly different (x 2 = 6·865, p < 0·01). after standardization according to the numbers of people of different ages and genders in the population of wuhan from the national census of 2017, the age-and gender-adjusted seroprevalence of igg was all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 19, 2020. . https://doi.org/10.1101/2020.06.16.20132423 doi: medrxiv preprint higher in females than in males and the differences were significant (x 2 = 2,060·3, p < 0·01). after adjusting for ages and genders, and assay sensitivity and specificity, including ci, the overall adjusted seroprevalence of igg was higher in females than in males. the difference between genders was significant (x 2 = 5,871·0, p < 0·01). the age-and gender-adjusted seroprevalence of igg positivity and /or igm positivity was higher in females than in males, and the difference was significant (x 2 = 979·26, p < 0·01). after adjusting for ages and genders, and assay type, the overall adjusted serum rate for igg and /or igm antibodies was 2·80 (95% ci: 2·56-3·04%) with 2·40 (95% ci: 2·11-2·68) for males and 3·23 (95% ci: 2·82-3·64) for females. numbers were higher for females than males, and the difference was significant table 2 . a significant difference was seen in seroprevalence of igg among people from different units (x 2 = 198·44, p < 0·01), with no significant difference for igm (x 2 =28·124, p>0·05), and a significant difference for igg positivity and /or igm positivity (x 2 = 200·21, p < 0·01). among the tested individuals, the seroprevalence of igg was highest for those who voluntarily came for examinations, followed by those reinforced by their work units, including real estate property companies, urban construction companies, telecommunications companies, banks, securities and insurance companies, law firms, and procuratorates. a significant difference was seen in seroprevalence of igg by urban area (x 2 = all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 19, 2020. . https://doi.org/10.1101/2020.06.16.20132423 doi: medrxiv preprint 43·660, p < 0· 01), with no significant difference for igm (x 2 = 14·783, p > 0·05), and a significant difference for igg and/or igm (x 2 = 45·110, p < 0·01). the wuchang and jianghan districts had higher seroprevalences of igg than other urban areas. detection of asymptomatic or subclinical novel human coronavirus sars-cov-2 infections is critical for understanding the overall prevalence and infection potential of covid-19 21 according to a study in denmark, 9,496 blood donors (17-69 years old) who gave blood during april 6-17, 2020 were tested for sars-cov-2 igm and igg antibodies using a commercial lateral flow test. the seroprevalence adjusted for assay sensitivity and specificity was 1·7% (ci: 0·9-2·3%), and differed by region. 22 a similar cross-sectional study conducted in japan had an igg seroprevalence of 3·3% (95% ci: 2·3-4·6%) using 1,000 samples from patients at outpatient settings. after adjusting for ages and genders, the igg seroprevalence was 2·7% (95% ci: 1·8-3·9%), and the estimated number of infections was 396 to 858 times the number of confirmed cases at the time. 23 the seroprevalence estimated in our study was adjusted by age and gender, and then for assay sensitivity and specificity, which was comparable to the studies in japan and denmark, but lower than preliminary findings for iran of 22%, new york city of around 14%, italy of 10%, and germany of 14%. [24] [25] [26] [27] all these studies indicated that the number of asymptomatic infections was much higher than the number of confirmed cases reported based on pcr results. our study found that the number of new infections was reduced by 64· 8% to a relatively lower level of 1·46 (95% ci: 0·93-1·98%) of the igg seroprevalence among the urban population aged 16-64 years on (attachment 2). of note, the officially reported number included people under age 16 and over age 64, yet was lower than the calculated number in this study, implicating underestimation due to omitted detection of asymptomatic infections. data from a detailed surveillance study from the chinese center for disease control and prevention indicates that 80% of confirmed cases were mild, and a number of patients can remain asymptomatic with very low symptomatology. 28 thus, epidemiological studies of asymptomatic infections should receive sufficient attention. some studies find an average level of igg antibodies that is higher in females than in males. 29 in our all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 19, 2020. . https://doi.org/10.1101/2020.06.16.20132423 doi: medrxiv preprint study, the igg seroprevalence was higher in females than in males, indicating that women were more likely to have asymptomatic infections. people living or working in the wuchang and jianghan districts had a higher igg seroprevalence of 4·60 (95% ci:3·21-5·99) and 4·18 (95% ci:3·80-4·56) respectively than people from other districts of wuhan in our study. based on the cumulative number of reported cases of covid-19 and the number of residents in each district in wuhan on march 25 and april 28, we estimated an average incidence rate per 100,000 people of 2·98 (95% ci: 2·97-2·99) during this period. incidence rates were higher in the jianghan and wuchang districts, at 8·09 (95% ci: 8·02-8·15) and 7·25 (95% ci: 7·20-7·29) per 100,000 people, respectively, which were the same as our regional distribution analyses (attachment 2). our study found significant differences in igg seroprevalence among people going back to work by types of jobs, with the highest seroprevalence in volunteer medical examinees who came for tests without a mandate from their job supervisors. these self-motivated individuals had close contacts with covid-19 patients, and therefore, had a higher risk of infection. other individuals with high igg seroprevalence were easy to identify due to the nature of their jobs. they undertook substantial voluntary work in response to government calls during the covid-19 pandemic, to assist in, for instance, administering in the local residential communities, transporting covid-19 patients, and screening the general population for epidemic incidence. thus, they faced a greater chance of contacting infected people during their work, and were more likely to be infected, even with personal protection. this study had a few limitations. first, this study had selection bias since the analyzed medical records were based on examinees directed by their work units. most of the examinees came from governmentowned institutions and agencies instead of private businesses. therefore, the sample was incompletely randomized and insufficiently representative, compromising the assessment accuracy of the prevalence of asymptomatic infections in wuhan. second, as the examinees were only from the back-to-work population, people under age 16 and over age 64 were not covered in analyses. therefore, we could not estimate covid-19 in these two groups. our study provides information to herd immunity investigation to help design targeted strategies for prevention. research on serological antibodies has great value for covid-19 prevention. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. previous studies following the rogan gladen methods, to correct for effects from accuracy of the serum antibody test. according to the rogan gladen methods, p=(t + β -1)/(α + β -1), in which p is adjusted seroprevalence, α is sensitivity of the antibody test (colloidal gold method ), β is specificity of the antibody test by colloidal gold method, t is age-and gender-adjusted seroprevalence or positive test frequency. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. n is the total number of individuals, n1 is the number of igg-positive individuals, n2 is the number of igm-positive individuals, n3 is the number of iggpositive or igm-positive. real estate includes real estate agencies, residential property management firms, and urban construction corporations. all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june 19, 2020. . https://doi.org/10.1101/2020.06.16.20132423 doi: medrxiv preprint epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study an invited commentary on "world health organization declares global emergency: a review of the 2019 novel coronavirus (covid-19)": emergency or new reality? a novel coronavirus from patients with pneumonia in china a new coronavirus associated with human respiratory disease in china the epidemiology and pathogenesis of coronavirus disease (covid-19) outbreak covid-19 case tracker the incubation period of coronavirus disease from publicly reported confirmed cases: estimation and application estimating the asymptomatic proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess cruise ship population-based age-stratified seroepidemiological investigation protocol for covid-19 virus infection molecular and serological investigation of 2019-ncov infected patients: implication of multiple shedding routes. emerging microbes & infections 2020 temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study antibody responses to sars-cov-2 in patients of novel coronavirus disease 2019. clinical infectious diseases : an official publication of the infectious diseases society of america viral kinetics and antibody responses in patients with all rights reserved. no reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted characterization of spike glycoprotein of sars-cov-2 on virus entry and its immune cross-reactivity with sars-cov protocol and reagents for pseudotyping lentiviral particles with sars-cov-2 spike protein for neutralization assays clinical evaluation and application of detection for sars-cov-2 igm and igg antibodies with colloidal gold immunochromatography assay population grouped by age estimating prevalence from the results of a screening test seroprevalence of immunoglobulin m and g antibodies against sars-cov-2 in china estimation of seroprevalence of novel coronavirus disease (covid-19) using preserved serum at an outpatient setting in kobe what the first data of robbio reveal, the only italian country to take immunity tests on all citizens blood tests show 14% of people are now immune to covid-19 in one town in germany new york antibody study estimates 13.9% of residents have had the coronavirus, gov. cuomo says the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) a comparison study of sars-cov-2 igg antibody between male and female covid-19 patients: a possible reason underlying different outcome between gender acknowledgments we acknowledge the work and contribution of all the health providers from the hubei key: cord-302159-exexcag6 authors: wei, yanqiu; lu, yanjun; xia, liming; yuan, xianglin; li, gang; li, xinying; liu, li; liu, wenhua; zhou, peng; wang, cong‐yi; zhang, huilan title: analysis of 2019 novel coronavirus infection and clinical characteristics of outpatients: an epidemiological study from a fever clinic in wuhan, china date: 2020-06-16 journal: j med virol doi: 10.1002/jmv.26175 sha: doc_id: 302159 cord_uid: exexcag6 background: since the outbreak of 2019 novel coronavirus (sars‐cov‐2) pneumonia, thousands of patients with fever or cough were flocked into fever clinic of designated hospitals in wuhan, china. to date, no data have ever been reported to reflect the prevalence of corona virus disease 2019 (covid‐19) among these outpatients. moreover, it is almost unknown to discriminate covid‐19 and nucleic acid negative patients based on clinical features in the fever clinics. methods: the infectious status of sars‐cov‐2 was estimated among the outpatients. the epidemiological and clinical characteristics were compared between covid‐19 and nucleic acid negative patients. results: the nucleic acid positive rate for sars‐cov‐2 in the outpatients from our fever clinic was 67·1%, while the majority of covid‐19 patients were mild cases. the predominant initial symptom in those covid‐19 patients was fever (78.2%), followed by cough (15.6%). very significantly lower number of eosinophils was characterized in covid‐19 patients as compared to that of nucleic acid negative patients. more importantly, the proportion of subjects with eosinophil counts lower than normal levels in covid‐19 patients was much higher than that of nucleic acid negative patients. fever combined with bilateral ground‐glass opacities in ct imaging and eosinophil count below the normal level are probably a valuable indicator of covid‐19 infection in those outpatients. conclusions: those findings may provide critical information for the regions such as europe and united states that are facing the same situation as wuhan experienced, and could be valuable to prevent those nucleic acid negative patients from misdiagnosis before antibody testing. this article is protected by copyright. all rights reserved. by who, 7 and now became a global pandemic along with patients diagnosed in more than 190 additional countries. the first case of covid-19 was characterized in wuhan, hubei province in december 2019. its clinical manifestations are very similar to those infected by the severe acute respiratory syndrome coronavirus (sars-cov) occurred in 2003. 8, 9 although the mortality rate of covid-19 in china is 3%, far lower than that of sars (10.0%), 10, 11 the mortality rate in wuhan, unfortunately once reached 9.0% in the early stage of the outbreak, and similarly in italy now. however, the mortality in wuhan gradually decreased, suggesting that early diagnosis and treatment could significantly reduce its death rate. upon the supports from the outsides of wuhan, increasing cases with respiratory symptoms were accessible to laboratory tests and medical treatments from the fever clinics. nevertheless, no data have been reported in terms of the proportion of covid-19 patients among all outpatients in fever clinics, or the proportion of severe cases among all covid-19 patients. similarly, no convincing evidence has been suggested to discriminate covid-19 from nucleic acid negative patients, or mild case from severe case of covid-19. as a leading hospital in hubei province, tongji hospital serves as one of the main designated hospitals to carry out fever clinic. this study is designed to analyze the infection rate of sars-cov-2 in patients visiting fever clinic in wuhan, and to compare the clinical features between covid-19 and nucleic acid negative patients based on the epidemiological, clinical, laboratory and ct scan results. to further provide more information that could be considered as a worthy reference for the frontline clinicians, a "clinical rapid and preliminary sorting score system" was proposed in case that the results for nucleic acid assays are not available or negative because of inappropriate sample collection. this system was designed to assess the possibility of covid-19 positivity based on the clinical characteristics and laboratory results in outpatients. in this retrospective study, we recruited all febrile patients from the fever clinic of tongji hospital in wuhan, china, from january 30 to february 4, 2020, the peak time period of this pandemic in wuhan. the covid-19 nucleic acid assays were conducted in tongji hospital. throat-swab specimens from the upper respiratory tract were collected from all outpatients twice with a 24h interval. fever was defined as axillary temperature reached 37.3 o c or above. due to the strong transmission potency of those newly infected were plotted as a figure. proportions for categorical variables were compared using the χ2 test, although the fisher exact test was used when the data were limited. means for continuous variables were compared using the mann-whitney test. a "clinical rapid and preliminary sorting score system" was proposed to assess the possibility of covid-19 positivity based on the clinical characteristics and laboratory results in outpatients. specifically, the predictive proportions of covid-19 positivity were carried out based on the mean positive predictive value in different combinations of clinical charts, ct scan and eosinophil count. all statistical tests were two-sided, and p<0·05 was considered as statistically significant. since tongji hospital is almost located in the center of covid-19 epidemic, its fever clinic received 936 visitors between january 30 th to february 4 th of 2020, which was the peak period of this outbreak. all of those 936 visitors were undergone at least twice of covid-19 nucleic acid assays with a 24h of interval, and 628 of whom were positive for the assays, and thus diagnosed as covid-19 (67·1%), while the rest 308 visitors were negative (32·9%). in terms of age distribution, the average age for the diagnosed covid-19 patients was 53 years (±14.8 years), while the average age for nucleic acid negative patients was 49 years (±13.0 years), which was significantly younger than that of covid-19 patients (p < 0.01). among those covid-19 patients, 296 are males (47.1%) and 332 are females (52.9%). in those nucleic acid negative patients, 142 are males (46.1%) and 166 are females (53.9%). no significant difference was noted between the covid-19 patients and nucleic acid negative patients in terms of genders (table1). it was noted that fever was the predominant initial symptom in covid-19 patients, which accounted for 78.2%, followed by cough (15.6%). other symptoms including fatigue (6·7%), chest tightness (2.4%), diarrhea (1.9%), muscle ache (1.3%), and dyspnea (1.0%) were also observed. only a very small proportion of covid-19 patients also manifested anorexia (0.5%), rhinobyon (0.3%), vomiting (0.2%), sore throat (0.2%), aversion to cold (0.2%), nausea (0.2%), hypersomnia (0.2%), expectoration (0.2%), dizziness (0.2%) and xerostomia (0.2%). however, fever was also characterized to be the major initial symptom for those nucleic acid negative patients as well, which accounted for 73.1%, and cough accounted for 21.1% (table 1) . among all 936 visitors, 460 of them conducted routine blood tests, and 309 were covid-19 patients, while the rests were nucleic acid negative patients. the average number of lymphocytes in covid-19 patients was 1·2×10 9 /l, while it was 1·4×10 9 /l for the nucleic acid negative patients, and no significant accepted article difference was observed between the two groups (p=0·062). in sharp contrast, covid-19 patients displayed significantly lower number of platelet counts as compared to that of nucleic acid negative patients (195·30×10 9 /l vs. 216·00×10 9 /l; p=0.026). remarkably, very significantly lower number of eosinophils was characterized in covid-19 patients as compared to that of nucleic acid negative patients (0.02×10 9 /l vs. 0.03×10 9 /l; p=0.002). more importantly, the proportion of subjects with eosinophil counts lower than normal levels in covid-19 patients was much higher than that of nucleic acid negative patients (74·11% vs. 59·60%; p=0·002) ( table 2) patients, while only 58·0% of nucleic acid negative patients displayed the above manifestation. characteristically, the covid-19 patients were more likely to have both lungs involved (90·2% vs. 80·7%; p<0·001). further analysis of the lesion sites revealed that those nucleic acid negative patients were more likely to exhibit lesions in the right upper lobe (17·8% vs. 11·7%, p=0·019) of right lung (42·8% vs. 34·8%, p=0·030), and lower lobe of left lung (19·7% vs 13·5%, p=0·023) ( table 3) . as aforementioned (table 1) , fever and cough were the primary symptoms in both covid-19 and nucleic acid negative patients. to better discriminate the initial symptoms in those two types of patients to improve diagnostic feasibility, we further analyzed their initial symptoms by classifications. remarkably, patients manifested muscle ache in the initial symptoms had the highest nucleic acid detection rate (80·0%; 95% ci: 45·9-95·0), followed by the initial symptoms coupled with dyspnea (75·0%; 95% ci: 37·7-93·7), while the detection rate in patients with initial symptoms of fever (68.6%; 95% ci: 65.1-71.9) or diarrhea (66.7%; 95% ci: 42.8-84.2) was relatively lower. however, the number of patients with initial symptoms including muscle ache (10/936) or dyspnea (8/936) was relatively small and, therefore, the above conclusion is worthy of further large-scale clinical observations. to further provide a risk assessing system that could be considered as a worthy reference for the frontline clinicians, a "clinical rapid and preliminary sorting score system" was proposed, which was constructed by combination of symptomatic manifestations such as fever, chest ct scan with bilateral ground-glass accepted article opacities and eosinophil count. interestingly, the results indicated that if the patients manifested these four characteristics (fever, bilateral ct imaging, ground-glass opacity and eosinophil count below the normal level), the possibility for a covid-19 positivity could reach up to 79·8% (95% ci: 71.97-87.7), and the or ratio was 2.782 (95% ci: 1.578-4.905). similarly, once patients only manifest bilateral lung ground-glass changes and eosinophil count below the normal level, the possibility for a positive result in nucleic acid assay could also reach 77.0% (95% ci: 71.0-83.0) ( table 4) . among 628 diagnosed covid-19 patients, 553 cases were mild cases (87·9%), while 75 were severe cases (11.9%). in general, the mild cases (52 years ± 15·1 years) were significantly younger than that of severe cases (57 years ± 11·5 years) (p = 0·004). among 553 mild cases, 262 of them (47·4%) were males, and 291 (52·6%) were females. similarly, 34 out of 75 severe cases (45·3%) were males, and the rest 41 (54·7%) were females. no preferential distribution in terms of genders was observed in either mild or severe/critical cases was observed. however, it seemed that more severe cases manifested cough in their initial symptoms as compared to that of mild cases (24% vs. 14·5%; p=0.033) ( table 5 ). this is the first retrospective study with large sample size of visitors from a single fever clinic in wuhan, china. based on the analysis of the initial clinical symptoms of 936 visitors in the fever clinic of tongji hospital and the estimation of basic reproductive number (r0) in previous studies, 14, 15 person-to-person transmission, particularly in the crowded public places, is likely the major style contributing to the covid-19 outbreak. this transmission style exacerbated the outbreak in wuhan significantly from late january to early february of 2020. given that tongji hospital is located in the center of this epidemic, the number of visitors in its fever clinic was far beyond of its capacity. in particular, from january 30 th to february 4 th of 2020, 5,686 covid-19 cases were confirmed in wuhan, while 628 of which were diagnosed in tongji hospital, which accounted for 11.0% of the total diagnosed cases. 16, 17 among 936 visitors included in this study, the detection rate for sars-cov-2 reached up to 67% (628/936). interestingly, there is no statistical difference in gender distribution between covid-19 patients and nucleic acid negative patients, suggesting that sars-cov-2 is susceptible to both genders. this finding is different from chen and his colleagues reported, 18 but consistent with the data published by wang and his colleagues. 14 this discrepancy is likely caused by the small sample size included by chen and his colleagues. however, all studies including our own indicated that aged subjects are more susceptible to sars-cov-2 infection. the primary symptoms of covid-19 patients were fever and cough, which were similar to the clinical manifestations of sars and mers. [19] [20] [21] in general, covid patients are difficult to be discriminated from nucleic acid negative patients based on symptoms such as fever, cough and others. therefore, we first assessed the relationship between the first symptom(s) and the positive rate of sars-cov-2 detection. remarkably, visitors initially complained with muscle ache displayed up to 80% positively of sars-cov-2, followed by dyspnea (75%), indicating that initial symptoms manifested by muscle ache or dyspnea could be more critical for a quick assessment for possibility of sars-cov-2 infection, as fever and cough are also common in those nucleic acid negative visitors. however, only 8 patients (1.3%) were found with aching muscle in our study, while a study in the hospitalized patients revealed that around 23.1% covidin general, antibodies specific for covid-19 virus could not be detected until day 10 following infection, and track records for all of our outpatients revealed that none of them had more than day 6 of the initial symptoms before visiting the fever clinic (1 to 6 days). therefore, it seems that nucleic acid assay is the only way to reach a confirmative diagnosis of covid-19 during the early stage of infection. unfortunately, false negative result could be produced in certain patients, which would delay the diagnosis and give timely treatment for saving their lives. in order to make a preliminary assessment whether a patient was covid-19 in case that nucleic acid assays are not available or negative because of inappropriate sample collection, we proposed a system by combining the initial symptoms, laboratory tests, and chest ct scans. remarkably, fever combined with muscle ache can reach a 75.0% possibility for a positive result in nucleic acid assays, while the possibility of nucleic acid positive could reach up to 79.8% once fever combines with bilateral lung ground glass-like changes in ct scans and eosinophil count below normal level. in particular, by combining bilateral lung ground glass-like changes in ct-scans with eosinophils below normal level only can also reach 77.0% possibility to be positive for nucleic acid assay. together, this system could be useful for helping those nucleic acid negative patients and regions lack of nucleic acid detection kits from misdiagnosis before antibody testing. one major limitation for our study is that we could not track their records after visiting our fever clinic. once a confirmative diagnosis reached, only those severe and critical covid-19 patients were arranged for hospitalized treatment by the outbreak control center under city government based on the available bed units in the designated hospitals in wuhan, and the purpose of this policy was designed to increase the efficiency for the use of limited bed units at that time. for those patients with mild symptoms or nucleic acid negative patients were advised for home quarantine for 14 days. therefore, we cannot track those patients for their location of admission and for obtaining additional medical histories. however, the situation was changed later upon the arrival of medical staff from outsides and the establishment of cabin hospitals and two additional infectious hospitals. in summary, this retrospective study included 936 visitors from the fever clinic of tongji hospital from january 30th to february 4th of 2020, which was the peak time of this outbreak. the detection rate for covid-19 was as high as 67.1%. by analysis with different groups, we demonstrated that muscle ache and fever could be two independent markers for early assessing the possibility of covid-19, while eosinophil counts below normal levels could a viable marker to assess the possibility of a patient being diagnosed as covid-19 by combining other initial symptoms, laboratory tests and chest ct scan. those data may provide critical information for the regions such as europe and united states that are facing the same situation as wuhan experienced, and could be valuable to prevent those nucleic acid negative patients from misdiagnosis before antibody testing. table 1 the clinical features of patients infected with 2019 novel coronavirus in wuhan, china the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle pattern of early human-to-human transmission of wuhan a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster the latest situation of new coronavirus pneumonia as of 24:00 on february date last updated: feburary 25 2020. date last accessed: feburary second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novelcoronavirus-(sars-cov-2). date last updated: feburary a novel coronavirus from patients with pneumonia in china a novel coronavirus associated with severe acute respiratory syndrome pathogenicity and transmissibility of sars-cov-2-a quick overview and comparison with other emerging viruses the epidemiology of severe acute respiratory syndrome in the 2003 hong kong epidemic: an analysis of all 1755 patients notice on issuing a new coronavirus infected pneumonia diagnosis and treatment plan (trial version 5) histopathologic changes and sars-cov-2 immunostaining in the lung of a patient with covid-19 clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia pneumonia epidemic situation of c sars-cov-2 infection in hubei province pneumonia epidemic situation of sars-cov-2 infection in hubei province, china -hubei provincial health committee epidemiological and clinical characteristics of 99 cases of 2019 novel coronaviruspneumonia in wuhan,china:a descriptive study clinical features and short-term outcomes of 144 patients with sars in the greater toronto area sars and other coronaviruses as causes of pneumonia middle east respiratory syndrome epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan, china eosinophils contribute to innate antiviral immunity and promote clearance of respiratory syncytial virus ct imaging features of 2019 novel coronavirus (sars-cov-2). 2020. p radiology of severe acute respiratory syndrome (sars): the emerging pathologic-radiologic correlates of an emerging disease thin-section ct 12 months after the diagnosis of severe acute respiratory syndrome in pediatric patients optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in eastern china detection of covid-19 in children in early notice on issuing a new coronary virus pneumonia diagnosis and treatment plan (trial version 7) key: cord-304710-gjb6zo81 authors: khan, s.; nabi, g.; han, g.; siddique, r.; lian, s.; shi, h.; bashir, n.; ali, a.; shereen, m. adnan title: novel coronavirus: how things are in wuhan date: 2020-02-11 journal: clin microbiol infect doi: 10.1016/j.cmi.2020.02.005 sha: doc_id: 304710 cord_uid: gjb6zo81 nan wuhan, a metropolis of 11 million people and home to thousands of foreign students, scientists, teachers and businessmen, is currently facing one of the deadliest outbreaks of a novel coronavirus (2019n-cov). the newly emerged coronavirus, 2019n-cov, was detected in december 2019 and the first fatality was reported at the start of 2020 [1] . during first month of the outbreak, there were 16 500 confirmed cases, 360 fatalities and over 20 000 suspected cases [2] . the government declared an emergency and wuhan and several cities nearby are in lockdown to prevent the rapid spread of the virus. currently, healthcare workers are in a critical stage. there is a great risk of medical and clinical staff (and workers) becoming infected with 2019n-cov because of their direct interaction with infected and suspected individuals. a total of 15 medical staff have been infected, and one doctor has died from 2019n-cov infection in wuhan hospital [3] . at hubei general hospital (one of the most famous hospitals in wuhan, also known as renmin hospital), a large number of clinical workers have been infected and admitted to the hospital; however, some of them have asked to be isolated at home due to the scarcity of sickbeds and clinical supplies. every day the dramatic increase in the number of infected individuals is causing a huge burden on the medical staff. there is a shortage of doctors and nurses, who are compelled to work longer without taking enough rest. working for long hours, disturbed daily routines including eating and sleeping schedules and fear of being infected are key factors that increase the risks of stress and anxiety for doctors and nurses, and may lead to their working less efficiently in terms of providing better treatment and care to patients. under these pressures, some medical staff have experienced an emotional breakdown at the frontline [4] . the situation worsened for medical staff after the death of dr liang wudong, who contracted 2019n-cov. the increasing number of suspected individuals every day and the shortage of laboratory staff could increase the workload and may delay routine clinical tests for infected or suspected individuals. furthermore, the shortage of protective coverings further increases the chances of getting the infection [5] . staff have been asked to use substandard masks, putting them at greater risk [4] . the healthcare authorities have stepped up efforts to overcome the problems and have sent thousands of medical personnel including army medical staff to wuhan. to cope with further shortages, the designated hospitals have transferred medical and clinical testing staff to frontline departments from other departments such as oncology, orthopaedics and medicines. in addition, healthcare workers from several undesignated healthcare units have been transferred to designated hospitals for coronavirus-infected patients. in order to increase the space and availability of sickbeds, regular hospital patients (not infected with 2019n-cov) are being moved out of hospitals, and admissions for new regular patients are being delayed. several hospitals are setting up online medical consultations for these patients to discuss their conditions and seek help. furthermore, some companies are working to make diagnostic kits available on a large scale, but it may take some time. however, the increasing number of patients every day and the expected peak in the coming days [6] may cause a further shortage of medical staff and health and logistic issues for the frontline healthcare provider. specific areas have been set aside inside designated hospitals to provide services according to the severity of the disease. suspected and confirmed cases are given diagnostic and treatment facilities in an isolated and protected environment; however, individuals in a critical condition are given treatment on a priority basis. in some cases, allopathic medicines are advised in combination with chinese medicine such as huoxiangzhengqi (for gastrointestinal problems), jinhua qinggan, lianhua qingjia, shufengjiedu and fangfengtongsheng (for fatigue and fever). psychological counselling is now available to handle the anxiety and fear among patients. confirmed patients have been given access to the internet and provided with healthy food; communication with relatives is through mobile video calls. online assistance using a video chat between doctor and patient (suspected or confirmed) is also used in some hospitals. some doctors and nurses prefer to communicate via mobile phone rather than direct contacting with the admitted patient. patients are discharged and sent back home in protected and disinfected vehicles after they have recovered from the fever, respiratory symptoms are improved and the nucleic acid test is negative. despite these services, new suspected and/or confirmed individuals are facing problems. the scarcity of sickbeds is causing confirmed patients to wait for a long time before they are admitted to a hospital, while the availability of sickbeds depends on recovery of already admitted patients. however, failure to provide admitted patients with protection measures such as goggles and suits, the shortage of medicines and the lack of isolated rooms are negatively affecting the recovery of patients. in some places, rapid measurement kits are not available. a pharyngeal swab-based test needs to be repeated for confirmation, which delays the process of admitting infected patients. this may increase the severity of symptoms and the risk of fatality. some of the infected individuals were found to have mild symptoms and rather than admitting them they were offered therapy and were advised to stay in isolated rooms. to cope with the increasing number of infected people, two new hospitals are nearing completion and will be able to house about 2300 beds [7] . however, the daily the numbers of confirmed and suspected cases are increasing in the thousands, thus raising concern about future treatment and management strategies. scientists in china are working efficiently, as observed by the early detection of the virus, sequencing of its first genome, designing of rapid detection kits, isolation of the virus in the laboratory and developing a vaccine [1, 8, 9] . a group of researchers in the wuhan institute of virology is studying the genome complexity, which may lead to uncovering unique structural features and drug target sites. moreover, research groups from the wuhan institute of virology and academy of military medical sciences have identified some broad-spectrum antiviral drugs that may have potential inhibitory effects against 2019-ncov. researchers and scientists at the wuhan institute of virology, wuhan university, huazhong university of science and technology and several other laboratories in wuhan and across the country are working to find ways of prevention and treatment in order to prevent further spread. broad range combinational therapies including lopinavireritonavir and interferon antiviral peptides are being evaluated for use against 2019n-cov. overall the current measures to control the 2019n-cov are being implemented with care and strictness. the entrances of residential communities, dormitories and public places are restricted and residents entering are monitored for temperature and related symptoms. people from wuhan are registered and kept under medical observation in some cities in china; meanwhile, their suspected contacts may be tracked to isolate them for monitoring purposes. farmers are being directed to maintain hygiene, and seafood markets are being monitored in major cities. the authors declare that there is no conflict of interest. no external funding was received for this article. the continuing 2019-ncov epidemic threat of novel coronaviruses to global health e the latest 2019 novel coronavirus outbreak in wuhan, china coronavirus claims first life outside china as wuhan enforces quarantine for all suspected patients china coronavirus: wuhan medical staff being infected at much faster pace than reported as national death toll hits 26 clinical features of patients infected with 2019 novel coronavirus in wuhan, china wuhan calls for more material help to deal with virus. china: daily dramatic hong kong data predicts coronavirus outbreak infecting 150,000 every day china building two hospitals in just a few days to tackle virus coronaviruses: genome structure, replication, and pathogenesis health workers in wuhan under growing risk as medical supplies run low the authors acknowledge the postdoctoral grant from the second affiliated hospital of zhengzhou university for s. khan. key: cord-336546-wcxqn5z2 authors: xi, aiqi; zhuo, ma; dai, jingtao; ding, yuehe; ma, xiuzhen; ma, xiaoli; wang, xiaoyi; shi, lianmeng; bai, huanying; zheng, hongying; nuermberger, eric; xu, jian title: epidemiological and clinical characteristics of discharged patients infected with sars‐cov‐2 on the qinghai plateau date: 2020-05-21 journal: j med virol doi: 10.1002/jmv.26032 sha: doc_id: 336546 cord_uid: wcxqn5z2 since the outbreak of coronavirus disease 2019 (covid‐19), caused by the severe acute respiratory syndrome coronavirus 2 (sars‐cov‐2) was first reported in wuhan, a series of confirmed cases of covid‐19 were found on the qinghai‐tibet plateau. we aimed to describe the epidemiological, clinical characteristics, and outcomes of all confirmed cases in qinghai, a province at high altitude. the region had no sustained local transmission. of all 18 patients with confirmed sars‐cov‐2 infection, 15 patients comprising 4 transmission clusters were identified. three patients were infected by direct contact without travel history to wuhan. of 18 patients, 10 patients showed bilateral pneumonia and 2 patients showed no abnormalities. three patients with comorbidities such as hypertension, liver diseases or diabetes developed severe illness. high c‐reactive protein levels and elevations of both alt and ast were observed in 3 severely ill patients on admission. all 18 patients were eventually discharged, including the 3 severe patients who recovered after treatment with non‐invasive mechanical ventilation, convalescent plasma and other therapies. our findings confirmed human‐to‐human transmission of sars‐cov‐2 in clusters. patients with comorbidities are more likely to develop severe illness. this article is protected by copyright. all rights reserved. coronavirus disease 2019 , caused by infection with the novel severe acute respiratory syndrome coronavirus 2 (sars-cov-2), emerged in wuhan, hubei, china in december 2019 [1] [2] [3] [4] and rapidly spread worldwide. 5 the outbreak spread to 209 countries and the global number of reported cases surpassed 1,210,000 as of april 6, 2020. 6 with evidence that sars-cov-2 is spread by human-to-human transmission, 7-9 the increasing number of cases and widening geographical spread of the disease raise a global health concern. 10 so far, several studies have described the epidemiological and clinical features of covid-19, but the data mainly came from wuhan. 4, 11 qinghai province, located on the qinghai-tibet plateau with accepted article an average altitude of more than 3000 meters above sea level and a population of 6.03 million, reported a total of 18 confirmed cases by april 6. during the outbreak, qinghai rapidly instituted a number of strict control measures to lower transmission, including the enforcement of quarantine measures, early detection, reducing passenger flow, and strong social messaging. by april 6, 2020, no new confirmed cases had been found in qinghai province for 60 consecutive days since feb 6, 2020. more importantly, all 18 patients including 3 severely ill cases had been discharged after treatment by feb 21, 2020 ( figure 1 ). in this study, we report the epidemiological and clinical characteristics, and outcomes of all 18 confirmed covid-19 patients in qinghai including family clusters who returned to qinghai from wuhan, and family members who did not travel to wuhan. for this retrospective study, we enrolled all 18 patients infected with sars-cov-2 from the hospitals designated for treatment by the health commission of qinghai province from jan 21 to april 6, 2020. 15 patients were from the fourth people's hospital of qinghai province and 3 patients were from the third people's hospital of xining. all confirmed patients enrolled in this study were diagnosed with covid-19 according to world health organization interim guidance 12 . a confirmed case of covid-19 was defined as a positive result on real-time reverse-transcriptase polymerase chain reaction (rt-pcr) assay from nasopharyngeal swab specimens. under the condition of tertiary protection, nasopharyngeal swabs of patients were collected in the isolation ward for sars-cov-2 nucleic acid detection. all biological samples were sealed and transferred to the laboratory of qinghai center for diseases prevention and control in strict accordance with the standard process. total rna was extracted using rna isolation kit (tianlong science technology, xi'an, china). in order to target the nucleocapsid (n) gene and open reading frame lab (orf1ab) gene, a sars-cov-2 real-time pcr kit (bio-germ, shanghai, china) was used in fluorescent pcr method. both internal controls and negative controls were routinely performed with each batch of tests. incubation period was defined from the first point of contact with a symptomatic case to illness onset. this study was approved by the ethics commissions of the two hospitals. oral consent was obtained from patients. the epidemiological, demographic, clinical, laboratory and radiological characteristics and treatment and outcomes data were obtained from patients' medical records. information recorded included demographic data, exposure history, comorbidities, symptoms, laboratory findings and mild cases: clinical symptoms were mild without pneumonia manifestation through image results. moderate cases: having fever and other respiratory symptoms with pneumonia manifestation through image results. severe cases: meeting any one of the following: respiratory distress, rr> 30/min; spo2 ≤90% at rest in xining adjusted according to altitude; pao2/fio2≤ 300mmhg needed to be corrected according to altitude as mentioned above. all treatment measures were collected during the hospitalization, such as antiviral therapy, antibacterial therapy, corticosteroid therapy, traditional chinese medicine therapy, immune support therapy, convalescent plasma therapy, and respiratory support. discharge criteria were based on covid-19 guidelines (5th version) by nhcc as follows: body temperature normal for more than 3 days, respiratory symptoms and pulmonary imaging improved significantly, and respiratory tract accepted article specimen nucleic acid amplification test negative on two consecutive occasions at least 24 hours apart. categorical variables were described as proportions and percentages, and continuous variables were described using median and range (min-max) values. statistical analyses were done using the graphpad prism software, version 8.02, unless otherwise indicated. for unadjusted comparisons, a 2-sided α of less than 0.05 was considered statistically significant. median values were compared by mann-whitney test. all 18 patients identified as confirmed sars-cov-2 cases were included in this study from january 25 to february 5, 2020 ( figure 1 ). among them, 3 (17%), 13 (72%) and 2 (11%) patients were categorized into severe, moderate and mild groups, respectively, during hospitalization. of 3 severe patients, 2 were initially classified as moderate and then changed to severe as disease progressed. in total, 15 patients returned from wuhan, hubei province of china. of the 3 remaining cases, 2 patients had contact with a confirmed case and 1 patient had contact with a family member who returned from wuhan with a negative result on nucleic acid amplification test. in total, 4 clusters of sars-cov-2 infection were identified, involving 15 cases. the median age was 32 years (range, 7-47 years), and 12 (67%) were men. five (28%) patients, including 3 severe patients, had chronic diseases, including hypertension, hyperlipidemia, diabetes, liver injury and polymyositis (table 1 and 2). on admission, the most common symptoms were cough (9 [50%]), sputum production (6 [33%]), chest tightness (6 [33%]), fever (3 [17%] ) and fatigue (3 [17%] ). all and showed fever, cough and fatigue when they contacted. two second-generation patients contacted with one source patient for 2 days and the incubation periods were 14 days and 15 days separately. the third second-generation patient contacted with the other source patient for 5 days and the incubation periods was 5 days. therefore, three second-generation cases had incubation periods of 5, 14 and 15 days, respectively. the median time from departure from wuhan to admission was 8 days (range, 1-16). chest x-ray or ct examination was performed on all patients on admission. of 18 patients, 10 (56%) patients showed bilateral pneumonia while 6 (33%) patients showed unilateral pneumonia, and 2 (11%) patients showed no abnormalities ( table 1 ). the most common abnormalities were ground-glass opacities (12 [67%]) and patchy shadows ( figure 2 ). on admission, 3 (17%), 3 (17%), 4 (22%) and 5 (28%) patients had leucopenia, lymphopenia, neutropenia and eosinophilia, respectively (table 3 ). hemoglobin was above the normal range in 6 (33%) patients, which may be attributed to high altitude. both alanine aminotransferase (alt) and aspartate aminotransferase (ast) concentrations were elevated in 4 patients including 3 severe patients ( table 2 ). elevated levels of lactate dehydrogenase (ldh) and creatine kinase were found in 6 (40%) and 2 (13%) cases, respectively. one patient with polymyositis showed abnormal (table 4) . with supportive care, the condition of all 18 patients improved significantly and ct images showed obvious regression of ground glass opacities ( figure 2 ). all patients including 3 severe cases were discharged. the median time for conversion of nucleic acid amplification test from positive to negative was 9 days (range, 5-18) and the median length of hospital stay was 13.5 days respectively. the remaining one had fever several hours before admission but no pneumonia symptoms on ct imaging. according to covid-19 guidelines made by the national health commission of the people's republic of china at that time, they were admitted before february 5. it is worth noting that one second-generation patient (47 years old, male) had contact with, and presumably contracted covid-19 from, his son who returned from wuhan withnegative nucleic acid test. his son had mild symptoms including fever, cough and fatigue at the next day after returning from wuhan. however, the nucleic acid tests for sars-cov-2 were negative at four different time points and ct imaging showed normal. so his son was quarantined at home and only contacted with him for 5 days. then the second-generation patient showed cough, fatigue and sore throat and was confirmed of covid-19 by nucleic acid test. we observed a greater number of men than women among the 18 cases of sars-cov-2 infection, consistent with a previous study 15 . additionally, 3 children were infected with sars-cov-2 and showed mild or moderate symptoms. all 3 severe cases had comorbidities such as hypertension, liver disease or diabetes. sars-cov-2 infects host cells through angiotensin-converting enzyme 2 (ace2) receptors. 2 ace2 is highly expressed in the heart and lungs, which is involved in heart function and the development of hypertension and diabetes. 16 liver injury in patients with sars-cov-2 infections might be also directly caused by the viral infection of liver cells. 17 elevation of both alt and ast was observed in 4 patients including 3 severe cases and 1 case with polymyositis on admission. therefore, liver damage is more prevalent in severe cases than in mild and moderate cases of covid-19 consistent with previous reports. 4, 14 as the elevated amount of c-reactive protein may be associated with the inflammatory response and cytokine storms caused by the virus in the blood vessels 18 , a previous study showed that the c-reactive protein level was positively correlated with the severity of the pneumonia. 19 similarly, we found that the amount of c-reactive protein was higher in 3 severe patients than the other 15 mild and moderate patients. qinghai is located on an elevated plateau with lower ambient oxygen levels. compared to those living at lower altitudes, patients at high altitude are less tolerant to hypoxia and lung diseases are more likely to cause respiratory failure. 20 therefore, oxygen supply is important for patients with covid-19, especially severe patients. our study has several limitations. first, there was no detailed collection of symptom data at different phases of illness. there is no detailed serial rt-pcr sampling depicted to show the viral dynamics in this small cohort. second, with the limited number of cases in qinghai, the results should be interpreted with caution. third, there was no control group for any of the treatments given, so no conclusion can be drawn about their role in recovery. at the time of convalescent plasma transfusion, the antibody level test (igg, igm et al) had not yet been routinely introduced at the hospital and no treatment guideline for using convalescent plasma was released. we did not measure the antibody concentrations in severe patients before and after convalescent plasma transfusion, so it is difficult to accurately evaluate the efficacy related to convalescent plasma. in summary, all 18 patients including 3 severely ill patients with covid-19 were discharged after treatment on qinghai plateau. patients with comorbidities are more likely to develop severe illness. high c-reactive protein levels and elevations of both alt and ast were observed in 3 severely ill patients on admission. the strategies of early detection, early diagnosis, early isolation, and early treatment of covid-19 in qinghai are useful to prevent the transmission and improve the cure rate. all authors declare no competing interests of this study. 4 -j a n -2 0 2 0 2 5 -j a n -2 0 2 0 2 6 -j a n -2 0 2 0 2 7 -j a n -2 0 2 0 2 8 -j a n -2 0 2 0 2 9 -j a n -2 0 2 0 3 0 -j a n -2 0 2 0 3 1 -j a n this article is protected by copyright. all rights reserved. a new coronavirus associated with human respiratory disease in china a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus from patients with pneumonia in china clinical features of patients infected with 2019 novel coronavirus in wuhan, china characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72314 cases from the chinese center for disease control and prevention who. coronavirus disease 2019 (covid-19) situation report -77 a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia sars-cov-2) and coronavirus disease-2019 (covid-19): the epidemic and the challenges a novel coronavirus outbreak of global health concern clinical characteristics of 138 hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance (ncov)-infection-is-suspected acute respiratory distress syndrome: the berlin definition clinical characteristics of coronavirus disease 2019 in china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study covid-19 and the cardiovascular system liver injury in covid-19: management and challenges this study was funded by science and technology department of qinghai province (number 2020-sf-158). we acknowledge all health-care workers involved in the diagnosis and treatment of patients in qinghai. we thank all patients involved in the study. we thank qinghai center for provincial people's hospital for detection of coronavirus antibody. this article is protected by copyright. all rights reserved. key: cord-319770-ddq2q1pg authors: wen, ying; wei, lan; li, yuan; tang, xiujuan; feng, shuo; leung, kathy; wu, xiaoliang; pan, xiong-fei; chen, cong; xia, junjie; zou, xuan; feng, tiejian; mei, shujiang title: epidemiological and clinical characteristics of covid-19 in shenzhen, the largest migrant city of china date: 2020-03-23 journal: nan doi: 10.1101/2020.03.22.20035246 sha: doc_id: 319770 cord_uid: ddq2q1pg we conducted a retrospective study among 417 confirmed covid-19 cases from jan 1 to feb 28, 2020 in shenzhen, the largest migrant city of china, to identify the epidemiological and clinical features in settings of high population mobility. we estimated the median incubation time to be 5.0 days. 342 (82.0%) cases were imported, 161 (38.6%) cases were identified by surveillance, and 247 (59.2%) cases were reported from cluster events. the main symptoms on admission were fever and dry cough. most patients (91.4%) had mild or moderate illnesses. age of 50 years or older, breathing problems, diarrhea, and longer time between the first medical visit and admission were associated with higher level of clinical severity. surveillance-identified cases were much less likely to progress to severe illness. although the covid-19 epidemic has been contained in shenzhen, close monitoring and risk assessments are imperative for prevention and control of covid-19 in future. the coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) is emerging as a major infectious disease epidemic globally. initially detected in a cluster of patients with unexplained pneumonia in wuhan, hubei province of china in early december 2019, sars-cov-2 rapidly spread not only within china but also around the globe within just three months. as of mar 10, 2020, 113,702 confirmed cases and 4,012 deaths have been reported in 109 countries (1) . although the natural reservoir of sars-cov-2 is still unknown, early confirmed cases are strongly associated with exposures to wild animals in the huanan seafood wholesale market (2) , and sustained human-to-human transmission is observed particularly among close contacts (3, 4) . due to the surging number and rapid spread of covid-19, world health organization (who) has increased the risk assessment of covid-19 to 'very high' at the global level on feb 28, 2020. as one of the most developed and commercialized cities in china, shenzhen is the largest migrant city where over 80% of its population (20 million) are migrants. the risk of case importation in shenzhen was therefore high, especially because the covid-19 epidemic occurred around the chinese lunar new year holiday season during which intra-city mobility of the migrant population was extremely high. since the first case of covid-19 in shenzhen was confirmed on jan 20, 2020, local authorities activated the highest level of emergency response to the disease. although there have been several studies on the transmission, epidemiology and clinical symptoms of covid-19 in wuhan (3, 5, 6) , data from other epidemic areas are still lacking (7) . in particular, information and knowledge of covid-19 from a migrant city with high population mobility like shenzhen can inform effective prevention and control strategies in other similar settings. as such, we investigated the epidemiological and clinical characteristics of all 417 cases that were confirmed in shenzhen is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. . https://doi.org/10.1101/2020.03.22.20035246 doi: medrxiv preprint as of feb 28, 2020. we conducted a retrospective study of the epidemiological and clinical characteristics of covid-19 cases in shenzhen from jan 1 to feb 28, 2020. covid-19 case was defined in accordance with the who interim guidelines and the national guidelines in diagnosis and treatment scheme for covid-19 (sixth edition) (8, 9) . sputum, blood, broncho-alveolar lavage fluid, nasopharyngeal swab, or oropharyngeal swab were collected from each patient and tested using real-time polymerase chain reaction (rt-pcr) for sars-cov-2. a cycle threshold value less than 37 was defined as pcr test positive. virus detection was first done by hospitals or districted centers for disease control and prevention (cdc), and positive results were further confirmed by guangdong provincial cdc (before jan 30, 2020) or shenzhen cdc (after jan 30, 2020). for each confirmed case, detailed epidemiological investigations were conducted by local epidemiologists and public health workers. all confirmed cases were immediately reported to the national infectious disease information system for covid-19, which was amended as a class b notifiable infectious disease on jan 20, 2020. we compiled the epidemiological and clinical data from both local epidemiological investigation reports and the national infectious disease information system. patients' information including sociodemographic characteristics, exposure history, close contacts, time-lines of illness onset, medical visit, hospitalization, and pcr confirmation, symptoms, and clinical outcomes, was extracted to construct a dataset with no personal identity. all confirmed covid-19 cases in shenzhen were included in the current analyses with no prespecified exclusion criteria. data collection in the epidemiological investigation was part of the continuing public health investigation of an emerging outbreak and therefore the . cc-by-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint patients were defined as having wuhan exposure if they were wuhan residents or visited wuhan within the past 14 days before symptom onset, and were defined as having shenzhen exposure if they had not left shenzhen within the past 14 days before symptom onset, while all others exposed elsewhere were defined as having exposure elsewhere in mainland china other than wuhan or shenzhen. based on the national guidelines in diagnosis and treatment scheme for covid-19 (9), the seriousness of clinical presentations of covid-19 cases was categorized as mild, moderate, severe, and critical. mild cases were those with virological confirmation but without an evidence of having pneumonia. moderate cases were mild cases at the same time with a diagnosis of pneumonia. severe was defined when one of the following criteria was met: dyspnea (respiratory frequency≥30/minute); blood oxygen saturation ≤93%; pao2/fio2 ratio <300; and/or lung infiltrates >50% within 24-48 hours. critical cases were defined when patients had respiratory failure; and/or septic shock; and/or multiple organ dysfunction/failure. in addition, we categorized cases into self-identified and surveillance-identified ones. the former referred to covid-19 cases who were identified when they sought medical care at the hospitals, while the latter referred to cases who were identified through active surveillance efforts including screening of close contacts of the confirmed patients and recent travelers from hubei; fever monitoring at airport, train station, docks, and highway checkpoints; and registration and report of fever by community workers. we defined a cluster as occurrence of two or more confirmed cases in a socially-close setting (such as a family, a school, or a company) within the past 14 days, which may be caused by human-to-human transmission through close contacts within such setting or infection via a common external exposure. other cases not from a cluster were defined as scattered cases. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint demographic and clinical characteristics as categorical variables were presented as numbers and percentages, while continuous variables were presented as means and standard deviations or 95% confidence intervals (ci), or medians and interquartile ranges (iqr) if appropriate. inter-group differences in the characteristics were tested by using pearson's χ 2 test or fisher's exact test for categorical variables, and by using student's t-test or analysis of variance for continuous variables showing a normal distribution, and kruskal-wallis and wilcoxon tests for continuous variables with non-parametric distribution. the incubation period was estimated by using a previously described parametric accelerated failure time model (10). patients with detailed information on the time of exposure, the date of illness onset, or the first time of presentation were included for this analysis. we fitted lognormal, gamma, and weilbull distributions using markov chain monto carlo in a bayesian framework (11). we estimated the serial interval by using the time difference of illness onset between the infector and infectee. initial reproductive number was estimated by using the best fit model based on date of illness onset of the early (jan 10-23) local exposed cases without relation to the imported cases and the estimated serial interval of covid-19. logistic regression models were applied to identify factors associated with the clinical severity of covid-19. all statistical tests and analyses of the incubation period, serial interval, and initial reproductive number were performed in r software (r foundation for statistical computing). a total of 417 cases had been confirmed as of feb 28, 2020 in shenzhen. in terms of potential source of exposure, 224 (53.7%) were exposed in wuhan, 75 (18.0%) were exposed in shenzhen, and 118 (28.3%) were exposed elsewhere (table 1 ). in addition, 161 (38.6%) cases were identified by surveillance, and 247 (59.2%) cases occurred in 92 clusters (common is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. . https://doi.org/10.1101/2020.03.22.20035246 doi: medrxiv preprint exposure or secondary transmission). none of the patients had been to the huanan seafood wholesale market within the past 14 days before illness onset, which was initially thought to be the index location of zoonotic infections of sars-cov-2 that started the covid-19 epidemic (12). days assuming the incubation time followed a lognormal distribution. estimates from models with other distributions (gamma and weilbull) were 5.4 to 5.5 days (see supplemental materials). using information on the date of illness onset from 28 pairs of infector and infectee, we estimated the mean serial interval to be 5.5 (95% ci: 4.1-7.0) days. we estimated the initial reproductive number to be 2.5 (95% ci: 1.4-4.3) using information from the cases that exposed in shenzhen. demographic characteristics, clinical symptoms and outcomes were presented in table 1 . the mean age was 45.4 years old, and 220 (52.8%) cases were female. patients with wuhan exposure were older than those with exposure in shenzhen or elsewhere (48.2 vs 42.9, 41.6, . cc-by-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. . https://doi.org/10.1101/2020.03.22.20035246 doi: medrxiv preprint p<0.05). patients identified by surveillance were younger than those self-identified cases (40.5 vs 48.4, p<0.001). in total, there were 29 (7.0%) pediatric patients aged below 15 years, of whom 26 were identified by surveillance and 28 were cases from clusters. the most common symptoms of covid-19 were fever (67.4%), dry cough (34.3%), and myalgia (28.5%). patients who were exposed in wuhan (78.1%), identified by surveillance (83.6%), or scattered (78.2%) were more likely to have fever (p<0.001). patients with shenzhen exposure were less likely to have dry cough (21.3%) than patients with wuhan exposure (35.7%) and elsewhere exposure (39.8%); they were also less likely to have myalgia (26.7%) than those with wuhan exposure (33.5%). patients who were identified by surveillance were less likely to have symptoms than the self-identified, such as fever (41.6% vs 83.6%), dry cough (23.0% vs 41.4%), myalgia (10.6% vs 39.8%), sore throat (8.1% vs 19.1%), and headache (8.1% vs 16.4%). is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint in this study, we reported the epidemiological and clinical characteristics of confirmed covid-19 cases in shenzhen, a large migrant city with the highest gdp per capita in mainland china. our results can be used to improve the prediction of transmission risk, design and implementation of intervention measures and strategies, and assessments of intervention effectiveness in similar settings. the epidemic curve of covid-19 in shenzhen had practical implications. overall, the rapid increase of cases in shenzhen was interrupted by the massive control measures implemented since jan 23 and followed by a sustained downward trend. the majority of the cases were imported and the local transmission was limited. furthermore, most cases were self-identified at the beginning, while cases were more likely to be identified by surveillance is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. fever and cough were the most common symptoms of covid-19 on hospital admission in shenzhen, which was in accordance with findings from a study that included 1099 patients from 30 provinces of china (14) . this county-wide study also reported that the proportion of patients with fever increased (88.7%) after hospital admission, although the proportion (43.8%) on admission was lower than that in our study (67.4%) (14). the overall proportion of patients with cough was lower than that of other study (59.4%) (5); meanwhile, more patients had dry cough (34.3%) than cough with phlegm (15.1%) in our study. the main symptoms were significantly different regarding different exposure sources; patients with shenzhen exposure were less likely to have fever and cough compared to those with wuhan exposure. in addition, the patients in our study were less likely to have symptoms compared to those patients reported in wuhan (15). interestingly, surveillance-identified patients showed fewer symptoms at the time of identification than those self-identified patients in our study. this might be because active surveillance identified cases at an early stage of covid-19. our study reported preliminary findings on the clinical severity of covid-19 in is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint other studies also suggested that these factors were associated with poorer outcomes in patients in wuhan and elsewhere (5, 15) . furthermore, the longer time from the first medical visit to hospital admission was associated with higher clinical severity on admission, while surveillance identification was associated with lower clinical severity. thus the low proportion of severe or critical cases in our study might be explained by the large number of cases identified by surveillance and the short time interval from the first medical visit to hospital admission. of note, 33 (83.3%) of the severe or critical cases were selfidentified, which might be due to delayed hospital admission. through active surveillance efforts such as screening of high-risk populations, a large proportion of covid-19 patients were identified at the early stage of their illness, thus decreasing the possibility of progression to a severe illness. the hospital fatality rate of covid-19 in shenzhen (0.7%) was much lower than 14% reported from wuhan (16), and also lower than 1.4% reported in a countywide study (15). since data on clinical outcomes were censored in our study, the hospital fatality rate may be underestimated. although our study had major strengths such as population-wide case identification in a major migrant city, a large sample size, and complete profiling of epidemics along the timeline of population interventions, there were several limitations that should be acknowledged. first, since some patients were still under treatment so far, we could not yet report the complete data of the disease progression on severity or assess predictors of clinical outcomes. second, important information, such as timelines of possible exposure, illness onset, and medical visits, was self-reported in the epidemiological investigations, which might be subject to recall bias. third, we did not have enough information on comorbid conditions, is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint (70.0) *elsewhere exposed refers to cases have been exposed in cities in mainland china other than wuhan or shenzhen. . cc-by-nd 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint .47) *aor, adjusted or; the model is constructed using the stepwise logistic regression (entry probability 0.05; removal probability 0.10) with variables including age, fever, cough with phlegm, sore throat, headache, breath problem, diarrhea, days from illness onset to the first medical visit, days from the first medical visit to admission, identification mode, and cluster. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. . https://doi.org/10.1101/2020.03.22.20035246 doi: medrxiv preprint figure 1 the epidemic curve of covid-19 cases by the date of illness onset and pcr confirmation in shenzhen. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 23, 2020. . https://doi.org/10.1101/2020.03.22.20035246 doi: medrxiv preprint novel coronavirus (2019-ncov) situation reports genava2020 a new coronavirus associated with human respiratory disease in china early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the 2019-ncov outbreak joint field epidemiology investigation team ql. an outbreak of ncip (2019-ncov) infection in china-wuhan hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan clinical features of patients infected with 2019 novel coronavirus in wuhan clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series clinical management of severe acute respiratory infection when novel coronavirus (2019-ncov) infection is suspected: interim guidance key: cord-304839-lesa5u2n authors: jiang, fang; deng, liehua; zhang, liangqing; cai, yin; cheung, chi wai; xia, zhengyuan title: review of the clinical characteristics of coronavirus disease 2019 (covid-19) date: 2020-03-04 journal: j gen intern med doi: 10.1007/s11606-020-05762-w sha: doc_id: 304839 cord_uid: lesa5u2n in late december 2019, a cluster of cases with 2019 novel coronavirus pneumonia (sars-cov-2) in wuhan, china, aroused worldwide concern. previous studies have reported epidemiological and clinical characteristics of coronavirus disease 2019 (covid-19). the purpose of this brief review is to summarize those published studies as of late february 2020 on the clinical features, symptoms, complications, and treatments of covid-19 and help provide guidance for frontline medical staff in the clinical management of this outbreak. in december 31, 2019, hospitals reported a cluster of cases with pneumonia of unknown cause in wuhan, hubei, china, attracting great attention nationally and worldwide. 1 on january 1, 2020, wuhan public health authorities shut down the huanan seafood wholesale market, where wild and live animals were sold, due to a suspected link with the outbreak. on january 7, 2020, researchers rapidly isolated a novel coronavirus (sars-cov-2, also referred to as 2019-ncov) from confirmed infected pneumonia patients. real-time reverse transcription polymerase chain reaction (rt-pcr) and next-generation sequencing were used to characterize it. 2 on january 23, 2020, owing to the large flow of people during the chinese spring festival, public transport was suspended in wuhan and, eventually, in all the cities in hubei province to reduce the risk of further transmission. the number of rt-pcr-confirmed cases has increased rapidly. on january 30, 2020, the world health organization (who) declared covid-19 (as it would be officially known as of february 11) to be a public health emergency of international concern (pheic) and declared an epidemic. as of february 24, 2020, 80,239 cases were confirmed worldwide causing 2700 deaths. mainland china, and especially hubei province, has borne the brunt of the epidemic, reporting 77,780 cases. outside of mainland china, 33 countries have reported 2549 confirmed infections and 34 fatalities. 3 we reviewed the published clinical features, symptoms, complications, and treatments of patients with covid-19 to help health workers around the world combat the current outbreak. we searched pubmed for all published articles regarding covid-19 up to february 19, 2020. keywords used were "covid-19," "2019 novel coronavirus," "sars-cov-2," "2019-ncov," "wuhan coronavirus," and "wuhan seafood market pneumonia virus." after careful screening, six published articles with confirmed cases were identified and included in this review. the summary of included clinical studies is shown in table 1 . huang et al. 4 first reported clinical features of 41 patients confirmed to be infected with covid-19 on january 2, 2020, which include 13 icu cases and 28 non-icu cases. more than half of the cases (66%) had been exposed to the huanan seafood wholesale market. almost all the patients had bilateral lung ground glass opacity on computed tomography imaging. the initial symptoms included fever (98%), cough (76%), dyspnea (55%), myalgia or fatigue (44%), sputum production (28%), headache (8%), hemoptysis (5%), and diarrhea (3%). only one patient did not present fever in the early stage of disease. twelve (29%) cases progressed to acute respiratory distress syndrome (ards), 5 (12%) had acute cardiac injury, 3 (7%) had acute kidney injury (aki), and 3 (7%) had shock. at the data cutoff date, 28 (68%) patients were discharged and 6 (15%) had died. on january 20, 2020, chen et al. 5 reported 99 cases with sars-cov-2-infected pneumonia. this case series revealed that older males with comorbidities as a result of weaker immune function were the most susceptible to covid-19 incidence. the symptoms, complications, and treatments in this study were similar to the previous published study by huang and colleagues. 4 at the data cutoff date, 31 (31%) were discharged and 11 (11%) died, and 57 (58%) of the patients table 1 summary of included clinical studies to date author huang et al. 4 chen et al. 5 li et al. 6 song et al. 7 chen et al. 8 wang et al. 9 study setting were still hospitalized. a study of li et al. 6 reported on 425 covid-19 cases in wuhan confirmed between january 1 and 22, 2020. the mean incubation period was 5.2 days, with the 95th percentile of the distribution at 12.5 days, though uncertainty remains. two subsequent studies confirmed the pattern of signs and symptoms. 7, 8 at the time of this writing, the most recent published case series 9 of 138 confirmed cases included 36 requiring intensive care by the data cutoff date of february 3, 2020. it also found the common presenting symptoms of fever (136, 99%), fatigue (96, 70%), and dry cough (82, 59%), though there were two patients who did not present any signs of fever at the onset of illness. a higher proportion of cases presented with gastrointestinal symptoms including diarrhea and nausea (14, 10%) than in previous series. forty-seven (34%) were discharged while 6 (4%) died, while the remainder were still hospitalized. the organ failure complications were similar to the original studies. taken together, these studies indicate the main clinical manifestations of covid-19 are fever (90% or more), cough (around 75%), and dyspnea (up to 50%). a small but significant subset has gastrointestinal symptoms. preliminary estimates of case fatality, likely to fall as better early diagnostic efforts come into play, is about 2%, mostly due to ards, aki, and myocardial injury. coronaviruses are widespread in humans and several other vertebrates and cause respiratory, enteric, hepatic, and neurologic diseases. notably, the severe acute respiratory syndrome coronavirus (sars-cov) in 2003 and middle east respiratory syndrome coronavirus (mers-cov) in 2012 have caused human epidemics. comparison with the current virus shows several significant differences and similarities. both mers-cov and sars-cov have much higher case fatality rates (40% and 10%, respectively). though the current sars-cov-2 shares 79% of its genome with sars-cov, it appears to be much more transmissible. 10 both sars-covs enter the cell via the angiotensinconverting enzyme 2 (ace2) receptor. 11, 12 the sars-cov-2 first predominantly infects lower airways and binds to ace2 on alveolar epithelial cells. both viruses are potent inducers of inflammatory cytokines. the "cytokine storm" or "cytokine cascade" is the postulated mechanism for organ damage. the virus activates immune cells and induces the secretion of inflammatory cytokines and chemokines into pulmonary vascular endothelial cells. the preliminary estimate of r0 (the expected number of cases directly produced by one person in a population susceptible to author huang et al. 4 chen et al. 5 li et al. 6 song et al. 7 chen et al. 8 wang et al. 9 invasive mechanical ventilation and ecmo, na not applicable, aki acute kidney injury, ards acute respiratory distress syndrome, crrt continuous renal replacement therapy, ecmo extracorporeal membrane oxygenation, imv invasive mechanical ventilation, niv noninvasive ventilation infection) for covid-19 is 2.2 (95% ci, 1.4 to 3.9). 6 fomites are suspected as the main source of infectious particles, though some uncertainty remains. other coronaviruses have been shown to persist for days on uncleaned surfaces. 10 additionally, sars-cov-2 rna was detected in the stool specimen in a person who had symptoms while the serum specimen tested negative. 13 recently, sars-cov-2 was isolated from a swab sample of a confirmed patient's feces by chinese researchers, 14 indicating the potential for fecal-oral transmission. studies have shown effective person-to-person transmission of 2019-ncov even in the presence of isolation efforts in medical facilities. 15, 16 a case series of nine infected pregnant women did not reveal evidence of third trimester vertical transmission after cesarian section. 17 transmission in health settings is a very serious threat. the most recent case series reported 57 (41%) of 138 patients were infected hospital settings, including 40 (29%) medical staff. 9 while further study is needed, it appears that asymptomatic persons are also potential sources of 2019-ncov infection. 18, 19 handwashing is the mainstay of viral control. contact isolation gear such as masks, gowns, and gloves are also recommended. transmission via ocular surface is possible, 20 so eye protection should also be used. several efforts to develop vaccines are underway, but the who estimates it will take 18 months for the covid-19 vaccines to be available. 21 at present, most treatment is symptomatic and supportive, though anti-inflammatory and antiviral treatments have been employed. supportive treatment for complicated patients has included continuous renal replacement therapy (crrt), invasive mechanical ventilation, and even extracorporeal membrane oxygenation (ecmo). no specific antiviral drugs have been confirmed effective. the first reported patient with 2019-ncov infection in the usa was treated with remdesivir, 13 and others have used antiretrovirals like ritonavir, with trials of both in progress. 22 a recent study conducted by the "front-line" health care providers combating covid-19 in wuhan indicated that systemic corticosteroid treatment did not show significant benefit. 23 baricitinib has been suggested as a potential drug for the treatment in the hope that it might reduce the process of both virus invasion and inflammation. 24 despite some diversity in initial symptoms, most covid-19 patients have fever and respiratory symptoms. for now, travel history to epidemic areas is important to the diagnosis and should be obtained on all patients with flu-like syndromes. if positive, timely referral to the public health authorities for testing is crucial. frontline medical staff are at risk and should employ protective measures. treatment is mainly supportive and symptomatic, though trials of vaccines and antivirals are underway. healthcare providers should follow subsequent reports as the situation will likely change rapidly. a novel coronavirus outbreak of global health concern a novel coronavirus from patients with pneumonia in china world health organization clinical features of patients infected with 2019 novel coronavirus in wuhan epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia emerging coronavirus 2019-ncov pneumonia analysis of clinical features of 29 patients with 2019 novel coronavirus pneumonia clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan sars and mers: recent insights into emerging coronaviruses a pneumonia outbreak associated with a new coronavirus of probable bat origin receptor recognition by novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars first case of 2019 novel coronavirus in the united states chinese researchers isolate novel coronavirus strain from feces importation and human-to-human transmission of a novel coronavirus in vietnam a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records transmission of 2019-ncov infection from an asymptomatic contact in germany evidence of sars-cov-2 infection in returning travelers from wuhan, china 2019-ncov transmission through the ocular surface must not be ignored who says vaccines against novel coronavirus 18 months away, pushes global research a randomized, open-label, blank-controlled trial for the efficacy and safety of lopinavir-ritonavir and interferon-alpha 2b in hospitalization patients with novel coronavirus infection. available from www.chictr.org. cn/showprojen.aspx?proj=48684 clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province baricitinib as potential treatment for 2019-ncov acute respiratory disease key: cord-304490-q9ab1pji authors: iqbal, najaf; fareed, zeeshan; shahzad, farrukh; he, xin; shahzad, umer; lina, ma title: nexus between covid-19, temperature and exchange rate in wuhan city: new findings from partial and multiple wavelet coherence date: 2020-04-22 journal: sci total environ doi: 10.1016/j.scitotenv.2020.138916 sha: doc_id: 304490 cord_uid: q9ab1pji abstract this study attempts to document the nexus between weather, covid-19 outbreak in wuhan and the chinese economy. we employ 24-h daily average temperature, daily new confirmed cases of a covid-19 in wuhan, and rmb exchange rate to represent the weather, covid-19 outbreak, and chinese economy, respectively. the methodology of wavelet transform coherence (wtc), partial wavelet coherence (pwc), and multiple wavelet coherence (mwc) is used to analyze the daily data collected from 21st january 2020 to 31st march 2020. results reveal significant coherence between series at different time-frequency combinations. overall results show the insignificance of an increase in temperature to contain new covid-19 infections. the renminbi exchange rate showed a negative coherence at specific time-frequency spots suggesting a negative but limited impact of the covid-19 outbreak in wuhan on the chinese export economy. our results are contrary to many earlier studies, which show a significant impact of increased temperature in slowing down covid-19 spread. these results can have important implications for economic and containment policy making regarding the covid-19 outbreak. the world is passing through an unprecedented situation as novel corona-virus (covid-19) is sweeping across -massive population of the world recently. the first case was reported in china's wuhan during december 2019, and a statement from who confirmed the novel nature of the virus on 9 th january 2020 (zhu et al., 2020) . within the same month, who declared public health emergency of international concern (pheic) on 29 th january 2020, citing concerns for the response capacity of countries with weaker health systems (sohrabi et al., 2020) . due to the highly contagious nature of covid-19 (r 0 =2-5) and an ever-increasing number of cases in other parts of the world, soon it became a pandemic (liu, gayle, wilder-smith, & rocklöv, 2020) . the total number of confirmed cases and deaths worldwide amount to 2,127,873 and 141,454 respectively at 04:33 hours beijing time on 17 th april 2020, according to data from johns hopkins university. a recent study in madrid suggests that covid-19 may become more contagious along time, implying that r 0 may increase (garcia-iglesias & de cos juez, 2020) . the health impact is severe enough to put more than half of the world's total population under some form of restric tion, while the economic impact is being called worse than the 2008-09 global financial crisis and compared with the great depression of 1930. stock markets around the world have seen a worse decline for decades (baker et al., 2020) . researchers across the globe are struggling to document the nascent knowledge acquired through primary j o u r n a l p r e -p r o o f observation and experience of the situation. efforts on a global scale are being made to know more about this virus and to slow down and ultimately stop the spread of this menace. figure 1 shows the daily time trend of new confirmed cases in wuhan city. [ insert figure 1 here] a sudden huge increase in new cases on 13 th february 2020 is due to the inclusion of new criterion (clinical symptoms) in detecting confirmed covid-19 cases. figure 2 showing the map where the coronavirus originated. novel corona-virus belongs to the family of severe-acute-respiratory-syndrome (sars) and bears flu like symptoms. since the weather is a key variable in predicting flu, hence it is likely to be an important factor for covid-19 too (sajadi et al., 2020) . since severe cold, wind speed and rain (weather variables) are expected to contribute to flu, cold, fever, cough and pneumonia etc. all of which are possible symptoms of covid-19, it is imperative to know how weather is associated with daily new confirmed infections of covid-19 in wuhan during this outbreak. figure 3 displays the 24-hourly daily average temperature of wuhan city. covid-19 has severely restricted peoples' mobility and disturbed routine-life-activities of almost more than half of the world population. in this scenario, the negative economic impact of this disease is imminent, especially in the country where it was reported first (china) and which is also amongst the worst affected (82,341infected and 3,352 dead till 17 th april 2020). as china is a production house of the world and a major portion of its gross domestic product (gdp) depends on exports, the renminbi (rmb, chinese currency) exchange rate is expected to be also affected (feng, li, & swenson, 2016) . due to lockdown in hubei (central chinese province of which wuhan is the capital), the movement of people and goods to and from this place was completely halted. due to the novel nature of covid-19, it became difficult to ascertain if the virus could be spread through goods transport or not. in this uncertainty, other countries felt reluctant to allow chinese made products to enter their borders. production had already suffered due to complete lockdown in a whole province and then reduced demand overseas added further to declining exports in china. all these factors can affect the exchange rate of rmb, which is primarily linked to foreign trade flows (li, ma, & xu, 2015) . in such a scenario, it is interesting to know how the chinese rmb exchange rate moved with the emerging situation of the covid-19 outbreak, explicitly speaking the number of new daily confirmed cases in wuhan during this period. figure 4 shows the daily time trend of the rmb exchange rate against usd. this study attempts to document the relationship between local weather (temperature), economy (exchange rate of rmb), and covid-19 outbreak (daily number of new confirmed covid-19 cases) in the chinese city of wuhan where it was first reported, using wavelet analysis. as it is an emerging situation, the research on different aspects of this global outbreak is still naive at the moment. soon after reporting of early cases of covid-19, it is established that human-to-human transmission is taking place lai, shih, ko, tang, & hsueh, 2020) . temperature is an important factor in infectivity reduction of the human coronavirus (lamarre & talbot, 1989) . experience with sars had demonstrated that the disease disappeared in warm weather during late july (wallis & nerlich, 2005) . similar behavior has been expected by some in the case of covid-19, also due to its relationship with the same family i.e., corona-virus (wilder-smith, chiew, & lee, 2020). temperature and humidity is an important factor in the survival of coronavirus on metal and other surfaces (casanova, jeon, rutala, weber, & sobsey, 2010) . higher humidity, lower temperature and tropical areas were found to be more feasible for the coronavirus spread during sars outbreak (chan et al., 2011) . a recent study finds an association between meteorological factors, air pollutants and number of deaths in wuhan during covid-19 outbreak using the generalized additive model (ma et al., 2020) . weather is found to be associated with the daily number of covid-19 cases in the indonesian capital city of jakarta also (tosepu et al., 2020) . research studies on the sars outbreak found that daily infections could increase as higher as 18.18 times at low temperatures as compared to high temperatures (merlo et al., 2006) . a study involving 429 cities around the world suggests that temperature may be an important factor in covid-19 infection and transmission and regions with similar weather conditions as of wuhan should be extra cautious in preventing an outbreak . the same study suggests that there may be the best temperature for covid-19 transmission and low temperature is more feasible for this infection and transmission. another research, including data from all cities of china suggests that increase in temperature leads to increase in doubling time of covid-19. this implies that high temperatures may reduce the speed of transmission of covid-19. although the model from this study explains only 18% of the variation in doubling time of covid-19 cases, it still provides an important insight into how temperature can play a role in the containment of this outbreak (oliveiros, caramelo, ferreira, & caramelo, 2020 ). while the above mentioned studies suggest a decisive role of increased temperature in reducing covid-19 spread, the current spread around southern hemisphere suggests there may be only little if any role of temperature in this regard. according to research on global scale, high temperature does not seem to slow down the covid-19 spread (jamil, alam, gojobori, & duarte, 2020) . another study on community outbreaks j o u r n a l p r e -p r o o f throughout the world suggests that covid-19 is a seasonal respiratory virus, spreading along similar latitude (sajadi et al., 2020) . in this uncertain situation where literature is inconclusive about the role of temperature in the covid-19 spread, we attempt to analyze the number of daily new covid-19 cases and average daily temperature in this regard. a better-modeled association helps to understand the behavior of this disease in varying weather conditions which can ultimately help to save precious human lives by taking preventive measures. what has happened in wuhan is important for the rest of the world to know to enable them to making informed and better decisions related to covid-19 containment. a recent study cited measures taken in wuhan as a model to contain the covid-19 elsewhere in the world (m. . a few recent studies confirmed the negative impact of the covid-19 outbreak on the chinese economy during its early stages (al-awadhi, al-saifi, al-awadhi, & alhamadi, 2020; mckibbin & fernando, 2020) . the chinese economy is export-oriented, and significant changes in exports due to covid-19 can affect its exchange rate. a lot of research is available on the relationship between the exchange rate and exports of a country, especially in the case of china (burdekin & willett, 2019; taylor, 2016) . a lot of studies conclude a positive relationship between the depreciation of rmb and chinese exports (park, yang, shi, & jiang, 2010) while others are inconclusive (cheung, chinn, & qian, 2012) . however, the current situation may be different as compared with the classical exchange-rate-exports relationship due to its novel nature. in the ongoing scenario, the rmb exchange rate is expected to show some coherence with the covid-19 outbreak, both directly and indirectly. weather is represented by "average daily temperature" in wuhan and calculated by taking 24-hourly local observations and then averaging throughout every day. covid-19 outbreak is represented by the "number of daily new confirmed infections" of covid-19 and the numbers are taken from national health commission of china's official website. data on chinese exchange rate v/s us dollar is taken from imf website. all data values are collected on daily basis from 21 st january 2020 (lockdown start date of wuhan city) to 31 st march, 2020. we have employed continuous wavelet transform (cwt), wavelet transform coherence (wtc), partial wavelet coherence (pwc) and multiple wavelet coherence (mwc) to analyze the association between the average daily temperature of wuhan, number of daily new confirmed covid-19 cases in wuhan city and rmb exchange rate. wavelet methodology is used mostly in geophysics and recently j o u r n a l p r e -p r o o f getting footprints in weather, environment, economics, and finance studies also (afshan, sharif, loganathan, & jammazi, 2018; ng & chan, 2012 ; wu, tan, guo, li, & chen, 2019) . it can capture non-linear association between multiple series of data (benhmad, 2012) . such methodology has not been employed in any studies related to covid-19 up to the best of our knowledge till now. there are several advantages of using wavelet methodology in multiple time series analysis; 1) assumption of stationarity can be relaxed. 2) a series with non-normal distribution can be used. 3) events localized in time can be captured efficiently. 4) analysis is done from a time-frequency perspective. 5) its very efficient in capturing non-linear relationships (which is the case most frequently in real world scenarios). 6) it can determine strength and direction of association and distinguish between short, medium and long term relationships at the same time. 7) different types of wavelet functions can be used depending upon the nature of data which allows more efficient and accurate tracking of the association. 8) it can capture bi-directional (lead-lag) relationship at the same time at different time-frequency domains between two time series (grinsted, moore, & jevrejeva, 2004; ng & chan, 2012; vacha & barunik, 2012) . the mathematical equation for wavelet transforms coherence is presented below; (1) the wavelet coherence ranges from 2 0 ( , ) 1 r m n  . zero means no coherence at all and one means perfect coherence. the method of monte carlo simulation is employed. in this methodology, the coherence is studied between two variables while controlling for the common effects of third variable. the mathematical representation of this method is given as under; the simplest way of understanding multiple wavelet coherence to compare it with multiple correlation. in this method, coherence is studied between one dependent variable y and the combination of two other x1 and x2 variables. the mathematical representations of mwc is shown below; ; descriptive statistics show that average number of daily cases of covid-19 is 704.31, ranging from minimum "0" to maximum 12,523 during our observation period. average daily temperature is 10.7 degree celsius, ranging from a minimum of 3 degree to a maximum of 21 degree centigrade. exchange rate average is rmb 6.99 per usd fluctuating between 6.90 and 7.115 which shows limited variation (maximum 3%) during this period. correlation between all three variables is positive and significant at the 1% level. coefficient for correlation is 0.61 between covid-19 and temperature, 0.56 between covid-19 and exchange rate and 0.53 between temperature and exchange rate respectively. inside from the light ones outside is called "cone of influence" and represents essential "edge effects" along its borders. figure 5(b) shows the significant variations in temperature that can be seen in frequency bands of 0-4, 4-8 and 8-16 during 3 rd , 3 rd -4 th and 8 th , and 3 rd -6 th weeks of observation respectively represented by an "l" and a long oval shaped dark red contours. can be interpreted as a correlation that is loca lized in time-frequency domain in simple terms but possesses many advantages as compared to simple correlation (grinsted et al., 2004) . the direction of clusters of small arrows observed in the figure 6(b), represents the direction of association between covid-19 and temperature while the colored bar on the right side tells us the strength of this association. arrows pointing towards right side mean a positive association (in phase) between these variables while negative (out phase) towards the left. arrows inside the circle (contour) mean a significant association. rightward direction of arrows inside the contour represents positive association between temperature and covid-19 in frequency band of 8-16 periods during third week of observation. red color inside the circle matches with a correlation of almost 0.80 which is shown on the colored bar on the right side representing a strong association. black cone shape lining from top to bottom on both sides is called "cone of influence" and represents significance level. temperature and exchange rate are in phase as shown by the arrows point ing towards right in the circle shown on the base of the figure 6(c) inside the cone of influence. red color inside is matching with almost 0.80 shown on the colored bar on the right which means a strong association in the frequency range of 16 and onwards during 4 th and 5 th week of observation. there are notable edge effects also in the same frequency band before and after 4 th and 5 th week. there is another very small cluster of arrows j o u r n a l p r e -p r o o f pointing left and downwards in the frequency range of 0-4 periods during 2 nd week which implies an out-phase association running from exchange rate to temperature. figure 7a-1 shows result of partial wavelet coherence (pwc) involving covid-19, temperature and exchange rate. it shows wavelet coherence between covid-19 and temperature while controlling for exchange rate. one small and the other large red colored contour can be observed in frequency domain of 0-4 and 8-16 periods respectively showing short and long term coherence within the given time period. short term coherence is observed during 1st week while long term between 2nd and 3rd week of the observation. red color inside contour matches with almost 0.80 on the colored bar on the right side of the figure showing a strong association. if we compare this result with wtc result of covid-19 and temperature from figure 6a, both are almost same. this implies that exchange rate has no significant impact on the relationship between covid-19 and temperature and results of wtc show true coherence between covid-19 and temperature. mwc shows how good the linear combination of independent variables co-moves with a dependent variable. figure 7a -2 presents result of mwc involving covid-19 as dependent while temperature and exchange rate as independents. linear combination of both independent variables explains variation (small and large red circles with black outlining) in covid-19 in almost all frequency bands including 0-4, 4-8, 8-16 and 16 to onwards during 1 st , 3 rd -4 th , 2 nd -3 rd and 4 th -5 th weeks of observation respectively. figure 7b-2 shows mwc results of temperature as dependent while exchange rate and covid-19 as independent variables. here also red colored islands with black outline can be observed in all frequency bands including 0-4, 4-8, 8-16 and onwards during 1 st -2 nd and 9 th , 3 rd , 3 rd -4 th and 5 th week of observation respectively. these small and large red colored contours show the strength of combination of exchange rate and j o u r n a l p r e -p r o o f covid-19 in predicting temperature. the more red the color, the more the variation can be explained in temperature by the combination of exchange rate and covid-19. figure 7c-2 shows mwc results involving exchange rate as dependent while temperature and covid-19 as independent variables. two small circles can be observed in the frequency band of 0-4 during 2 nd and last week of observation respectively while a large red circle in frequency band of 16 and above during 4 th and 5 th week of observation. these red areas show the association between exchange rate and a linear combination of temperature and covid-19 in that particular time-frequency space. average daily temperature of wuhan shows a positive (in phase) coherence with daily new number of covid-19 cases in medium term considering the given observation time period. this suggests that increase in temperature did not play any significant role in reducing the covid-19 spread in wuhan. this result is contrary to a lot of other studies suggesting that increase in temperature may help to contain covid-19 spread. our results are applicable for a temperature range between 3 degree and 21 degree centigrade which is the minimum and maximum temperature observed during the observation period. although exchange rate and covid-19 show a significant negative (out phase) coherence for a short period of time during 4 th and 5 th weeks of observation, the impact of covid-19 on rmb exchange rate is not very large. the mwc results downplay any huge combined impact of covid-19 and temperature on rmb exchange rate suggesting little impact on chinese exports during the observation period. overall results show a significant co movement and coherence between covid-19, exchange rate and weather in wuhan. although wavelet analysis is relatively new and better than correlation and many other time series techniques from many aspects as stated above in methodology section, results from this approach still need a caution in interpretation while talking about causality. in absence of any sound economic/scientific/social theory, there may not be any causation and data may show correlation and co-movements merely. modeling nonlinear granger causality between the oil price and us dollar: a wavelet based approach china's global interdependence: international reserves, capital inflows, financial market transmission, and exchange rate determination effects of air temperature and relative humidity on coronavirus survival on surfaces the effects of temperature and relative humidity on the viability of the sars coronavirus clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records are chinese trade flows different 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surface temperature and landscape pattern based on wavelet coherence: the case of metropolitan beijing a novel coronavirus from patients with pneumonia in china j o u r n a l p r e -p r o o f key: cord-325012-yjay3t38 authors: chen, ze-liang; zhang, qi; lu, yi; guo, zhong-min; zhang, xi; zhang, wen-jun; guo, cheng; liao, cong-hui; li, qian-lin; han, xiao-hu; lu, jia-hai title: distribution of the covid-19 epidemic and correlation with population emigration from wuhan, china date: 2020-02-28 journal: chin med j (engl) doi: 10.1097/cm9.0000000000000782 sha: doc_id: 325012 cord_uid: yjay3t38 background: the ongoing new coronavirus pneumonia (corona virus disease 2019, covid-19) outbreak is spreading in china, but it has not yet reached its peak. five million people emigrated from wuhan before lockdown, potentially representing a source of virus infection. determining case distribution and its correlation with population emigration from wuhan in the early stage of the epidemic is of great importance for early warning and for the prevention of future outbreaks. methods: the official case report on the covid-19 epidemic was collected as of january 30, 2020. time and location information on covid-19 cases was extracted and analyzed using arcgis and winbugs software. data on population migration from wuhan city and hubei province were extracted from baidu qianxi, and their correlation with the number of cases was analyzed. results: the covid-19 confirmed and death cases in hubei province accounted for 59.91% (5806/9692) and 95.77% (204/213) of the total cases in china, respectively. hot spot provinces included sichuan and yunnan, which are adjacent to hubei. the time risk of hubei province on the following day was 1.960 times that on the previous day. the number of cases in some cities was relatively low, but the time risk appeared to be continuously rising. the correlation coefficient between the provincial number of cases and emigration from wuhan was up to 0.943. the lockdown of 17 cities in hubei province and the implementation of nationwide control measures efficiently prevented an exponential growth in the number of cases. conclusions: the population that emigrated from wuhan was the main infection source in other cities and provinces. some cities with a low number of cases showed a rapid increase in case load. owing to the upcoming spring festival return wave, understanding the risk trends in different regions is crucial to ensure preparedness at both the individual and organization levels and to prevent new outbreaks. emerging infectious diseases are a major challenge in the 21st century. in recent years, worldwide outbreaks of ebola and middle east respiratory syndrome caused great health and economic losses. [1, 2] the ongoing new coronavirus pneumonia (corona virus disease 2019, covid-19) outbreak is becoming a global public health problem. the covid-19 outbreak is highly similar to the severe acute respiratory syndrome (sars) outbreak that occurred in 2003; both outbreaks were caused by new coronaviruses during time periods overlapping with the chinese spring festival. [3] on december 31, 2019, the wuhan municipal health committee reported 27 cases of pneumonia with an unknown cause, and many cases were traced to the wuhan southern china seafood market, which was subsequently closed on january 1, 2020. [4] on january 7, 2020, laboratory tests showed that the pathogen causing the previously unexplained pneumonia was a new type of coronavirus; this pneumonia was then officially named covid-19 by the world health organization. [5, 6] the covid-19 outbreak started in wuhan and spread rapidly to other provinces and countries. [7, 8] as of january 30, 2020, a total of 34 provinces and regions in china had reported 9692 cases, and nearly all imported cases were derived from wuhan in hubei province. [9, 10] covid-19 has been defined as a class b infectious disease but has been managed as a class a infectious disease by the chinese government. daily case reports are being released, and any omission or concealment is punishable by law. currently, the number of cases is still increasing, and the epidemic has not yet reached its peak; however, the situation differs from province to province. information on the temporal and spatial distributions of cases is important for developing targeted treatment and prevention strategies. because the return peak of spring festival travel is approaching, information on the possible changes in the incidence of covid-19 in different cities will help in better preparation for disease prevention and management. therefore, in this study, we investigated the temporal and spatial distributions of the early covid-19 epidemic to reveal the dynamic changes and trends in reported cases. these results will provide valuable information for disease prevention at both the individual and organization levels. all officially reported confirmed and suspected cases of covid-19 and related deaths were collected from the official website of health departments or articles citing their reports. case data were imported into microsoft excel (microsoft corporation, redmond, wa, usa) and analyzed. the national and hubei province shapefiles were used for arcgis (environmental systems research institute, redlands, wa, usa) analysis. the map was linked to an excel file containing time and location information. location data were available for 34 provinces of china and 17 prefecture level cities of hubei province. the time span was from january 16 to january 30, 2020. the covid-19 risk analysis was based on the bayesian space-time model of the winbugs (microsoft corporation) software. [11, 12] the model was divided into three levels: (1) data model the statistical data on low incidence were assumed to follow a poisson distribution for the parameters n i and m it : y it ∼ poisson (n i m it ), where the hubei province y it was i (1, ..., 17) cities with t (1, ..., 15) days number of cases occurring during the day, and the nationwide y it was the number of cases occurring in t (1, ..., 15) days in i (1, ..., 34) provinces. we assumed that there was no change in the number of people at risk in each city during the study period, such that n i was the number of people at risk in the town (i), and m it was the corresponding disease risk in the city (t) per day (i). (2) process model m it 's logarithmic transformation of disease risk allows the relative risk to be expressed as a linear combination of spatial, temporal, and spatiotemporal interaction components. the mathematical expression is shown in equation (1). where a is the fixed effect of the overall relative risk in the entire study area within 11 days, and t * = t -5.5 is the time span relative to the intermediate time point. in this model, the risk of disease is broken down into three parts: spatial change, temporal change, and space-time interaction; s i is a component of spatial variability, describing the urban disease risk relative to the risk in the entire study region over an 11-day observation period; b 0t * + y t is the change over time, which represents the overall trend of disease risk in the entire study area relative to that on the medium-term observation day, including the linear trend b 0t * and the time random effect y t ; b 0 is the time coefficient, representing the time trend in the study area; and b 1i t * allows each city to have different time-varying trends and is part of the spatiotemporal interaction. relative to b 0 , it represents the trend of local change in each city based on b 0 ; e it is used to explain local changes that cannot be explained by spatiotemporal random effects. [13] (3) parametric model according to the besag york and molliè (bym) model, [14] a spatial structure effect is defined by a prior conditional autoregressive (car) structure. in this process, a spatial adjacency weight matrix needs to be defined. if adjacent, the weight w ij = 1; otherwise the weight w ij = 0, and the special w ij = 0. similarly, b 1i is also assumed to follow bym characteristics. for the time structure effect y t , a car process is used, and the adjacency weight matrix in time is defined. for the over-discrete parameter e it , according to gelman, the normal distribution with a mean value of 0 and a variance of s 2 e, is generally assumed and the variance of each parameter obeys gamma (a, b). [15] based on this model, through the spatial component s i and its posterior probability, high-or low-risk cities (identified based on the average risk [a] in the entire study area) can be identified. by calculating the probability that spatial relative risk exp(s i ) is greater than 1, regions can be divided into five categories: those with probability >0.8, 0.6-0.8, 0.4-0.6, 0.2-0.4, and <0.2 are defined as hot spots, secondary hot spots, warm-spots, subcold spots, and cold-spots, respectively. similarly, based on the probability threshold, the differences in these regions can be identified considering the trend over time. further, based on the probability that exp (b 1i ) is greater than 1, regions can be divided into five categories: cities with an incidence risk probability greater than 0.8 show a trend for a rapid change in risk relative to the overall change, and those with an incidence risk probability between 0.6 and 0.8 show a trend for a greater change in the incidence risk than the overall change. a value between 0.4 and 0.6 indicates that the change in the occurrence risk is the same as the overall risk change; 0.2 to 0.4, that the trend of change in disease risk is lower than the overall risk change; and less than 0.2, that the trend of change in disease risk is much lower than the overall risk. population migration data were collected from the baidu website (http://qianxi.baidu.com/). data on emigration from wuhan city and hubei province to other cities and provinces were extracted and edited with microsoft excel for windows (microsoft corporation). emigration intensity was calculated using the migration index multiplied by the migration proportion in the province or city. correlation analysis was performed using ibm spss statistics software (version 22; international business machines corporation, armonk, ny, usa). p values less than 0.05 were considered statistically significant. pearson correlation coefficients greater than 0.2 were considered indicators of a positive correlation. to obtain a general profile of the case distribution, we first analyzed all the available cases during this covid-19 outbreak. [16] as shown in figure 1a , the number of cases remained stable from january 11 to 15, 2020, and the number of new and cumulative cases increased rapidly after january 16. the first death was reported on january 10, and the number of deaths began to increase rapidly from january 17 onwards, with the cumulative number of deaths reaching 213 on january 30 [ figure 1b ]. [6] after the nucleic acid assay became available, suspected cases waiting for laboratory confirmation could be diagnosed rapidly. [17] after january 19, the number of suspected cases increased rapidly, and about 40% to 50% of these suspected cases were then confirmed [ figure 1c ]. before january 19, the number of severe cases remained low, but they increased steadily from january 20 onwards [ figure 1d ]. because wuhan is the capital city of hubei province and the virus spread throughout the province quickly, we also analyzed the changes in number of cases in hubei province. on january 9, 41 cases were first reported, and by january 30, 5806 cases had been reported, accounting for 59.91% (5806/9692) of the total cases in china [ figure 1e ]. the cumulative number of figure 1f ]. these data indicated that both the incidence and mortality of covid-19 disease were the highest in hubei province. [18] before january 16, cases were mainly reported in hubei province. from january 17 onwards, the outbreak spread to many provinces and the number of cases increased rapidly. therefore, our spatial and temporal analyses used data from january 17 to 30, 2020. the location of each case was extracted from official reports and mapped onto the national map at the city level using arcgis. of the 362 cities, 307 (84.8%, 307/362) had reported cases. in general, the core outbreak area, wuhan, and its surrounding cities had the highest number of cases, followed by cities with a high population which are transportation hubs. spatial distribution was then analyzed with a bayesian model using winbugs. after nearly 100,000 iterations, the model converged successfully. after the model converged, it was iterated another 110,000 times to obtain parameter estimations. generally, a ratio close to 1 indicates that the two chain iterative sequences are close, and that the model has a good convergence and is stable [ figure 2a ]. using the established model and parameters, hot and cold spots were identified. the results showed that sichuan, yunnan, guizhou, hainan, and taiwan were hot spots, and inner mongolia, gansu, ningxia, qinghai, xinjiang, chongqing, hunan, and guangxi were secondary hot spots. generally, hot spots clustered in the midwest, and cold spots clustered in the southeast [ figure 2b ]. the overall temporal trend was calculated using the time risk model (exp(b 0t * + v t )), which described the general incidence risk according to time between january 16 and 30, 2020. through the analysis, b 0 was estimated to be 0.4604, that is, the disease risk on the following day was found to be approximately 1.585 times higher than that on the previous day. the relative risk according to time increased steadily from january 20 onwards and the upward trend continued as of january 30 [ figure 2c ], indicating that the number of cases nationwide is on the rise. as shown in figure 2d , heilongjiang, hebei, beijing, tianjin, xinjiang, ningxia, jiangsu, hunan, taiwan, and hainan showed a faster increase in the number of cases than was observed overall in the country. the increase in the number of cases in jilin, liaoning, shaanxi, guangxi, and fujian provinces also occurred relatively fast [supplementary table 1 , http://links.lww.com/cm9/a210]. the increase in other provinces was consistent with or lower than the overall national trend [ figure 2d ]. since hubei province had the highest number of cases, we analyzed the temporal and spatial distribution in different cities of hubei province. wuhan had the highest number of cases, followed by huanggang and xiaogan cities. suizhou, jingmen, and xianning were part of the second group with a high number of cases. the spatial convergence analysis had 100,000 iterations [ figure 3a ]. hot spots were identified in the east regions and cold spots were identified in the west regions [ figure 3b ]. the overall temporal trend in the change in the number of cases was calculated using the model. the average time trend coefficient b 0 was estimated to be 0.6727, indicating the time risk (occurrence probability in time) on the following day was 1.960 times higher than that on the previous day, suggesting that the daily number of cases in hubei province is on the rise [ figure 3c ]. xiangyang, suizhou, yichang, and ezhou showed the highest increase rates, and shiyan, shennongjia, xiaogan, and huangshi showed relatively high increase rates [ figure 3d ]. other cities had a growth slower than the overall growth in the province [supplementary table 2 , http://links.lww.com/cm9/ a210]. the increase rate in hubei province (1.960) was higher than that in the whole country (1.585), indicating that the rate of increase in hubei province was significantly higher than that in other provinces in china. the outbreak started from wuhan, and nearly all early cases were derived from this city, which is located in hubei province. because the outbreak occurred just before the spring festival, large-scale population migration during this period influenced the subsequent epidemic. from january 1 to 23, 2020, the population that migrated out of wuhan city and hubei province increased steadily, peaking on january 21 and 22 [ figure 4a ]. wuhan city was under lockdown on january 23, and after that, population migration was greatly inhibited. as observed in 2019, high population migration occurred on january 31; the timely city lockdown prevented a subsequent outbreak burst. we analyzed the migration into and out of wuhan city and hubei province. the top targets for emigration included henan and hunan provinces [ figure 4b ]. more people migrated out of wuhan than into the city [ figure 4c ]. to analyze the correlation between the number of cases and the emigration in wuhan city and hubei province, population migration data were collected from baidu qianxi. the correlation coefficient between the provincial number of cases and emigration from hubei province was 0.719 [ figure 4d ]. the correlation coefficient between the provincial number of cases and emigration from wuhan increased to 0.943, with the highest coefficient of 0.996 observed between wuhan and other cities of hubei provinces [ figure 4e and 4f; supplementary tables 3 and 4 , http://links.lww.com/ cm9/a210]. these data strongly indicated that the number of cases was highly related to population emigration from wuhan. although we do not know the exact number of people emigrating from wuhan, 5 million is an astonishing number, considering that each individual may be a potential virus carrier. if no control measures were implemented, the number of cases would exponentially increase. of the 5 million emigrants, 74.22% emigrated to other cities of hubei province [supplementary because the outbreak duration overlaps with the spring festival transport waves, large-scale migration will be a strong determinant of the characteristics of this outbreak. we analyzed the migration in the 3 days before the spring cities with high immigration were relatively scattered. chongqing experienced the highest immigration, accounting for 1.50% of the total number of immigrants [ figure 4 ]. as immigrants will be traveling back to work after the spring festival, the cities showing high "emigration" may be at a high risk of another wave of new cases owing to the return of the migrants. covid-19 is causing great public health and economic losses in china. the number of cases has increased rapidly, with over 70% coming from hubei province. [16, 19] as of january 30, the number of cases has exceeded the total number of cases of the sars-cov outbreak. [20] until february 15, 2020, the cumulative number of confirmed cases was 70,533, nearly ten times that noted during the sars outbreak. prevention and control of the outbreak has required concerted action from the whole population of china. although all individuals have participated in the campaign against the outbreak, people in areas with a low number of cases assumed that they were safe from the disease. therefore, awareness of high-risk regions is important for preparing individuals, particularly in regions with low incidence. further, it must be noted that 5 million persons emigrated from wuhan to all over the country. [21] we do not know exactly how many of them are virus carriers, and it is impossible to track and diagnose them all. evidence from previous cases showed that asymptomatic patients in the incubation period are also infectious, making it a greater challenge to track virus carriers. therefore, isolation at home and less contact with others is the most efficient measure to prevent infection and transmission. to reduce transmission, the spring festival holiday has been extended from january 31 to february 2. the opening time for all schools and universities has been delayed, and online teaching programs have been launched. factories have been required to delay resumption or allow work from home. we analyzed the temporal and spatial distribution of reported cases. in general, the number of cases is still on the rise. for hubei province, which has the highest number of cases and deaths, the growth trend is relatively stable. conversely, in other hot spots, the number of cases was not very high, but the growth continued. hence, these areas should be closely monitored. [22] it is particularly noteworthy that the cities with the fastest change in temporal risk, such as chongqing, have large population movements and rapid temporal risk. if they are not strictly monitored, there may be more outbreaks. to prevent disease outbreaks caused by the return travel wave after the spring festival, the country has extended the spring festival holiday. correlation analysis showed that early incidence was closely related to the emigration waves from wuhan, that is, the higher the migrating population index, the larger chinese medical journal 2020;vol(no) www.cmj.org was the number of cases. this also proved that the first generation of cases in each province mainly came from wuhan. however, with the progress of the epidemic, migrants are spreading the virus to other people and are becoming an important source of local community transmission. therefore, it is necessary to strictly implement isolation and related control measures in accordance with the guidelines. particularly, control measures must be taken to prevent the spread of diseases in communities, which is crucial to prevent a large-scale outbreak. very soon, many company staff will return to their workplaces. because many enterprises in china are labor intensive, with large populations, human-to-human transmission is extremely easy. therefore, workers need to meet requirements for isolation after returning to the city and use personal protection at work to prevent clustered outbreaks. at present, there have been several reports of employee infections caused by resumption of work; these represent a warning for all enterprises. super megacities such as guangzhou, shenzhen, and shanghai, which have the largest number of migrant workers, need to be prepared for this. from february 16, the number of new cases began to decrease, but the epidemic did not stop completely. therefore, we must act together to stop the spread of the disease. at present, the state has adopted mobility control measures to encourage people to avoid going to public places and wear masks when going out to reduce the risk of human-to-human transmission. we believe that with the joint efforts made by everyone, the number of cases and losses will be kept to a minimum. the challenge of emerging and re-emerging infectious diseases risks to healthcare workers with emerging diseases: lessons from mers-cov, ebola, sars, and avian flu bats are natural reservoirs of sars-like coronaviruses origin of viruses: primordial replicators recruiting capsids from hosts first case of 2019 novel coronavirus in the united states a novel coronavirus from patients with pneumonia in china novel wuhan (2019-ncov) coronavirus drug treatment options for the 2019-new coronavirus (2019-ncov) emerging understandings of 2019-ncov early transmission dynamics in wuhan, china, of novel coronavirusinfected pneumonia space-time mixture modelling of public health data temporal and spatial analysis of neural tube defects and detection of geographical factors in shanxi province joint prior distributions for variance parameters in bayesian analysis of normal hierarchical models bayesian image restoration, with two applications in spatial statistics interpreting posterior relative risk estimates in disease-mapping studies the extent of transmission of novel coronavirus in wuhan, china, 2020 updated understanding of the outbreak of 2019 novel coronavirus (2019-ncov) in wuhan preparedness and proactive infection control measures against the emerging wuhan coronavirus pneumonia in china real time data report of epidemic situation severe acute respiratory syndrome-associated coronavirus infection preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak distribution of the covid-19 epidemic and correlation with population emigration from wuhan, china the authors thank andre kiesel for critical revision of this manuscript. none. key: cord-321727-xyowl659 authors: wang, lishi; li, jing; guo, sumin; xie, ning; yao, lan; cao, yanhong; day, sara w.; howard, scott c.; graff, j. carolyn; gu, tianshu; ji, jiafu; gu, weikuan; sun, dianjun title: real-time estimation and prediction of mortality caused by covid-19 with patient information based algorithm date: 2020-07-20 journal: sci total environ doi: 10.1016/j.scitotenv.2020.138394 sha: doc_id: 321727 cord_uid: xyowl659 the global covid-19 outbreak is worrisome both for its high rate of spread, and the high case fatality rate reported by early studies and now in italy. we report a new methodology, the patient information based algorithm (piba), for estimating the death rate of a disease in real-time using publicly available data collected during an outbreak. piba estimated the death rate based on data of the patients in wuhan and then in other cities throughout china. the estimated days from hospital admission to death was 13 (standard deviation (sd), 6 days). the death rates based on piba were used to predict the daily numbers of deaths since the week of february 25, 2020, in china overall, hubei province, wuhan city, and the rest of the country except hubei province. the death rate of covid-19 ranges from 0.75% to 3% and may decrease in the future. the results showed that the real death numbers had fallen into the predicted ranges. in addition, using the preliminary data from china, the piba method was successfully used to estimate the death rate and predict the death numbers of the korean population. in conclusion, piba can be used to efficiently estimate the death rate of a new infectious disease in real-time and to predict future deaths. the spread of 2019-ncov and its case fatality rate may vary in regions with different climates and temperatures from hubei and wuhan. piba model can be built based on known information of early patients in different countries. • the mortality rate determines whether a highly infectious disease becomes a public concern. • summarizing information after the fact does not contribute to real-time readiness to deal with the disease. • the patient information based algorithm (piba) estimates the death rate of a disease in real-time. • piba can be used to estimate the death rate of a new infectious disease in real time and to predict future deaths. a b s t r a c t a r t i c l e i n f o the mortality rate is the most important factor that determines whether a highly infectious disease becomes a public concern and carries risks causing a pandemic. different virus epidemics take place throughout the world every year, but only a few rise to the level of public concern (schlagenhauf and ashra, 2003; viboud and simonsen, 2012; who ebola response team, 2014) . severe acute respiratory syndrome (sars), swine influenza a h1n1 virus (h1n1), and zaire ebolavirus (ebola) brought on the public's attention because they caused many severe infections and thousands of deaths (dawood et al., 2012; nicholls et al., 2003; who ebola response team, 2014) . similarly, the disease covid-19 caused by a coronavirus (2019-ncov) brought world-wide attention and caused public panic because many deaths had been reported without being put in the context of the many mild infections and its potentially low case fatality rate (chan et al., 2020; huang et al., 2020; wang et al., 2020; wu et al., 2020) . for example, despite being a common infection, influenza rarely causes public concern because even though it is common, it leads to death in only 0.1% of cases. a variety of reports indicate that 2019-ncov is highly infectious through multiple routes huang et al., 2020; wu et al., 2020) . while the high infection rate is certain, the mortality rate of covid-19 has not been definitively determined. it is reasonable to suspect that the deaths of six of the first 41 patients (15%) in wuhan (huang et al., 2020) in the earliest reports by chinese scholars were inaccurate. when the initial mortality rates were reported, only patients who were critically ill were included. patients with mild symptoms, as well as those with asymptomatic infections, were not analyzed huang et al., 2020; wu et al., 2020) . case-fatality rates reported by huang et al. (2020) analyzed a skewed patient sample since it included only a small number of patients who had been transferred from other hospitals due to their critical condition. therefore huang et al.'s sample was skewed towards a concentration of severely ill patients, while the general patient population includes more patients with covid-19 who are asymptomatic or only have mild symptoms and who have not been hospitalized. chen et al. (2020) reported an 11% death rate, again based on patients with severe conditions. we have estimated the mortality rate using a patient information based algorithm (piba). the piba uses patient data in real-time to build a model that estimates and predicts death rates for the near future. piba uses data of patients identified early in the disease process to calculate the average number of days from hospitalization to death for those hospitalized. another feature is to take into account variations based on mathematical models. the piba calculation method does not divide the total number of patients on a day by the number of deaths on the same day. instead, the piba calculation method divides the number of deaths on that day by the number of possible patients of a day or days when the patients have just begun to develop the disease. thus, piba comprehensively and reasonably estimates the mortality rate based on the actual number of deaths and estimates the number of patients on a specific day. as time goes on, large amounts of data from northern and southern china have been accumulated through continuous reporting, all of which are used by piba, which then becomes more accurate as data accumulates. we conclude that it is time to utilize the accumulated data to estimate the case fatality rate of covid-19 infection. based on national data from the china national health center, the covid-19 death rate is much lower than that reported in huang et al. (2020) . holistic data covering all of wuhan, the epicenter city of covid-19, also indicates a death rate lower than that reported by huang et al. these data sources cover a larger patient sample, and include patients displaying symptoms with varying levels of severity. therefore, the updated estimation of the death rate should reference these larger scale and more representative data. our study contributes to knowledge on covid-19 death rate by building on huang et al.'s (2020) estimation and available data from official websites and addressing the limitations with a larger and more representative sample. 2.1. steps for estimating and predicting mortality using piba 1) to collect data from the patient's initial admission to death. strive to collect data for a certain number of patients. 2) to calculate the average number of days (μ) from hospital admission to the death and the number of days between one standard deviation (μ ± σ) interval and two standard deviations (μ ± 2σ). 3) to use these parameters (μ, μ ± σ, μ ± 2σ) to calculate the daily mortality during the epidemic. 4) to predict the mortality of infectious diseases in the future based on the calculated known mortality combined with the number of patients in a region. the predicted numbers are compared with real mortality to test and correct model data. 5) to conduct following-up modification of the piba model according to different nationalities and regions. in particular, the initial patient data collected may vary significantly from country to country, one ethnic group to the other, and region to region. the calculation based on the number of deaths and the number of patients on the same day does not reflect the real death rate because most patients with covid-19 do not die on the same day that they entered the hospital (chan et al., 2020; huang et al., 2020; wang et al., 2020) . with the piba method, we recognize that the patient population size was inaccurate in the early days but trust the published information of patients who died right after covid-19 outbreaks. the estimation is built upon data from patients with a normal distribution model. based on information about patients in wuhan who died during the period between dec 16, 2019, to jan 2, 2020 (huang et al., 2020) , two parameters were used to estimate days from onset of symptoms to death and days from admission to the intensive care unit (icu) to death. these two parameters are adopted in the estimation and prediction of covid-19 death rate. each parameter has five values including the mean, μ, one standard deviation from the mean, μ ± σ, and two standard deviations from the mean, μ ± 2σ. we collected data from covid-19 patients in china from three public websites. the data from the whole country are collected and made available on the official website of the health emergency office of the national health commission of the people's republic of china at http://www.nhc.gov.cn/yjb/new_index.shtml. the data from hubei province and wuhan are from the health commission of hubei province at http://wjw.hubei.gov.cn/fbjd/dtyw/. these data include the number of patients with covid-19 who were confirmed as having the disease, who died from the disease, whose condition was severe, and who were admitted to the hospital or icu. other collected data included daily new cases, new deaths, people who were in close contact with an infection source, and accumulated number of patients. we paid particular attention to data from wuhan, plus two additional cities in hubei province, xiaogan, and huanggang, in which the number of patients was higher than in other cities in hubei province. information from a northern province, heilongjiang province, was collected from the official website of outbreak information of the health commission of heilongjiang province at http://wsjkw.hlj.gov.cn/index. php/home/zwgk/all/typeid/42. data of heilongjiang province and harbin city were included because the province is located in the northern high-altitude zone. these data are used to assess whether the covid-19 is more, less, or equally likely to spread to an area with a cold climate. collected information included numbers of patients and numbers of deaths from each city and in the whole province. for any missing data in any day, a formula was used to estimate the data in that day: ni = {(n(i + j) + (n(i − j)) / (j + 1)} + (n(i − j), where ni = the estimated value of the missing data of the day i. j is the number of days of missing data, usually is 1; in the rare case, data of two consecutive days may be missing. if the data of two days are missing, the first day will be considered as the day i, the second day n (i + 1) will be calculated as n(i + 1) = ni + {(n(i + j) + (n(i − j)) / (j + 1)}. based on the days between confirmation of covid-19 and the days of death in the hospital, calculated from wuhan, as mentioned in method 1 and information from the whole country and hubei province, we tested the number of days from diagnosis to death, that most likely reflects the actual death rate. the estimated days are used to estimate the death rate using data from hubei province and wuhan city with the five values from above (μ, μ ± σ, μ ± 2σ). in consideration of the contribution of a variety of sources for the estimation, we fractured the data from (μ, μ ± σ and μ ± 2σ) into the piba and built the testing model as follows. 1) m i = (d i − d i−1 ) / (p i−n − p i−n−1 ) (death rate at increments) 2) m i = d i / p i−n (death rate at accumulative numbers) where m i = mortality rate, d i = the cumulative numbers of deaths on day i, p i = the cumulative numbers of patients on day i , i = the current day for calculating the death rate, n = the number of days from severe infection to death. when we considered these five partial values in normal distribution as a good indicator with a width of one standard deviation, each one of the five death rates calculated above on each day would have its own weight as the possible normal distribution (μ = 38.2%, μ − σ = μ + σ = 24.2%, and μ + 2σ = μ − 2σ = 6.7%). from here, we could give the death rate for every single day just a single value that results from the weighted average of all five cohorts of patients, as defined by time from severe illness to death. the equation is as follows: where d = death rate, mμ = mortality rate with μ days, wμ = weight with μ days gap, μ = mean in normal distribution, σ = standard deviation. 2.5. confirmation of the best estimation of the days to calculate the death rate in the other cities the same formula was then used to estimate the death rate from the other two cities in hubei province, namely xiaogan and huanggang. the piba model was developed using data from hubei province, including a. distribution of days between disease symptoms and death and between time of icu admission and death. vertical axis: days, horizontal axis: cases. b. estimated days from first symptoms to death and days from icu admission to death. c. lagging days (days from first symptoms to the day of death), μ, μ ± σ and μ ± 2σ and their weight (in percentages) used for the estimation of death rate in the broader patient population. note: among these values above, the lagging day μ − 2σ from symptom confirmation to death in panel b that equals to −3 has been set to 0. wuhan, xiaogan, and huanggang, and was further validated using data from heilongjiang province and harbin city. piba was then used to predict trends in new number of deaths. in order to further test the validity of our piba method in predicting actual mortality, we used a combination of the curve trend data and the overall mortality rate of the country, hubei, wuhan, and the rest of the country (china overall except hubei). based on our prediction of the days from actual hospitalization to death, we separately predicted the number of deaths in each day of the coming week. that is, from the comprehensive information of the number of new patients on the seventh day, the 13th day, and the 19th day before the targeted prediction day, we obtained three numbers of deaths for each of the predicted days. then from three of these numbers, the lower and upper values of the number of deaths on that day are used as the minimum and the maximum number of predicted deaths on that day, respectively. also, the same formula was used to predict the death number of a week in south korea. using information published by wuhan, we calculated the days between icu admission and death. we obtained the actual data from 33 patients who died in the hospital in wuhan. the days from onset of symptoms to deaths ranged from 6 to 30 (see fig. 1a ). from icu intake to death, the shortest number is one day, and the longest is 22 days. we derived two parameters, each from the 33 death cases, i.e., the days from onset of symptoms to death and the days from inpatient admission to death. since there are six patients out of these 33 death cases who have the same date of symptoms' appearance and inpatient, there were 33 values in the dataset related to inpatient and 27 values in another dataset related to symptoms' appearance (fig. 1a) . the results indicated that the average time from onset of the symptoms to death is 13 days (m = 13, s.d. = 6) (see fig. 1b ). accordingly, the lagging days from the day of death and their weight in the calculation of death rate were derived based on the new inpatient days (fig. 1c) . the prediction of death rate is based on data from wuhan city in which patients diagnosed with covid-19 had been confirmed since january 19, 2020 and where deaths had occurred, which were among the first confirmed cases of coronavirus. 3.2. estimated death rate for the whole country and hubei province using piba formula according to our five estimation parameters, from illness (i.e., symptom appearance) to death, the maximum number of days is 25 days. the earliest reported data in wuhan was published on january 19, 2020. based on these data, we were able to calculate the mortality rate from february 8, 2020, to the present. however, on february 12, the national health committee revised the data again (see appendix table 1 ). because of this amendment, the number of confirmed cases appeared to have changed significantly in only one day. we chose the calculation results from february 14 up to february 25 (appendix table 2 ), considering that the death rates on february 12 and february 13 are likely distorted by this sharp rise within a short term. fig. 2a through d provide information about the overall death rates in mainland china (hereafter referred to as country), hubei, wuhan, and rest of country (excluding hubei) (appendix table 3 ). we noticed that the death rate at increments based on piba in the whole country (in blue) in fig. 2a is below 10%, with most values between 2.7% and 6% in the last five days. the death rate in hubei province is similar to that of the whole country because 90% of the patients in the whole country were from hubei province (see appendix table 1 ) (fig. 2b) . in wuhan, the accumulated death rate was still high, as much as 20% (fig. 2d ). when we used the data from the rest of the country to test our piba formula, as expected, the curve is different from the curves from hubei and wuhan. unlike in hubei and wuhan, the death rate of the rest of the country is much lower and stable, mostly lower than 1% (fig. 2c) . the predicted death rate will remain between 1% and 2% for the near future. xiaogan and huanggang are the two cities in hubei province. the number of patients with covid-19 in these two cities is higher than in other cities in hubei except wuhan. they also are the cities with the largest number of patients with covid-19 in china. we, therefore, tested the piba formula using data from these two cities. currently, the death rate based on the increment data is around 3%, lower than that in wuhan but higher than that in the rest of the country. however, according to piba, the rate of deaths may decrease in the near future. heilongjiang province, including its capital city, harbin, is the province outside of hubei with the largest number of diagnosed patients. harbin city is located in the northeast of china and is in the coldest area in china. no patients from harbin city or the heilongjiang province were reported during the sars epidemic period. we used the piba formula to estimate the death rate in both the heilongjiang province (fig. 3c) and harbin city (fig. 3d) . the death rate of harbin decreased sharply in the past several days, into 0%. the low rate of less than 1% will possibly remain for the future. based on the piba and the death rate of accumulated numbers, the expected final death rate of the whole country, hubei, wuhan, and rest of the country except hubei, is predicted as follows (see table 1 ). the predicted values are from the intersection points between the incremental estimation and net values estimation. we used the predicted death rate to calculate the potential number of deaths per day in the coming week. because our initial estimation on the lagging days between inpatient and death was only based on 33 fig. 3 . death rate estimations of four places. the blue curve represents the mortality calculated by the actual increase in deaths per lagging day divided by the increase in actual patients on the previous corresponding day. the gray curve represents the total number of deaths per lagging day, divided by the total number of identified actual patients on the corresponding previous day. the orange curve shows the number of deaths per day divided by the total number of patients the same day. numbers on the vertical axis represent the death rate; on the horizontal axis is the date. a. the death rate of xiaogan city in hubei province b. death rate of huanggang city in hubei province. c. the death rate in heilongjiang province. d. the death rate in harbin city. patients, we, therefore, used the days of average 13 days plus (19 days) and minus one standard deviation (7 days) as the range of number of deaths on a given day in the coming week (see appendix table 4 . predicted number of deaths in the days of the coming week after february 25, 2020). as shown in fig. 4 , the actual number of deaths in the past four days fell into the predicted range. in the country (fig. 4a) , hubei (fig. 4b) , and wuhan (fig. 4c) , the numbers of actual death were near the predicted minimum numbers. while, for the rest of the regions of the country except hubei, the actual death data fluctuates between the predicted maximum and minimum values (fig. 4c) . due to the number of newly infected patients dropping in the last few days, the total number of patients tends to be constant or even less in the coming days if unexpected events do not occur. the peaks in these figures reflect sudden changes in numbers of patients (see fig. 4 ). we believe that the intersecting point between the trendlines could reasonably be considered one of the rates in its range of the death rate of patients infected in the future. as shown in the data above, the incidence in mainland china's provinces and cities was basically zero in late middle march. because of this, we were not able to prove the feasibility of this method in more regions in mainland china. however, because the environment, medical conditions, and population races in different countries are different, to test the usefulness of the piba model in other countries, we need to get the basic information of the initial population. this information includes the specific number of days from onset to death of a reasonable number of patients in different regions of different countries. at present, we could not access these data accurately. the only thing we can do is to test asian countries such as south korea and japan based on their ethnic similarities with populations in china. taking all aspects into consideration, we believe that south korea's data are more reliable. therefore, fig. 4 . comparison between the predicted number of deaths based on piba and the actual number of deaths. the blue color represents the estimated minimum number of deaths line. the orange color represents the estimated maximum number of deaths line. the gray line represents the actual number of deaths. panels a, b, c, and d showed these death numbers in the country, hubei, wuhan and the rest of country except hubei. we further tested our model using the affected population in south korea. as shown in fig. 5 , the trend of deaths in south korea in recent days is consistent with our prediction. first, piba is capable of accurately estimating the disease mortality and the number of future deaths. this real-time accurate prediction and estimation of disease mortality provide the public, government, and society with more accurate disease information. based on currently available data that includes patients with varying degrees of severity, the estimated prediction of the mortality rate of covid-19 is less than 3%, and less than the prior prediction based on limited available data. this finding may ease public concern and panic. updated scientific findings will be widely disseminated to broaden public awareness and contribute to helping fight covid-19. the medical, clinical, and research community should strive to publish scientifically rigorous findings related to urgent public health issues. publishing findings based on the availability of limited data contributes to unnecessary public concern and government action. in this particular case, the first report on the estimation of coronavirus death rate is an applaudable effort. however, it also had the limitations of a skewed dataset that focused on patients who were transferred from local hospitals because of their critical condition while excluding patients with less severe symptoms who remained at local hospitals. as soon as more data are available, we should provide updated reports and introduce improved estimation and prediction algorithms. this study indicates that as the number of transmissions of 2019ncov increases among the human population, its lethality will gradually decrease. indeed, the reasons are not necessarily all because of their reduced toxicity. there may also be improvements in treatments and implementation of early detection methods. therefore, a real-time estimate of death rate using patient information such as the piba method would demonstrate an appreciation of the importance of public and societal awareness. a critical issue to consider is that if the mortality rate of the covid-19 in a certain area is relatively high, the covid-19 in the area is still spreading and endemic. one of the most obvious questions is why the fig. 5 . test piba model using covid-19 population from south korea. a. estimation of death rate in the korean population using the piba method. the blue curve represents the mortality calculated by the actual increase in deaths per lagging day divided by the increase in actual patients on the previous corresponding day. the gray curve represents the total number of deaths per lagging day, divided by the total number of identified actual patients on the corresponding previous day. the orange curve shows the number of deaths per day divided by the total number of patients the same day. the number on the vertical bar represents the death rate, number on the horizontal bar shows the date. b. comparison between the predicted number of deaths based on piba and the actual number of deaths. the blue color represents the estimated minimum number of deaths line. the orange color represents the estimated maximum number of deaths line. the gray line represents the actual deaths. mortality rate in wuhan is considerably higher than in other places. based on our assessment, wuhan's medical equipment and rescue measures are comparable with other areas in china, and the pathogenicity of the virus is similar. we conclude that there is a large proportion of patients in wuhan who have mild illness and not been hospitalized at all. due to the uncertainty of the movement of infected people in the early stages of the onset, these mildly ill people move around in wuhan unidentified. this problem reminds other parts of the world that if the fatality rate of the covid-19 is found to be high, a large number of infected people have not been able to be identified or diagnosed. therefore, the work of controlling and isolating this infected group has not been completed, and the disease is still spreading and circulating in the area. the data on heilongjiang province and harbin show that, unlike some experts' predictions (cf. https://news.ifeng.com/c/7uhmhxcfhmq), it will occur more intensely in the high-altitude regions with a cold climate, and the mortality rate will be higher. with the development of the generations of 2019-ncov, its toxicity will gradually weaken, and we expect that the mortality rate in the cold northern regions will not increase, nor will it exceed that in wuhan or hubei province. our research has limitations, mainly due to available data. first, the estimation of number of patients from the date of hospital admission or icu intake to the date of death is based on data from official public websites. information from 33 individuals was estimated. if the information had been available regarding more patients, the initial estimate would have been more accurate. the second aspect is the accuracy of the number of patients diagnosed and the number of hospitalizations per day. due to the back and forth revision and correction of the data as announced by the official sources, we are not confident that all the data are error-free; however, we feel that these data as a whole are reliable. the third limitation of the piba method is that it depends on accurate patient information at the beginning of the epidemic. depending on different situations from different countries or regions, this information may or may not be available, or the information may not be accurate. the piba model accurately predicted a case fatality of 1.6% for symptomatic patients in china at a very early stage in the covid-19 pandemic. the model can be generalized to predict case fatality for any infection (including asymptomat), to predict the rate of severe disease, and to predict the death rate for patients who develop severe disease. these early, accurate predictions inform the public, society, and governments to estimate the extent of the disease's harm and to develop suitable strategies. supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2020.138394. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study estimated global mortality associated with the first 12 months of 2009 pandemic influenza a h1n1 virus circulation: a modelling study clinical features of patients infected with 2019 novel coronavirus in wuhan lung pathology of fatal severe acute respiratory syndrome severe acute respiratory syndrome spreads worldwide global mortality of 2009 pandemic influenza a h1n1 a novel coronavirus outbreak of global health concern ebola virus disease in west africa-the first 9 months of the epidemic and forward projections nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study this work was partially supported by funding from merit grant i01 bx000671 to wg from the department of veterans affairs and the veterans administration medical center in memphis, tn, usa and grant 90dduc0058 to cg from u.s. department of health and human services, administration for community living. revise and approve and manuscript: all authors. all the data of patients in this study are from official public websites. key: cord-337324-jxtch47t authors: qian, guo-qing; yang, nai-bin; ding, feng; ma, ada hoi yan; wang, zong-yi; shen, yue-fei; shi, chun-wei; lian, xiang; chu, jin-guo; chen, lei; wang, zhi-yu; ren, da-wei; li, guo-xiang; chen, xue-qin; shen, hua-jiang; chen, xiao-min title: epidemiologic and clinical characteristics of 91 hospitalized patients with covid-19 in zhejiang, china: a retrospective, multi-centre case series date: 2020-02-25 journal: nan doi: 10.1101/2020.02.23.20026856 sha: doc_id: 337324 cord_uid: jxtch47t background recent studies have focused initial clinical and epidemiologic characteristics on the covid-19, mainly revealing situation in wuhan, hubei. aim to reveal more data on the epidemiologic and clinical characteristics of covid-19 patients outside of wuhan, in zhejiang, china. design retrospective case series. methods 88 cases of laboratory-confirmed and 3 cases of clinical-confirmed covid-19 were admitted to five hospitals in zhejiang province, china. data were collected from 20 january 2020 to 11 february 2020. results of all 91 patients, 88 (96.70%) were laboratory-confirmed covid-19 with throat swab samples that tested positive for sars-cov-2 while 3 (3.30%) were clinical-diagnosed covid-19 cases. the median age of the patients was 50 (36.5-57) years, and female accounted for 59.34%. in this sample 40 (43.96%) patients had contracted the diseases from local cases, 31 (34.07%) patients had been to wuhan/hubei, 8 (8.79%) cases had contacted with people from wuhan, 11 (12.09%) cases were confirmed aircraft transmission. in particular within the city of ningbo, 60.52% cases can be traced back to an event held in a temple. the most common symptoms were fever (71.43%), cough (60.44%) and fatigue (43.96%). the median of incubation period was 6 (iqr, 3-8) days and the median time from first visit to a doctor to confirmed diagnosis was 1 (1-2) days. according to the chest computed tomography scans, 67.03% cases had bilateral pneumonia. conclusions social activity cluster, family cluster and travel by airplane were how covid-19 patients get transmitted and could be rapidly diagnosed covid-19 in zhejiang. coronavirus disease 2019 (covid-19) is highly contagious and spreads rapidly through human-to-human transmissions. 5, 6 as of 20 february, 75 571 confirmed cases had been reported in mainland china and 1083 confirmed cases in 24 other countries and regions. amongst the cases in mainland china, 2239 cases died, 11 cases of death was reported from out of mainland china. 7 there were 41 initial cases of covid-19 that were directly or indirectly linked to the wuhan huanan seafood wholesale market, as reported by huang and colleagues. 8 the clinical features include fever, dry cough, dyspnea, myalgia, fatigue, decreased leukocyte counts and computed tomography (ct) evidence of pneumonia. 8 subsequently, chen and colleagues reported 99 cases from a single centre of wuhan, but the severe and non-severe cases were not compared. 9 and then wang and colleagues published a study based on 138 hospitalized patients from wuhan. 10 however, all these studies are based on cases identified in wuhan. recently, guan and colleagues reported 1099 cases with laboratory-confirmed sars-cov-2 from 552 hospitals across 31 provinces/provincial municipalities. 11 they reported that the median age was 47.0 years, 41.90% were females, 31.30% had been to wuhan and 71.80% had contacted people from wuhan, and the average incubation period was 3.0 days. the most common symptoms were fever and cough. 11 together, several articles about cases from wuhan have reported epidemiologic and clinical manifestations and provided important initial background upon which we seek to furnish further in this paper. [8] [9] [10] 12 the clinical features of covid-19 of cases outside wuhan is still largely unknown. zhejiang province has consistently been one of the top three provinces with most cases in china and therefore provide a good basis to learn how covid-19 spreads outside wuhan. the cluster events, public transport transmissions, and clinical diagnosis of this new infectious disease are of great importance to be reported as it shred lights on of cases that occur outside wuhan. here, we report the epidemiologic and clinical characteristics of covid-19 patients from five hospitals in zhejiang province, china. we performed a retrospective, multicentre study on the epidemiologic history, clinical records, laboratory results, and chest radiological features of 88 laboratory-confirmed and 3 clinical-diagnosed patients with covid-19 that were diagnosed from 20 january 2020 to 11 february 2020. final follow-up for this report lasted until 16 february 2020. the primary method of diagnosis is to perform real-time reversetranscriptase polymerase-chain-reaction (rt-pcr) assay test using throat swab specimens that were collected from upper respiratory tracts. this test is done twice at 24-hour interval. of the 91 cases reported in here, 88 cases were tested positive for sars-cov-2 at least once. these laboratory confirmation assays for sars-cov-2 were performed at cdcs of various cities and at ningbo first hospital following the standard protocol. 8 three further cases were reported in ningbo cohort as clinical-diagnosed covid-19 pneumonia because of their epidemiological history, signs, symptoms and chest ct evidence according to national health commission of the people's republic of china guidance, though they tested negative for the sars-cov-2. 13,14 the incubation period was defined as the time from the exposure to the confirmed or suspected transmission source to the onset of illness. a team of doctors who had been treating these patients extracted the medical records of these patients and sent the data to working group in ningbo to further examine. when the data were not clear or missing, the working group in ningbo would clarify the details with the doctors in charge of treating these patients. the study has been reviewed and approved by the medical ethical committees (2020-r018). the requirement for written informed consent was waived because of the urgent need to collect clinical data and no harm could potentially be done to patients. doctors who treated the patients collected and recorded the epidemiological characteristics by interviewing each patient on their activity history during the two weeks before symptoms onset or admission into hospital. all patients underwent chest ct scans. the clinical symptoms, chest ct and laboratory findings on admission were extracted from electronic medical records. laboratory results included blood routine, blood chemistry, arterial blood gas, fibrinogen, liver and renal function, electrolytes, c-reactive protein, and procalcitonin. patients were divided into the diagnosed as severe group and mild group according to national treatment guideline. 13,14 questionnaires of mulbsta scores 15 were recorded by attending physicians according to six indexes, which are multilobular infiltration, lymphopenia, bacterial co-infection, smoking history, hypertension, and age. all data were checked by two experienced physicians (gq and ny). we present the summary statistics of continuous variables using the means and standard deviations (sd) or median (iqr), comparison across groups were performed using the mann-whitney u test. categorical variables were expressed as the counts and percentages in each category. chi-square tests was used for categorical variables as appropriate. all analyses were analyzed by ibm spss statistics version 26.0. this was a retrospective case series study, no patients and public were involved in the design, or conduct, or reporting, or dissemination plans of our research. of all 91 patients recruited as of 11 february, we detected 88 (96.70%) laboratory-confirmed covid-19 pneumonia with throat swab samples that positive for sars-cov-2 and 3(3.30%) clinical-confirmed covid-19 pneumonia since they had definite demographic history, typical symptoms and chest ct images. as shown in table 1 , the median age of the 91 patients was 50 years (iqr, 36.5 to 57.0), ranged from 5 to 96 years. there was 1 child (5 years . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . old), 1 student who were 17-years of age, and six cases of elderly patients aged 70 or above. adults account for most of the cases, with breakdown as follows: aged 18-39 (26 cases, 28.57%), aged 40-49 (16 cases, 17.58%), aged 50-59 (28 cases, 30.77%) and aged 60-69 (13 cases, 14.29%). there were 54 female patients (59.34%), with none of them pregnant. as for epidemiologic characteristics, 31 patients had been to wuhan/hubei within the past two weeks (g0). local cases are defined as follows: 8 patients had within the past two weeks had contact with personnel who had been in wuhan/hubei, these are the first generation of local cases (g1). following that 40 patients contracted the disease after having had contact with the local cases, these are defined as g2 local cases. in particular 23 of the g2 cases were all derived from an event where people collectively prayed for good luck in a temple for the new lunar year. there were 11 patients who were infected while air travelling. it is impossible to establish how the remaining 1 patient contracted the disease. none of the patients had a history of exposure to the huanan seafood wholesale market. no healthcare workers were found in our study. moreover, none of the health workforce in on admission, the most common symptoms were fever (65, 71.43%), cough (55, 60.44%) and fatigue (40, 43.96%) ( table 2 ). among them, 34 (37.36%) cases have temperature between 38.1-39℃, but none had a very high fever (body temperature > 41℃). other symptoms included expectoration (30, 32.97%), anorexia (23, 25.27%), diarrhea (21, 23.08%), neausea (11, 12 .09%) and vomiting (6, 6.59%). in a case, her abdominal discomfort was the only symptom. nine patients were diagnosed as severe pneumonia because of the development of pneumonia. as of 16 february, 60 (65.93%) patients were still isolated in our hospitals, and 31 (34.07%) patients had been discharged and no patients had died so far. the median of incubation period is 6 (iqr, 3-8) days, and number of days from first visit to a doctor till the case is confirmed is 1 (1-2). . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint according to data of laboratory tests, half of patients (49, 53.85%) demonstrated elevated levels of c-reactive protein (crp), but elevated levels of procalcitonin were detected in only a minority (14, 15.39%). data from blood routine showed that 14 (15.39%) patients had below the normal range of leucocyte, and 3 (3.97%) cases with elevated levels ( table 3) the serum level of albumin was suppressed in 43 (47.25%) patients. alt (7, 7.69%) and ast (9, 9.89%) were slightly elevated in minority of cases. suppressed calcium concentration and serum sodium concentration were less common. some patients had abnormality in arterial blood gas analysis, with decreased pao2 in 18 cases, increased levels of lactic acid in 25 cases, and increased ph in 14 cases. our study has stratified patients with covid-19 pneumonia based on the severity of symptoms on admission according to national guidelines. 13, 14 nine patients were diagnosed as severe pneumonia because of the development of pneumonia. compared with those mild patients, patients diagnosed as severe pneumonia had numerous differences in laboratory results (table 4) , including higher neutrophil, lower lymphocytes count, hyponatremia, hypocalcemia, as well as higher levels of crp. mulbsta score is used to predict mortality in viral pneumonia, amongst the 9 severe pneumonia patients their mulbsta scores were significantly higher, indicating they had higher mortality risks. this report, to our knowledge, is the largest case study to date of hospitalized patients with covid-19 in zhejiang province, which is outwith of wuhan and hubei. as of 16 february, 2020, of the 91 cases in the present study, 9 were diagnosed as severe pneumonia, 31 were discharged, 60 . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint the most common symptoms at the onset of coivd-19 were fever, cough, and fatigue. the median of incubation period was 6 (iqr, [3] [4] [5] [6] [7] [8] days and from first visit to a doctor to confirmed diagnosis was only 1 (1-2) days. our study provided further evidence that rapid human-to-human transmission of sars-cov-2 outside wuhan had occurred. none of the patient in this study had direct contact with wildlife or from huanan seafood wholesale market. while 8.79% had contact with people who had travelled from wuhan, more than 52.75% were local zhejiang residents with no travel history to wuhan and hubei. in particular, 23 cases of 38 cases of ningbo cohort were related to the outbreak of a temple cluster, including 11 patients had directly participated in a temple activity. our findings have provided strong evidence that large social events should be cancelled in order to prevent infection. notably, there is 54 (59.34%) female cases in our study compared to 27% of the first reported study 8 or 41.8% of a recently study 11 , and 44% of a recently study from zhejiang province. 16 however, it has been found that more males were infected by middle east respiratory syndrome (mers)-cov and sars-cov. 17, 18 whether it is related to endocrinology 9 , social activities, or religious activities still needs further research. fever (71.43%), cough (60.44%) and fatigue (43.96%) are the most comment clinical characteristics in our study and is similarly to the cohorts reported in the published literature. 8, 10, 16 furthermore, it is reported only 43.8% of covid-19 had fever onset and 87.9% reported having had fever during hospitalization. 11 fever is less widespread amongst those infected with covid-19 than those with sars-cov (99%) and mers-cov (98%). 19 as screening heavily on fever detection, patients that do not have fever might get suspected as being wrongly diagnosed. some covid-19 cases had atypical symptoms or were asymptomatic. furthermore, asymptomatic persons are potential sources of sars-cov-2 transmission. 20 it appears that transmission is possible during the incubation period, and the carrier cannot be spotted. 20 recently, a study reported that they detected sars-cov-2 in stool samples from patients with abdominal symptoms. 21 interestingly, we had detected sars-cov-2 in rectal swab of . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.02.23.20026856 doi: medrxiv preprint patients who were twice tested negative by throat swab specimens using rt-pcr. therefore, it is helpful to detect atypical symptoms covid-19 using both throat swab and rectal swab, particularly for patients who suffer symptoms with their digestive tract, like diarrhea. only 28 (30.77%) cases had lymphopenia in our study, while half the patients (49, 53.85%) demonstrated elevated levels of c-reactive protein, decreased platelet in 10 cases. most cases had normal serum levels of procalcitonin on admission (procalcitonin <0.04 ng/ml), except 14 cases had procalcitonin level higher than 0.04 ng/ml. all patients were scanned by chest ct scan. of the 91 patients, 61 (67.03%) had multilobe infiltration. the typical manifestation of lung ct were ground-glass opacification (ggo) of bilateral multiple lobular and subsegmental areas of consolidation (figures 1 and 2 ). our study provided three cases as clinical-confirmed covid-19 pneumonia because of their epidemiological history, signs, symptoms and chest ct evidence according to guidance, though they tested negative for the sars-cov-2. thus, ct could be used as an important differential method in cities where they are lacking nucleic acid kits, like wuhan, and help to bring forward the isolation period for the infected. currently, no anti-viral agents have been proven to be effective treatment for covid-19. it is reported that combination of lopinavir and ritonavir had been applied to sars-cov-2 patients with substantial clinical benefit. 22 as an emerging virus, all the patients received anti-viral agents in ningbo cohort, including kaletra (lopinavir/ritonavir) and umifenovir, 9 cases received methylprednisolone to treat high fever, spo2 ≤93% and hypoxiemia. the dose of methylprednisolone depends on disease severity between 1mg/kg to 2mg/kg. however, the outcome is still unclear. as of 16 february 2020, no death has been reported in zhejiang province as the government authority has taken unprecedented and effective effort to reduce the risk of transmission. early diagnosis, early isolation and early management all contributed to reducing transmission and mortality in zhejiang. however, 60 patients are still hospitalization and their cases should be followed up in the future. our study has some limitations. firstly, two thirds of patients are still hospitalized. for those who had been released their cases are being followed up for 2 weeks, and further information can be learnt from these individuals. secondly, we just have recruited 91 cases. increasing the number of cases is good for observing covid-19 outside of wuhan/hubei. thirdly, we did not . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.02.23.20026856 doi: medrxiv preprint have many severe cases to compare the differences of epidemiological and clinical features. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . . cc-by-nc-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.02.23.20026856 doi: medrxiv preprint a pneumonia outbreak associated with a new coronavirus of probable bat origin coronavirus infections -more than just the common cold genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding a novel coronavirus from patients with pneumonia in china coronavirus disease 2019 (covid-19) outbreak journey of a thai taxi driver and novel coronavirus chinese center for disease control and prevention. covid-19 pneumonia epidemic map clinical features of patients infected with 2019 novel coronavirus in wuhan, china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical characteristics of 2019 novel coronavirus infection in china ) 14. national health commission of the people's republic of china. the notice of launching guideline on diagnosis and treatment of the novel coronavirus pneumonia clinical features predicting mortality risk in patients with viral pneumonia: the mulbsta score clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series prevalence of comorbidities in the middle east respiratory syndrome coronavirus (mers-cov): a systematic review and meta-analysis sex-based differences in susceptibility to severe acute respiratory syndrome coronavirus infection middle east respiratory syndrome transmission of 2019-ncov infection from an asymptomatic contact in germany the digestive system is a potential route of 2019-ncov infection: a bioinformatics analysis based on single-cell transcriptomes role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings this work was supported by natural science foundation of zhejiang province (q17h010001), natural science foundation of ningbo (2017a610246), and shaoxing municipal science and technology plan project. this article has been accepted for publication in qjm: an international journal of medicine, published by oxford university press. key: cord-314273-xhnv5cje authors: lytras, theodore; panagiotakopoulos, georgios; tsiodras, sotirios title: estimating the ascertainment rate of sars-cov-2 infection in wuhan, china: implications for management of the global outbreak date: 2020-03-26 journal: nan doi: 10.1101/2020.03.24.20042218 sha: doc_id: 314273 cord_uid: xhnv5cje we sought to estimate the ascertainment ratio of sars-cov-2 infection in wuhan, china, using a modified bayesian seir model with publicly reported case data. we estimated it at 0.465% (95%ci: 0.464-0.466%), implying that the outbreak in wuhan was abated by depletion of susceptibles, rather than public health action alone. this suggests a high-transmissibility/low-severity profile for the current pandemic and raises doubt about whether suppression, rather than mitigation, is a feasible goal. the coronavirus disease 2019 (covid-19) outbreak originated at the end of 2019 in the city of wuhan, china, and is currently sweeping the globe, with more than 370,000 confirmed cases and 16,000 deaths. with the outbreak having already turned into the latest global pandemic, one of the key unknowns that will determine its public health impact is the infection fatality rate (ifr), i.e. the number of deaths as a proportion of all persons infected with the sars-cov-2 novel coronavirus, the causative pathogen of covid-19. the ifr is expected to be much lower than the case fatality rate (cfr), the proportion among confirmed cases, if many sars-cov-2 infections with mild or no symptoms are not being ascertained [1] . a low ascertainment rate has been previously suggested, based on epidemic modelling of exported cases: between 1.8% and 14% in wuhan [2] [3] [4] [5] , 28.4% in italy [6] and just 0.23% in iran [7] . after the lockdown that came into force on 23 january 2020, wuhan approximates a closed population in which the outbreak appears to have run its course, with cases on a steady decline since mid-february. we sought to estimate the ascertainment rate by applying epidemic modelling to publicly reported confirmed covid-19 cases in wuhan; a secondary objective was to estimate other epidemic parameters, including the basic reproduction number r0. we downloaded the most recent confirmed case data from wuhan using the r package 'ncov2019' [8] , for the period between 3 january and 9 march 2020. on 12 february there was a spike of 13,436 retroactively reported confirmed cases due to a change in the case definition; we addressed this by linearly interpolating the new confirmed cases for that date and distributing the remainder to all previous dates in proportion to the number of cases already reported. the median incubation period of covid-19 has been estimated at approximately 5-6 days, with a range between 1-14 days [9, 10] . according to the who-china joint mission report, the median time from symptom onset to laboratory confirmation in wuhan decreased from 15 days (range 10-21) in "early january" to 5 days (3) (4) (5) (6) (7) (8) (9) in "early february" [11] . to reflect the above, we modelled the time between case reporting and symptom onset with a weibull distribution with a shape/scale parameter of 8/15.7 on january 10, decreasing linearly to 4/5.5 on february 10 and after. we similarly modelled the time between case reporting and case exposure (infection with sars-cov-2) with a weibull distribution with shape/scale . cc-by 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 26, 2020. . 4.4/22.3 decreasing linearly to 2.6/12.1 (figure 1 ). these distributions were used to reconstruct estimated epidemic curves by infection date and by symptom onset, up until february 23, discarding the last two weeks available. to these data we subsequently fitted a discrete-time seir (susceptible-exposed-infected-removed) model, modified for underascertainment and fitted in a bayesian framework. the model assumes that cases are observed from only a fraction of the population (i.e. the ascertainment rate) that is stable over time. we further assumed that cases are isolated upon confirmation and are thus removed from the "infected" pool at that time. transition probabilities at time t between s-e, e-i and i-r are 1-exp(-β*it-1/n), 1-exp(-κ) and 1exp(-γ) respectively, where it-1 the total number of all infected at time t-1, n the population of wuhan (11 million people), β the contact rate, γ the removal rate and κ the incubation rate (the inverse of the incubation period). in this model, β/γ equals the basic reproduction number r0 and (1/κ + 1/2γ) equals the serial interval [12] . we used non-informative uniform(0,10) priors for β, γ and κ, and uniform(0,1) for the ascertainment rate. four sensitivity analyses were performed: (1) a model with a variable contact rate in three roughly equal periods, i.e. until the lockdown, until 10 february and until 23 february, (2) variable contact rate and an assumed 10% ascertainment rate, (3) assuming a 85% drop in contact rate after the lockdown, as recently suggested [13] , and (4) a simplified sir model (rather than seir). all analyses were done with r and jags, using 4 chains of 20000 iterations each and another 5000 as burn-in. model estimates are presented as posterior medians and 95% credible intervals (cri). the full analysis code is available on github: https://github.com/thlytras/ncovasc. a total of 49,948 confirmed covid-19 cases were reported in wuhan until 9 march, of whom 46,159 were reported until february 23. figure 2 illustrates the confirmed cases and the estimated epidemic curves by symptom onset and infection date. all model results for the main and sensitivity analyses are detailed on table 1 . the ascertainment rate was estimated at just 0.465% (95% cri 0.464-0.466%), meaning that for every confirmed case in wuhan there had been approximately 200 sars-cov-2 infections that were not detected. the r0 was estimated at 3.07 (95% cri 3.02-3.11), and the incubation period and serial interval at 4.4 and 8.8 days respectively; the latter remained identical in sensitivity analyses. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint assuming a variable contact rate over the study period, the r0 estimate would be as high as 5.33 until the wuhan lockdown, falling to 2.09 until 10 february then up again to 3.83, with an ascertainment rate of 0.48%. a nearly identical rate of 0.51% was obtained with a simplified sir model, and a slightly higher rate of 0.93% assuming an 85% drop in contact rate after the lockdown. on the other hand, if one assumes a fixed ascertainment rate of 10% and a variable contact rate, the r0 would need to be as low as 0.85 right after the lockdown, and yet lower to 0.45 after 10 february, in order to fit the data ( table 1 , sensitivity analysis 2). the projected course of the epidemic in wuhan, under the main analysis model, is shown in figure 3 . we estimate that half the population was already infected by 27 january, and by 23 february only 585,000 susceptibles remained (95% cri 555,000-617,000), meaning 94.7% of the population had been infected. assuming a 85% drop in contact rate after the lockdown (sensitivity analysis 3), the same percentage drops to 52.7% (95% cri 51.0-54.4%). it has been suggested that the covid-19 outbreak in wuhan was controlled via non-pharmaceutical measures and bold public health action that "changed the course of a rapidly escalating epidemic" [11]. our modelling suggests another plausible scenario: that the large majority of the population was infected, with consequent depletion of susceptibles, and only a very small percentage of infections were ascertained. otherwise, if ascertainment is assumed higher or not taken into account, very large reductions in transmissibility of sars-cov-2 are needed to account for the observed data, with about 80% of infections prevented immediately after the lockdown and 90% after february 10. it should be emphasized that in no way do our results diminish the value of non-pharmaceutical public health interventions in mitigating the outbreak, nor do they underestimate the immense efforts of the chinese people. their bold, large-scale action undoubtedly alleviated an already very difficult situation, and likely succeeded in "flattening the curve" of the pandemic to the maximum possible extent. accounting for case ascertainment is crucial for accurately assessing the true nature of the covid-19 pandemic. an ascertainment rate as low as 0.5% in wuhan suggests that the ifr of the sars-cov-2 virus is orders of magnitude lower than the cfr of covid-19 (although some underascertainment of covid-19 deaths should be taken into account as well). together with a r0 estimate of 3.07, it would make covid-19 . cc-by 4.0 international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 26, 2020. . https://doi.org/10.1101/2020.03.24.20042218 doi: medrxiv preprint the archetype of a high-transmissibility / low-severity pandemic, whose high impact is driven by the sheer number of infections rather than the virulence of the pathogen [14] . our result further implies a very large amount of transmission from asymptomatic or minimally symptomatic persons, raising doubts about the feasibility of suppressing, much less containing, the covid-19 pandemic [15] . currently the world health organization (who) still advocates for a "containment strategy", with laboratory testing for every suspected case, isolation of confirmed cases (including mild cases) in health facilities, and tracing all contacts [16] . laboratory testing is indeed a priority for surveillance purposes, and also for severely ill patients, healthcare workers and other selected groups [17] . given our findings, however, exhaustive testing and contact tracing are probably not optimal at this point in countries with ongoing epidemics, and risk detracting from the only eminently achievable end goal, which is mitigation: "flattening the curve" as much as possible, reducing stress on healthcare facilities and protecting the vulnerable. that is what is likely occurring in other lockeddown areas of china right now, with the virus on a slow and stealthy progression, rather than on a freeze. given the severity of the pandemic threat, no effort should be spared and no public health intervention discounted a priori. but at the same time, it is crucial to set realistic priorities and realistic expectations, as well as allocate resources optimally while advocating for more. our estimated ascertainment rate is on the lower end of previously published estimates for wuhan [4] . regardless of the precise rate though, the main conclusion about the feasibility of "containment/suppression" (or lack thereof) still holds, as also evidenced by the rapid worldwide spread of sars-cov-2. our result also highlights the urgent need for seroprevalence surveys in different populations, to formally elucidate the true prevalence of the infection and guide further management of this new global pandemic. striving for more timely data remains essential for optimal public health decisions. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted march 26, 2020. . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint communicating the risk of death from novel coronavirus disease (covid-19) novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions. medrxiv the rate of underascertainment of novel coronavirus (2019-ncov) infection: estimation using japanese passengers data on evacuation flights estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) estimation of covid-19 outbreak size in italy based on international case exportations. medrxiv estimation of covid-2019 burden and potential for international dissemination of infection from iran. medrxiv open-source analytics tools for studying the covid-19 coronavirus outbreak. medrxiv incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia report of the who-china joint mission on coronavirus disease epidemic modelling: an introduction. cambridge age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in china. medrxiv novel framework for assessing epidemiologic effects of influenza epidemics and pandemics substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) we gratefully acknowledge dr. vana sypsa for providing very useful comments on this manuscript none funding key: cord-306690-s5mxes4r authors: shangguan, ziheng; wang, mark yaolin; sun, wen title: what caused the outbreak of covid-19 in china: from the perspective of crisis management date: 2020-05-08 journal: int j environ res public health doi: 10.3390/ijerph17093279 sha: doc_id: 306690 cord_uid: s5mxes4r since the first known case of a covid-19 infected patient in wuhan, china on 8 december 2019, covid-19 has spread to more than 200 countries, causing a worldwide public health crisis. the existing literature fails to examine what caused this sudden outbreak from a crisis management perspective. this article attempts to fill this research gap through analysis of big data, officially released information and other social media sources to understand the root cause of the crisis as it relates to china’s current management system and public health policy. the article draws the following conclusions: firstly, strict government control over information was the main reason for the early silencing of media announcements, which directly caused most people to be unprepared and unaware of covid-19. secondly, a choice between addressing a virus with an unknown magnitude and nature, and mitigating known public panic during a politically and culturally sensitive time, lead to falsehood and concealment. thirdly, the weak autonomous management power of local public health management departments is not conducive for providing a timely response to the crisis. finally, the privatization of many state-owned hospitals led to the unavailability of public health medical resources to serve affected patients in the wuhan and hubei province. this article suggests that china should adopt a singaporean-style public health crisis information management system to ensure information disclosure and information symmetry and should use it to monitor public health crises in real time. in addition, the central government should adopt the territorial administration model of a public health crisis and increase investment in public health in china. since the first known case of a covid-19 infected patient in wuhan, hubei province, china on 8 december 2019 [1] , covid-19 has spread to more than 200 countries and infected over three million people worldwide (as of 28 april 2020), causing a worldwide public health crisis. however, the covid-19 pandemic has not only caused an unprecedented global health crisis, but has also triggered a worldwide economic downturn-"2020 is on track to witness the deepest global recession on a scale not seen since world war ii" [2] . one of the major reasons for the current global public health crisis is the failure in virus control during its early stages in wuhan and the remaining areas of hubei province. covid-19 can result in infectious diseases of the respiratory tract which is similar to sars [3] , but is spreading much faster and wider than sars. sars broke out in guangdong province, china on november 16 2002 , and spread to 24 of a total of 34 provinces, municipalities and autonomous regions in china in six months [4] , while covid-19 spread from a single city to the entire country (all 34 provinces, municipalities and autonomous regions) in just 54 days. from the typology of crises proposed by gundel [5] , it is easy to attribute the public health crisis caused by covid-19 to an unexpected crisis, which means the crisis is hard to predict but easy to influence. however, china failed to influence the rapid spread of covid-19 even though it had gained valuable experience in dealing with a public health crisis after sars and later established a disease control and prevention system led by the center for disease control & prevention (cdcp) [6] . this is a question worthy of reflection. the existing literature on covid-19 focuses on pathological characteristics of patients [7, 8] , gene sequencing of covid-19 [9, 10] , demographic features of the patients and fatality rate [11] [12] [13] . such research is largely based on clinical diagnosis, general epidemiological research, response tactics (isolation), social distancing and community containment. what is missing is the mismanagement factors contributing to the sheer speed of spatial expansion and dramatic increase in infected people. this article attempts to fill this research gap through analysis of big data, officially released information and other social media sources to understand the root cause of the crisis from the aspects of china's current management system and public health policy. to do so, this paper draws on structuralinstitutional perspectives to examine the coordination structure and mechanisms in the covid-19 crisis management system. crisis management involves multiple disciplines [14] including psychology, sociology, political science and management science [15] . the analytical methods of systemic approaches [16] and resilience engineering [17, 18] are usually adopted in crisis management. rasmussen adopted systemic approaches to build a crisis management system of socio-technical which is divided into three levels from top to bottom, namely: government, regulators and associations and company. they also explained the structure, goals, constraints, pressures and operating limits of the system [19] . based on resilience engineering, hollnagel et al. pointed out that a system that can resist a crisis requires four capabilities: (1) its ability to anticipate the occurrence of a perturbation; (2) its ability to monitor its operating condition to maintain control of its operations (during the perturbation); (3) its ability to respond when the disturbance is there; (4) its ability to learn from the occurrence of a perturbation [20] . thus, it can be seen that crisis management involves multiple subjects and they work together to prepare for, handle and recover from the crisis. in public health crisis management, five factors are usually considered [21] [22] [23] : (1) information disclosure or control; (2) assessment of dangers and threats; (3) establishment of crisis information communication channels and health education platforms; (4) the making of and implementation of strategic crisis response plans; (5) overall mobilization of critical resources. the first factor relates to crisis information disclosure and control, which is a choice for the authority to take. such a choice is viewed as having a direct impact on people's emotional reactions towards the crisis and thus is a foundation of crisis management. when an unknown crisis suddenly breaks out, people display negative psychological characteristics such as high anxiety, tension, depression, hostility, guilt and shame [24] . if these negative emotions are not well controlled, it will greatly hinder the effective implementation of crisis management [25] . rosenthal pointed out that the government usually has two choices in the management of people's emotions: controlling information and disclosing information. controlling information requires minimizing external participation, media attention, and public initiatives. when disclosing information, the government takes the opposite position and actively encourages the mobilization of various forces. information disclosure has obvious advantages, but the reality is that some governments take an information control approach to deal with a crisis [26] . perry's work shows that when a crisis cannot be quelled in the short term, controlling information normally causes even greater panic [27] . the second factor relates to scientific and effective assessment of the crisis which is performed for the later formulation of intervention policies [28, 29] . such crisis assessment should be based on accurate information because information deviation will directly lead to the expansion of the crisis [30] . therefore, in the early stages of the crisis, investigations should be carried out quickly to collect information and carefully verify the accuracy of all information. meanwhile, real-time monitoring of the crisis should be conducted to ensure the timeliness of information [31] . for a general epidemic, after collecting a large amount of data, experts and scholars will assess its infectivity, susceptible population and mortality [1] . some scholars also use mathematical models to estimate the number of people infected by the epidemic [32] . covid-19 has also been studied in mathematical modelling [33] . with the development of science and technology, the methods of crisis assessment have thus become diversified [21] . the third factor is establishment of crisis information communication channels and health education platforms, which is an important communication component in crisis management. their functions include the release of risk information, evacuation notices, risk prevention measures and available assistance by public institutions [34] . because different types of crises present different forms of threat, the emphasis on communication and education is different [35] . in a public health crisis, relevant agencies need to provide the public with information on the source of the disease, preventative measures, symptoms of the disease, treatment methods and routes of transmission in a timely manner [36] . through communication channels and health education platforms, the public can respond to the crisis autonomously, thereby helping the government control the crisis [37] . the fourth factor is the making and implementation of strategic crisis response plans, and this factor is crucial for the government [38] . theoretically, government departments can effectively curb the crisis by formulating corresponding policies based on scientific crisis assessment [39] , but for the government, the key of crisis control in crisis management is to gain time [40] . rosenthal et al. believe that the longer it takes for government decision-making to take place, the more political criticism and rumors may be induced [41] , and these factors often cause the collapse of the response policies [32] . therefore, government departments must intervene immediately when the crisis comes to light. delaying every second will negatively impact the government; however, it must take sufficient time to formulate efficient and reasonable policies. this presents a dilemma for the government. the fifth factor is overall mobilization of critical resources. during the bird flu and sars in china, resource allocation was far beyond the capacity of local resource management, causing shortages of medical substances and food supply [42] . timely and effective allocation and transportation of emergency resources can reduce losses caused by public crises [43] . as time, quantity and quality of the resources are the key limitation factors, emergency managers do have to find an optimal schedule for assigning resources to the affected areas [44] . a reasonable public health crisis response system should guarantee a certain reserve of medical space, medical materials and medical staff, which is also a prerequisite for resource mobilization [45] . based on the five factors of crisis management highlighted through a literature review, this paper intends to explain the problems in china's handling of the public health crisis caused by covid-19 and discusses the causes of such problems. all research data for this paper comes from several sources, including chinese government official reports and news, big data statistics, official statistical data and international journals and the media. (1) chinese government official reports and news chinese government official reports and news were mainly sourced from caijing (http://www. caixin.com/2020-01-20/101506242.html) and nanfang metropolis daily (https://m.mp.oeeee.com/h5/ pages/v20/ncovtimeline/?from = groupmessage&isappinstalled = 0), which are used to obtain the latest information and reports on covid-19. (2) big data statistics the big data statistics platform uses baidu (similar to google) can provide a media index (http://index.baidu.com/v2/index.html#/) of certain keywords reported by the media and emigration index (https://qianxi.baidu.com/). the media index reflects the number of keywords related to the news reported by the media and included in the baidu news channel. the keywords searched in this paper were "wuhan pneumonia" and "novel coronavirus," because the chinese media universally reported covid-19 using these words as the key title words. the emigration index reflects the scale of emigration and is the normalized value. in this paper, we searched the emigration index of wuhan and compared this index against the 25 days pre-chinese new year in 2020 and 2019: two periods of data comparison-1 january 2020 to 25 january 2020 (chinese new year was 25 january 2020) and 12 january 2019 to 5 february 2019-when there was no covid-19 (chinese new year for 2019 was 5 february 2019). our official statistical data was collected from relevant chinese departments, international journals and the media. china's official sources come from the official website of national cdcp (http://www.nhc.gov.cn/), the national health commission (hc, http://www.nhc.gov.cn/), and the national bureau of statistics (bs, http://www.stats.gov.cn/). our international journal references mainly cite publications by the lancet, which covers the largest volume of covid-19 papers. data from these departments and journal articles were used to obtain the number of people infected with covid-19, infection characteristics, control information and public health expenditure. tracing covid-19 development in china, we can see that 25 january 2020 is a dividing line. our study concentrates our research attention to the period from 8 december 2019 (the first known case) to 25 january 2020 when the central government commenced its tough lockdown policy. this was a stage of confusion and chaos. initially it was called wuhan pneumonia ("wuhan fei yan" in chinese pinyin). on the morning of 26 december 2019, mr. jixian zhang, the director of respiratory medicine of hubei provincial hospital of integrated chinese and western medicine (wuhan) found four abnormal cases of pneumonia and he reported this to wuhan cdcp the next day. on 28 and 29 december 2019, the outpatient department of that hospital admitted another three patients from the wuhan south china seafood market. the symptoms of these seven patients were similar. on 5 january 2020, the wuhan hc confirmed that there were 59 patients with an unexplained pneumonia diagnosed in wuhan. on 9 january 2020, chinese authorities officially confirmed the novel coronavirus as the pathogen of "wuhan pneumonia." since then, chinese media has described "wuhan pneumonia" as a new coronavirus (later named covid-19 by the world health organization). on 11 january 2020, the wuhan hc advised that there were 41 people infected with covid-19 and the number of infected people increased by 4, 17, and 59 on 16, 17 and 18 january, respectively. since 19 january 2020, new covid-19 infections occurred in other provinces, municipalities and autonomous regions in china. by then, a large-scale outbreak of covid-19 occurred in china. on 23 january 2020, the wuhan municipal government suspended city buses, subways, ferries, long-distance passenger transportation, airports and train stations in the city, prohibiting citizens from leaving wuhan. with the rapid spread of the virus in china, every level of government successively initiated first-level responses to major public health emergencies (the highest level of public health incident response) on 23-25 january 2020. on 25 january 2020, china officially entered the national epidemic control stage. thus, the problems in crisis management for china mainly occurred prior to 25 january 2020. this paper reports our key findings within the following five factors. research concludes that information control can temporarily prevent the spread of rumors in the crisis and eliminate the fear of the public [25] . however, the public experience greater fear if the crisis erupts in a large scale, so this is generally not advocated in crisis management [46] . the chinese case confirms that information control deprives people of their ability to prevent and resist crises. in fact, in the early stages of covid-19, the chinese government adopted information blockades and controls to prevent public panic, which resulted in most people being unprepared for covid-19. we searched baidu for the keywords "wuhan pneumonia" and there was no single media report on "wuhan pneumonia" prior to 31 december 2019 ( figure 1 ). there were very few reports during the period 1 january 2020 to 19 january 2020. our search of the media keyword "novel coronavirus" found no single report on the novel coronavirus prior to 8 january 2020. 20 and 21 january 2020 witnessed a large search for "wuhan pneumonia," which was replaced by "novel coronavirus" after 23 january 2020. in summary, the chinese government imposed a strict media blockade on the report of covid-19 before 31 december 2019 and controlled it from 1 january 2020 to 19 january 2020. it was not until 20 january 2020 that the chinese media began to cover it extensively. research concludes that information control can temporarily prevent the spread of rumors in the crisis and eliminate the fear of the public [25] . however, the public experience greater fear if the crisis erupts in a large scale, so this is generally not advocated in crisis management [46] . the chinese case confirms that information control deprives people of their ability to prevent and resist crises. in fact, in the early stages of covid-19, the chinese government adopted information blockades and controls to prevent public panic, which resulted in most people being unprepared for covid-19. we searched baidu for the keywords "wuhan pneumonia" and there was no single media report on "wuhan pneumonia" prior to 31 december 2019 ( figure 1 ). there were very few reports during the period 1 january 2020 to 19 january 2020. our search of the media keyword "novel coronavirus" found no single report on the novel coronavirus prior to 8 january 2020. 20 and 21 january 2020 witnessed a large search for "wuhan pneumonia," which was replaced by "novel coronavirus" after 23 january 2020. in summary, the chinese government imposed a strict media blockade on the report of covid-19 before 31 december 2019 and controlled it from 1 january 2020 to 19 january 2020. it was not until 20 january 2020 that the chinese media began to cover it extensively. due to the media blockade and control of information about covid-19, the baibuting community in wuhan held a banquet with more than 40,000 families on 18 january 2020, which was approved to be the single most serious infectious event in wuhan. knowing nothing about covid-19, people in wuhan still visited population-intensive places such as shopping malls, supermarkets and entertainment places in large numbers until 20 january 2020. this accelerated the rapid spread of covid-19. a few medical workers did try to warn of the outbreak, but all were silenced, including the famous "coronavirus whistleblower" dr li wenliang, who tried to warn his medical university classmates in his wechat circle of the outbreak, but was accused of spreading fake information by local police [47] , although afterwards, the chinese government acknowledged dr li 's contribution and recognised him as a martyr. in summary, the control of information and media silence directly resulted in most people being unprepared during the covid-19 outbreak. in a public health crisis, timely and effective access to information is critical. however, the hc in each province, municipality and autonomous region had concealed the epidemic in the early due to the media blockade and control of information about covid-19, the baibuting community in wuhan held a banquet with more than 40,000 families on 18 january 2020, which was approved to be the single most serious infectious event in wuhan. knowing nothing about covid-19, people in wuhan still visited population-intensive places such as shopping malls, supermarkets and entertainment places in large numbers until 20 january 2020. this accelerated the rapid spread of covid-19. a few medical workers did try to warn of the outbreak, but all were silenced, including the famous "coronavirus whistleblower" dr li wenliang, who tried to warn his medical university classmates in his wechat circle of the outbreak, but was accused of spreading fake information by local police [47] , although afterwards, the chinese government acknowledged dr li 's contribution and recognised him as a martyr. in summary, the control of information and media silence directly resulted in most people being unprepared during the covid-19 outbreak. in a public health crisis, timely and effective access to information is critical. however, the hc in each province, municipality and autonomous region had concealed the epidemic in the early stages of covid-19, which caused the national hc to make an incorrect assessment of the reality of the situation. figure 2 shows that the period from 20 january to 25 january 2020 registered the fastest spread of covid-19, whilst the official record shows no increase in the number of infected cases in hubei province from 11 january to 15 january 2020 with no emergency response measures applied, indicating that hubei hc had concealed the epidemic. some scholars have questioned the under-reporting of infected people by china [48] . by constructing a mathematical model, imai stages of covid-19, which caused the national hc to make an incorrect assessment of the reality of the situation. figure 2 shows that the period from 20 january to 25 january 2020 registered the fastest spread of covid-19, whilst the official record shows no increase in the number of infected cases in hubei province from 11 january to 15 january 2020 with no emergency response measures applied, indicating that hubei hc had concealed the epidemic. some scholars have questioned the under-reporting of infected people by china [48] . by constructing a mathematical model, imai et al. concluded that as of 12 january 2020, there should have been 1723 covid-19-infected patients (not the officially reported 41 patients in wuhan) [49] . wu et al. calculated that as of 25 january 2020, there had been 75,815 covid-19 infected patients in wuhan using the data of patients given by national hc from 31 december 2019 to 28 january 2019 [50] . under-reporting of chinese covid-19 cases can be contrasted to the experience of china's neighboring countries. as revealed in section 3.1, before 19 january 2020, covid-19 did not spread on a large scale in china, but only spread within the hubei province. this was impossible as there was one case of a covid-19 patient in thailand reported on 13 january 2020 and another case in japan on 16 january 2020. wuhan's connection to these two countries is far less frequent than other chinese provinces. how could there be no spread within china when it had spread to thailand and japan? in addition, according to spatiotemporal distribution of people infected with covid-19 as shown in figure 2 , guangzhou, shanghai and beijing, which are further away from hubei province, had covid-19 cases earlier than other provinces and municipalities around hubei province. however, according to a baidu search of wuhan's population emigration index, before 25 january about 400,000 people left wuhan moving to guangdong province, 120,000 to shanghai, 120,000 to beijing, and 680,000 to the provinces and municipalities around hubei province. this showed that the population who moved to the neighboring provinces and municipalities is almost equal to that of guangzhou, shanghai and beijing, so it is impossible for the provinces and municipalities around hubei to have had no infectious cases to report. this suggests that the hc of each province, municipality and autonomous region outside hubei province had initially concealed the epidemic. in a public health crisis caused by infectious diseases, public health agencies should establish communication channels and health education platforms in a timely manner and communicate the source, symptoms, transmission mode of the disease and isolation measures to the public [34] . however, the national cdcp did not fare well in the early debate about whether covid-19 can be transmitted from person to person. the explanation from the national cdcp about whether covid-19 can be transmitted from person to person is shown in table 1 below. official explanations no obvious human-to-human transmission found; no medical staff found to be infected 5/01/2020 no clear sign of human-to-human transmission found; no medical staff found to be infected 10/01/2020 no medical staff found to be infected 11/01/2020 no clear evidence of human-to-human transmission found 14/01/2020 limited human-to-human transmission is not excluded 16/01/2020 no clear evidence of human-to-human transmission found, the possibility of human-to-human transmission cannot be ruled out, but the risk of sustained human-to-human transmission is low 19/01/2020 the transmission route is not yet fully understood 20/01/2020 covid-19 can transmit from person to person source: chinese authoritative media. table 1 shows that the national cdcp did not explicitly point out that covid-19 could be transmitted from person to person before 19 january 2020. it was not until 20 january 2020 that nanshan zhong, an academic of the chinese academy of engineering, confirmed that covid-19 could be passed from person to person. the official media did not report this before 20 january 2020 despite cases of medical staff being infected by person-to-person transmission. interesting enough, authors including staff working in china's national cdcp and wuhan's cdcp published a paper in an english academic journal-the new england journal of medicine-with a conclusion that interpersonal transmissions had occurred among close contacts since the middle of december 2019 [7] . another english paper published in the lancet, whose leading author chen wang is an academic of the chinese academy of sciences, also mentioned 16 cases of medical workers infected with covid-19 in december 2019 [8] . another english paper published in the lancet by chen described in detail a case of family cluster transmission and demonstrated that covid-19 can be transmitted from person to person. the patients mentioned in the article were admitted to the hospital on 10 and 11 january 2020 [51] . the fact that seven medical staff were infected between 1 january 2020 to 11 january 2020, with eight more infected between 12-22 january 2020 was released to the public by various chinese media sources after the central government officially accepted interpersonal transmission [52] . generally speaking, the government plays an important role in crisis management, and it can respond to the crisis efficiently by formulating a unified response policy [46] . if the government fails to formulate a response in time, it will cause the public to panic and lose confidence in the government [40] . in the process of the crisis management of covid-19, the wuhan municipal government could have taken preventative measures at a much earlier time. based on various media reports, table 2 summarizes the key time points of other countries in taking preventative measures compared to the wuhan government who did not take measures at such times. as early as 1 january 2020, hospital doctors in wuhan found an unknown type of pneumonia based on medical testing reports (later it was confirmed that the nucleotide had the homology of covid-19, which is 82% similar to the sars virus [53] ). however, instead of strengthening the protective measures against covid-19, the wuhan local government accused the doctors of spreading rumors. at the same time, singapore and hong kong had already introduced quarantine measures on 3 and 4 january 2020, respectively. after 13 january 2020, covid-19 infected patients appeared in countries other than china, indicating that covid-19 had spread widely. however, the wuhan government did not introduce the lockdown policy until 23 january 2020. another fundamental mistake that the wuhan government made was that it allowed five million people to leave wuhan before china quarantined the city [54] . although many left due to the chinese new year, others also left to avoid quarantine. this is supported by our data comparison. using the chinese lunar calendar time table to compare to wuhan's emigration index (the emigration index here is the normalized value) from 1-23 january 2020 and the emigration index from january 2019 to 5 february 2019, we found that the emigration index in 2020 and 2019 is basically the same before lunar 22 december 2019 and shows the opposite trend from lunar 23 december 2019 to the chinese new year (see figure 3) . normally, the closer to chinese new year, the fewer people move out of wuhan, but the trend shows that the opposite occurred in 2020, indicating that many wuhan residents had been aware of the crisis and started to take the initiative to leave. the final part of this paper investigates the availability of public health crisis resources. public health crisis causes a surge in demand, especially for medical resources in the short term, so the government needs to coordinate the mobilization of resources [44] . starting from lockdown, under the leadership of the central government the chinese governments at all levels mobilized support to wuhan including transporting a large number of medical supplies and sending nearly 29,445 medical staff (excluding military medical staff) to wuhan. this also included building a "huosheng" mountain hospital (with 1000 beds) and a "leisheng" mountain hospital (with 1600 beds) in wuhan within 10 to 11 days. however, all these achievements do not overshadow the problem of a serious shortage of infectious disease medical facilities and materials in china. china is not ready to cope with a large-scale infectious disease. for a long time, china has had insufficient reserves of medical resources for infectious diseases. take wuhan as an example: the epidemic started and 14 million people (8.5 million local residents and over 5 million migrant workers or students whose hometowns are in other parts of china) were able to access only two hospitals which treat infectious diseases. the total number of beds in these hospitals is around 900 which equates to 0.64 beds per 10,000 people. this is far lower than the standard for the number of beds in infectious disease hospitals in china of 1.2 to 1.5 beds per 10,000 people [52] . on 23 january 2020, wuhan had no hospital beds available for infected people and those who suspected they were infected, so the "huosheng" mountain hospital was built, followed by the "leisheng" mountain hospital on 25 january 2020. because of the shortage of beds, doctors could only advise that patients who suspected they had covid-19 and those with mild symptoms be isolated at home. this led to a sharp increase in the number of family cluster transmissions [55] . in addition, the shortage of masks, goggles and protective clothing also caused a large number of medical staff to be infected in the early stages. according to the "analysis of epidemiological features of new coronavirus pneumonia" issued by the national cdcp, it is known that by 17 february 2020, a total of 3019 medical staff were infected with covid-19. this section will first identify what the problems in china's public health crisis management are, and then explain the key causes. the final part of this paper investigates the availability of public health crisis resources. public health crisis causes a surge in demand, especially for medical resources in the short term, so the government needs to coordinate the mobilization of resources [44] . starting from lockdown, under the leadership of the central government the chinese governments at all levels mobilized support to wuhan including transporting a large number of medical supplies and sending nearly 29,445 medical staff (excluding military medical staff) to wuhan. this also included building a "huosheng" mountain hospital (with 1000 beds) and a "leisheng" mountain hospital (with 1600 beds) in wuhan within 10 to 11 days. however, all these achievements do not overshadow the problem of a serious shortage of infectious disease medical facilities and materials in china. china is not ready to cope with a large-scale infectious disease. for a long time, china has had insufficient reserves of medical resources for infectious diseases. take wuhan as an example: the epidemic started and 14 million people (8.5 million local residents and over 5 million migrant workers or students whose hometowns are in other parts of china) were able to access only two hospitals which treat infectious diseases. the total number of beds in these hospitals is around 900 which equates to 0.64 beds per 10,000 people. this is far lower than the standard for the number of beds in infectious disease hospitals in china of 1.2 to 1.5 beds per 10,000 people [52] . on 23 january 2020, wuhan had no hospital beds available for infected people and those who suspected they were infected, so the "huosheng" mountain hospital was built, followed by the "leisheng" mountain hospital on 25 january 2020. because of the shortage of beds, doctors could only advise that patients who suspected they had covid-19 and those with mild symptoms be isolated at home. this led to a sharp increase in the number of family cluster transmissions [55] . in addition, the shortage of masks, goggles and protective clothing also caused a large number of medical staff to be infected in the early stages. according to the "analysis of epidemiological features of new coronavirus pneumonia" issued by the national cdcp, it is known that by 17 february 2020, a total of 3019 medical staff were infected with covid-19. this section will first identify what the problems in china's public health crisis management are, and then explain the key causes. (1) the media lost its supervisory function chinese media are directly managed by the chinese government, which leads them to serve the government. after the government monopolizes and controls the information resources, it can be selective in reporting and releasing information. this results in information submission errors [56] , which directly promotes the public's failure to obtain real and effective information in a timely manner. in this case, the chinese media did not help the government observe and warn of the public crisis, nor did it monitor the government's deficiencies in handling public crises. (2) a choice between addressing a virus with an unknown magnitude and nature, and mitigating known public panic during a politically and culturally sensitive time stage 1 was both politically and culturally sensitive given that nobody wanted to create any unnecessary public panic during the period leading up to chinese new year with a virus that was still relatively unknown in terms of magnitude and nature. wuhan and the rest of the local governments were getting ready in early january for the most important local yearly political meetings-the so-called "two sessions" (the national people's congress and the chinese people's political consultative conference (cppcc)). during the "two sessions," the top priority is to maintain stability and keep this period free from problems. this is also why when experts from beijing arrived to investigate the atypical pneumonia outbreak, wuhan officials tried to avoid two things: upsetting beijing and causing a public panic in advance of these two important meetings. therefore, they took a multipronged approach to control information about the outbreak [57] local officials concealed the facts due to the nature of the political climate and timing of when this was happening. china's public health management system does not allow local departments to declare infectious disease crises even in their own jurisdiction. it is the state council which possesses the power to declare a crisis involving a statutory infectious disease and to draft and implement contingency plans. meanwhile, local departments are asked to take appropriate measures to prevent diseases according to the epidemic prevention level set by the state council for infectious diseases. thus, in wuhan's case, wuhan hc and wuhan cdcp had no power to declare an infectious disease crisis or take any initial measures before authorization. more and more scholars believe that power concentration is not conducive to timely response to crises and multi-centralization of crisis management has become a trend [26] . it is important for the local departments to successfully combat any infectious disease because it obtains the information fast and should have the discretion to manage it to prevent a large-scale outbreak [40] . (4) privatization of public hospitals leads to insufficient public health medical resources a significant healthcare trend in china is the increasing privatization of medical hospitals and clinics based on a belief that private hospitals are more efficient [58] . up to 2020, the number of private hospitals in china account for over 66% of all chinese hospitals [59] . the privatization of public hospitals has attracted a large amount of social capital, effectively reducing government expenditure on health. as can be seen from figure 4 , the share of government investment decreased from 30.66% in 2011 to 27.74% in 2018, and the share of social investment increased from 34.57% in 2011 to 43.66% in 2018. however, the privatization of public hospitals has resulted in insufficient public health and medical resources. on the one hand, due to the low frequency of public health disease outbreaks, private hospitals have invested less in public health care based on market demand. on the other hand, due to the decrease in government investment in public health, a large number of technical personnel in public health have been drained, resulting in a serious shortage of public health staff [52] . based on rasmussen's socio-technical management system [19] , we can frame china's public health management systems into a three tiered hierarchical system. the chinese government is at the top level and they are both the makers and implementers of the law. the regulators and associations, such as hc and cdcp, respectively, are at the second level. they develop crisis management norms based on the law and oversee the implementation. at the very bottom level are the public who selectively cooperate with the above two levels of management based on personal interests. during the covid-19 crisis, the chinese public was generally considered to be cooperative with the government and relevant health management departments [60] , the public has little disturbance to the public health management system. using this framework, we have summarized the information flow path of china's public health management system in figure 5 . this figure shows the many checkpoints required for an infectious disease case to reach the public. we can use this to explain what caused the delay and ignorance of releasing early covid-19 information. after receiving confirmed cases from wuhan's hospital or clinic, the covid-19 infectious disease information followed two separate paths. wuhan municipal cdcp reported its first covid-19 case to wuhan municipal hc on december 8, 2019, but it could not report the same information to hubei provincial cdcp until after wuhan hc had submitted covid-19 information to hubei provincial hc. a similar prerequisite applied to hubei provincial cdcp which reported to national cdcp after hubei provincial hc reported to national hc. the most critical requirement for smooth information transmission was that any local hc could not pass covid-19 information to another upper level hc without permission from its local government. therefore, wuhan hc could report to hubei provincial hc only if wuhan municipal government approved it to do so. similar approval was required from the hubei provincial government as hubei provincial hc reported to national hc on 31 december 2019. the final stage is that state council released the covid-19 infectious disease information to the public after it received the confirmed information from the national hc on 11 january 2020. we can see that it took a total of 34 days from the first confirmed covid-19 patient reported by the wuhan municipal cdcp to the congress to the release of covid-19 information to the public. we can also see, as the most professional of all the disease management associations, wuhan municipal cdcp basically did not have any real authority to transmit disease information. it could neither issue an early warning of infectious diseases to the public nor take any emergency measures. the only authority able to release the early warning is the state council. the lack of independent management power by the local cdcps directly led to a serious lag in the release of disease information and the implementation of emergency measures. based on rasmussen's socio-technical management system [19] , we can frame china's public health management systems into a three tiered hierarchical system. the chinese government is at the top level and they are both the makers and implementers of the law. the regulators and associations, such as hc and cdcp, respectively, are at the second level. they develop crisis management norms based on the law and oversee the implementation. at the very bottom level are the public who selectively cooperate with the above two levels of management based on personal interests. during the covid-19 crisis, the chinese public was generally considered to be cooperative with the government and relevant health management departments [60] , the public has little disturbance to the public health management system. using this framework, we have summarized the information flow path of china's public health management system in figure 5 . this figure shows the many checkpoints required for an infectious disease case to reach the public. we can use this to explain what caused the delay and ignorance of releasing early covid-19 information. after receiving confirmed cases from wuhan's hospital or clinic, the covid-19 infectious disease information followed two separate paths. wuhan municipal cdcp reported its first covid-19 case to wuhan municipal hc on december 8, 2019, but it could not report the same information to hubei provincial cdcp until after wuhan hc had submitted covid-19 information to hubei provincial hc. a similar prerequisite applied to hubei provincial cdcp which reported to national cdcp after hubei provincial hc reported to national hc. the most critical requirement for smooth information transmission was that any local hc could not pass covid-19 information to another upper level hc without permission from its local government. therefore, wuhan hc could report to hubei provincial hc only if wuhan municipal government approved it to do so. similar approval was required from the hubei provincial government as hubei provincial hc reported to national hc on 31 december 2019. the final stage is that state council released the covid-19 infectious disease information to the public after it received the confirmed information from the national hc on 11 january 2020. we can see that it took a total of 34 days from the first confirmed covid-19 patient reported by the wuhan municipal cdcp to the congress to the release of covid-19 information to the public. we can also see, as the most professional of all the disease management associations, wuhan municipal cdcp basically did not have any real authority to transmit disease information. it could neither issue an early warning of infectious diseases to the public nor take any emergency measures. the only authority able to release the early warning is the state council. the lack of independent management power by the local cdcps directly led to a serious lag in the release of disease information and the implementation of emergency measures. china's covid-19 crisis management can be roughly divided into two stages. since 25 january 2020, the chinese central government launched an unprecedented national campaign to contain the disease. now, china is winning the battle and the rest of the world is fighting. however, china has paid a huge price for its initial delays and slow response. strict government control over information was the main reason for the early media silencing, which directly caused most people to be unprepared for covid-19. in fact, the same problem occurred during the sars outbreak [52] . we can see that chinese local government officials seem to be habitually choosing to underreport bad news for fear of economic losses or criticism from upper level officials, which would impact their personal political achievements. the weak autonomous management power of local governments is not conducive to taking a timely response to the crisis. critical decisions about combating covid-19 must be made and implemented under considerable time pressure. local authorities need to take action quickly. finally, the lack of appropriate medical assistance given by private hospitals to help manage covid-19 should inform chinese and relevant authorities to rethink china's health system and reform and invest more in its public health network. ultimately, this paper covers two broad dimensions of covid-19 crisis management: technical/physical and political. our findings further confirm that crisis management involves multiple subjects and they have to work together to prepare for, handle and recover from crisis. the five commonly considered factors in public health crisis management are a useful framework to analyze the problems and major causes of the covid-19 crisis in china. this crisis management analysis framework could be used to examine why china's powerful national campaign has successfully contained covid-19 in stage two and more interestingly, how some of the lessons learned from stage one had been immediately overcome in stage two. each of the five factors has been addressed differently compared with stage one. for example, the central government's china's covid-19 crisis management can be roughly divided into two stages. since 25 january 2020, the chinese central government launched an unprecedented national campaign to contain the disease. now, china is winning the battle and the rest of the world is fighting. however, china has paid a huge price for its initial delays and slow response. strict government control over information was the main reason for the early media silencing, which directly caused most people to be unprepared for covid-19. in fact, the same problem occurred during the sars outbreak [52] . we can see that chinese local government officials seem to be habitually choosing to underreport bad news for fear of economic losses or criticism from upper level officials, which would impact their personal political achievements. the weak autonomous management power of local governments is not conducive to taking a timely response to the crisis. critical decisions about combating covid-19 must be made and implemented under considerable time pressure. local authorities need to take action quickly. finally, the lack of appropriate medical assistance given by private hospitals to help manage covid-19 should inform chinese and relevant authorities to rethink china's health system and reform and invest more in its public health network. ultimately, this paper covers two broad dimensions of covid-19 crisis management: technical/ physical and political. our findings further confirm that crisis management involves multiple subjects and they have to work together to prepare for, handle and recover from crisis. the five commonly considered factors in public health crisis management are a useful framework to analyze the problems and major causes of the covid-19 crisis in china. this crisis management analysis framework could be used to examine why china's powerful national campaign has successfully contained covid-19 in stage two and more interestingly, how some of the lessons learned from stage one had been immediately overcome in stage two. each of the five factors has been addressed differently compared with stage one. for example, the central government's top-down system was able to mobilize nearly all relevant organizations and services to support the lockdown of the whole nation (factor 5); the public has been well informed: the government and media have provided continuous and clear covid-19 information to the public (factor 1); professional infectious disease control experts assess the virus threat regularly (factor 2); covid-19 public health education platforms are free for people to access (factor 3); and the officials' top priority on their daily agenda at every level of government is to make the right decisions at the right time-officials carefully listen to health experts in managing the local response action plan (factor 4). more importantly, the world could learn more from china's response to the covid-19 outbreak. late intervention to covid-19 is not an issue unique to china. in fact, countries like the united states and many european countries have also experienced some lag in the process of handling the crisis despite observing the chinese demonstrating the serious consequences of delaying any response during stage one. assigning blame is unproductive to the conversation, rather, this paper seeks the answer how china can or should make structural and management adjustments to its process of intervention so as to help the management of the future crises. therefore, it is time to consider the following policy recommendations: first, in the current organizational management structure in china, the main reasons for media loss and politics overruling the truth are information control and information monopoly. singapore's public health management system provides an idea for china's future information management. singapore has established a case management system (cms) which collects information on hospitals, ministry of health, ministries of education and general practitioners via the internet. the system can identify suspected and confirmed patients through the information collected and provide early warning flags. it also closely monitors close contacts of suspected and confirmed patients and makes available real-time information on patients, suspected cases and potential cases. china should adopt a similar system to make the epidemic information public. secondly, introducing a local territorial management model should be explored. the local public health management departments do not have autonomy to take timely action. china should adopt a local territorial management model such that as soon as a crisis occurs, local public health management departments can immediately release information to the public and take prompt measures according to the epidemic situation. any initial delay will result in large damage down the track. finally, increasing government public health investment is key. at present, china's cdcp is severely short of public health technical personnel and hospitals are short of public health medical resources. therefore, the chinese government should increase public health investments in training professional technicians and increasing medical resource reserves. to increase training, further investment in relevant education is required. to boost medical resource reserves, a medical emergency supply network system could be constructed [61] . this system could cover all cities and be funded by local governments in major infectious disease hospitals and general hospitals. each 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behavior of the public during covid-19 epidemic and its countermeasures can china's covid-19 strategy work elsewhere? science this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord-310676-125o0o7x authors: liu, qibin; fang, xuemin; tokuno, shinichi; chung, ungil; chen, xianxiang; dai, xiyong; liu, xiaoyu; xu, feng; wang, bing; peng, peng title: prediction of the clinical outcome of covid-19 patients using t lymphocyte subsets with 340 cases from wuhan, china: a retrospective cohort study and a web visualization tool date: 2020-04-11 journal: nan doi: 10.1101/2020.04.06.20056127 sha: doc_id: 310676 cord_uid: 125o0o7x background wuhan, china was the epicenter of the 2019 coronavirus outbreak. as a designated hospital, wuhan pulmonary hospital has received over 700 covid-19 patients. with the covid-19 becoming a pandemic all over the world, we aim to share our epidemiological and clinical findings with the global community. methods in this retrospective cohort study, we studied 340 confirmed covid-19 patients from wuhan pulmonary hospital, including 310 discharged cases and 30 death cases. we analyzed their demographic, epidemiological, clinical and laboratory data and implemented our findings into an interactive, free access web application. findings baseline t lymphocyte subsets differed significantly between the discharged cases and the death cases in two-sample t-tests: total t cells (p < 2.2e-16), helper t cells (p < 2.2e-16), suppressor t cells (p = 1.8-14), and th/ts (helper/suppressor ratio, p = 0.0066). multivariate logistic regression model with death or discharge as the outcome resulted in the following significant predictors: age (or 1.05, p 0.04), underlying disease status (or 3.42, p 0.02), helper t cells on the log scale (or 0.22, p 0.00), and th/ts on the log scale (or 4.80, p 0.00). the mcfadden pseudo r-squared for the logistic regression model is 0.35, suggesting the model has a fair predictive power. interpretation while age and underlying diseases are known risk factors for poor prognosis, patients with a less damaged immune system at the time of hospitalization had higher chance of recovery. close monitoring of the t lymphocyte subsets might provide valuable information of the patients condition change during the treatment process. our web visualization application can be used as a supplementary tool for the evaluation. 2020 received treatment according to the fifth edition of the ministry of health guidelines [8] [9] : 1. bed rest and supportive treatment; 2. regular examination on blood routine, crp, biochemistry, coagulation function, myocardial enzymes, lung ct; 3. oxygen therapy, including nasal catheter oxygen, transposal high-flow oxygen therapy, ventilator; 4. antiviral therapy, including lopinavir/ritonavir tablets, arbidol hydrochloride tablets, etc. if the patient maintained a normal body temperature for at least three days, and tested negative with covid-19 (including throat swab, stool, and sputum) at least twice and 24+ hours apart, as well as showing significant improvement in lung ct, the patient would be considered recovered and discharged from the hospital. the discharged patients were transported by the chinese government using designated vehicles and they were further isolated for at least two weeks. 2 ml venous blood samples were obtained from each patient to measure t cell subsets, and all the analyses were completed within 4 hours of sampling. facscalibur flow cytometer (bd biosciences, san jose, ca) was used for flow cytometry acquisition and analysis. the absolute count of each lymphocyte subset was determined using cd3/cd4/cd8/cd45 bd multitest reagents according to the manufacturer's protocol (bd biosciences). from january 31 to march 8, 2020, a total of 721 patients who tested positive of covid-19 were admitted to wuhan pulmonary hospital. among these patients, 430 completed the treatment and were discharged, 62 died, and 229 still remain in hospitalization. excluding four patients whose direct cause of death was not covid-19 infection, and selecting patients who had at least one t cell subsets test available, we had a total of 340 patients in the study, including 310 discharged cases and 30 death cases. we reviewed laboratory test results and chest ct examinations of these 340 patients, and collected all the t lymphocyte subsets tests data. if multiple t lymphocyte subsets tests were performed, we chose the earliest one as the baseline. two researchers independently reviewed the collected data to ensure data accuracy. there have been a number of descriptive analyses about the epidemiological, clinical, laboratory, and radiological characteristics of the covid-19 patients 10-14 . little as yet known about how these characteristics can be used in guiding the practice of the healthcare providers 15 . as the world face the expanding covid-19 pandemic, with the number of infected cases increase exponentially every day, any quick and easy method of understanding the patient's condition can be valuable. with this in mind we seek to build a statistical model with only a few strong predictive characteristics. as several other research teams pointed out, the potential risk factors of older age, high sofa score, and d-dimer greater than 1 µg/l could help clinicians to identify patients with poor prognosis at an early stage 12 . older patients (>65 years) with comorbidities and ards are at increased risk of death 14 . additionally, during our experience of treating the patients, we have noticed that the t lymphocyte subsets are closely correlated to the patient's progress. we found that all the patients showed varying degrees of decline in t lymphocyte subsets at hospital admission. and the patient's condition improved or worsened with the rise or fall of the t lymphocyte subsets. we have also considered some other immune indicators and inflammatory indicators, as well as the blood routine and lung ct, but they all . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.06.20056127 doi: medrxiv preprint have certain limitations. immune indicators and inflammatory indicators such as thyrotropin and white blood cells were not as sensitive as the t lymphocyte subsets; the blood routine is not specific enough to differentiate the condition of the patients 11 , and although lung ct is an accurate way to assess the patient's condition, it cannot be repeated too often especially for those critical patients who needed oxygen and ventilator. in conclusion, we decided to focus our research on patient's age, underlying disease status, and the t lymphocyte subsets measures: helper t cells, suppressor t cells, and th/ts among the 310 discharged cases, 155 were male and 155 were female. the average age was 56·4 years (sd 14·0). 107 (34·5%) of them had underlying diseases (the most common underlying disease is hypertension, 23·9% for male and 20·0% for female). the average duration of the hospitalization was 11·1 days (sd 6·94), and it took 15·1 days (sd 10·3) on average for them to reach our hospital since their first symptoms (table 1) . elderly patients tended to take longer to recover and they also had a (table 3) . among the 30 death cases, 17 were male and 13 were female. the average age was 69·0 years (sd 7·87). 23 (76·7%) of them had underlying diseases (the most common underlying disease is also hypertension, 64·7% for male and 38·5% for female). the average duration of the hospitalization was 15·1 days (sd 8·78), and it took 11·7 days (sd 8·20) on average for them to reach our hospital since their first symptoms ( table 2 ). the death event occurred more quickly among elderly patients ( we also performed a multivariate logistic regression model using age, underlying disease status, and the baseline t lymphocyte subsets test as the predictors to predict the patient outcome (death or hospital discharge). the significant predictors are age (or 1·05, p 0·04), underlying disease status (or 3·42, p 0·02), helper t cells on the log scale (or 0·22, p 0·00), and th/ts on the log scale (or 4·80, p 0·00). the mcfadden pseudo r-squared 16 for the logistic regression model is 0·35, suggesting the . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.06.20056127 doi: medrxiv preprint model has a fair predictive power (the mcfadden pseudo r-squared measure ranges from 0 to below 1, total lymphocyte did not turn out to be significant predictors in our logistic regression model (table 5) . we believe by looking at some of the patient's basic characteristics such as age and underlying diseases, together with the t lymphocyte subsets measures, could be a quick way to shed light on the patient's prognosis, during the time of pressure and emergency. in order for our findings to be more applicable for public health workers fighting at the frontline, we have developed an interactive web data visualization tool to implement the algorithm and made it accessible for the world at the following web address: https://rpubs.com/mindyfang/covid19. we did not use other lab tests such as the regular blood test items in our analysis because they are less differentiative than the t cell subset measures; and 3. we hope our interactive web tool could be utilized for quick use, therefore keeping as few input items as needed seems to be a more practical choice. figure 6b shows the k-means clustering result using the wuhan pulmonary hospital data. after multi-dimensional data transformation, the algorithm separates the death group and the discharged group as shown in the graph. a proportion of the discharged cases had similar profiles with the death cases, which had made it difficult for the algorithm to differentiate them apart. however, by using this algorithm, it is possible to identify a large number of patients with relatively good prognosis. we have also uploaded a dummy date set with de-identified and randomly modified patient data , as well as all the source code used for the current analysis as well as the interactive web application to: https://github.com/mindy-fang/covid-19. all of our source code were written with the r programming language and the interactive web application was developed with the shiny package [19] [20] [21] (rstudio version 1.2.1335, r version 3.6.0). other fellow researchers can substitute the dummy data with their own data, or modify the source code to make their own applications. meanwhile we will keep updating our reference panel as we include more patients, so that the algorithm would gain more and more statistical power over time. to our best knowledge, the current research is the largest retrospective study of covid-19 patients . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint . https://doi.org/10.1101/2020.04.06.20056127 doi: medrxiv preprint with known clinical outcomes so far. significant reductions in t cells are very common in severe covid-19 patients. age-dependent deficits in t cell and b cell functions and overproduction of type 2 cytokines may cause inadequate viral replication control and longer pro-inflammatory responses, which may lead to poor prognoses 22 . lymphopenia is a prominent part of sars-cov infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes [23] [24] [25] . we know that 2019-ncov was once called severe acute respiratory syndrome coronavirus 2 (sars-cov-20) [26] [27] . the level and the speed of t cell recovery are important factors of assessing disease prognoses and guiding early intervention in critically ill patients. in this study we have identified that older age, underlying diseases, and low t cell counts may be risk factors for poor clinical outcomes in covid-10 positive patients. we have also implemented an interactive web tool to visualize a new patient's risk using these risk factors. when a new patient's data is entered through the web ui, it will be shown where he is as compared to the 310 patients included in this study. it should be noted that our intension is not for the web tool to be considered as a 100% gold standard for determining the final clinical outcome of the patients. the visualization result simply suggests whether the new patient is more likely to recover or to have adverse outcomes. another important significance of our tool is the monitoring of patient's progress in real time during the treatment. for example, the patient's longitudinal profile gradually shifting towards the red centroid (poor outcome) or the green centroid (good outcome) may provide insight on the patient's progress ( figure 5 ). however, the actual final prognosis of the patient depends on many other factors, including the starting time of the treatment, treatment compliance, degree of treatment, and so on. our algorithm has the following limitations: it may not predict accurately for younger patients, or patients with no symptoms, since our training data contains relatively old and severe patients; secondly, the model was built based on a sample size of 340, which is not a large number. but we will keep updating our web application as we collect more data. in addition, the reference panel used in our analysis were infected population in wuhan, china. although there was no clear evidence that the underlying mechanism of the t cell depletion under the covid-19 infection is similar or different across ethnicity groups, it is only natural to assume that the baseline values and the degree of t cell depletion would be slightly different. we found that the t-lymphocytes, b-lymphocytes, and nk cells did differ among people in different regions [28] [29] [30] . we encourage researchers around the world to download the source code and customize it with their own data, as they accumulate more experience and knowledge with patients from their own hospitals or regions. to end our writing with the most recent update (march 13, 2020), the epidemic in wuhan has gradually passed its peak. all the cabin hospitals were closed, and other hospitals in wuhan started to return to their normal track. medical volunteer teams have returned to their home cities. we give thanks to all the support that we have received during our most difficult time and hope the situation would improve quickly for other parts of the world. . cc-by-nd 4.0 international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.06.20056127 doi: medrxiv preprint clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected coronavirus disease 2019 novel coronavirus in the united states the novel coronavirus originating in wuhan, china: challenges for global health governance persistence and clearance of viral rna in 2019 novel coronavirus disease rehabilitation patients clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance national health commission of the people's republic of china. chinese management guideline for covid-19 (version 6.0) clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study pathological findings of covid-19 associated with acute respiratory distress syndrome the assessment of fit in the class of logistic regression models: a pathway out of the jungle of pseudo-r²s application of k-means algorithm for efficient customer segmentation: a strategy for targeted customer services points of significance: principal component analysis web application development with r using shiny 1st edn r: a language and environment for statistical computing. (r foundation for statistical computing rstudio inc. shiny: web application framework for r il-23 and psma-targeted duo-car t cells in prostate cancer eradication in a preclinical model effects of severe acute respiratory syndrome (sars) coronavirus infection on peripheral blood lymphocytes and their subsets cellular immune responses to severe acute respiratory syndrome coronavirus (sars-cov cd4+ t cells are important in control of sars-cov infection long-lived memory t lymphocyte responses against sars coronavirus nucleocapsid protein in sars-recovered patients longitudinal intra-and inter-individual variation in t-cell subsets of hiv-infected and uninfected men participating in the la multi-center aids cohort study.medicine (baltimore) isolation of a novel coronavirus from a man with pneumonia in saudi arabia normal values of t, b and nk lymphocyte subpopulations in peripheral blood of healthy cuban adults our research was supported by medical teams from shanxi, inner mongolia and other parts of china. the authors would like to thank prof li ming, prof zhu qi, prof yang chengqing, prof guo guangyun, prof du juan, prof du ronghui for their technical support and prof chen xianxiang for guidance in interpretation of the results. key: cord-305422-t8azymo7 authors: yi, ye; lagniton, philip n.p.; ye, sen; li, enqin; xu, ren-he title: covid-19: what has been learned and to be learned about the novel coronavirus disease date: 2020-03-15 journal: int j biol sci doi: 10.7150/ijbs.45134 sha: doc_id: 305422 cord_uid: t8azymo7 the outbreak of coronavirus disease 2019 (covid-19), caused by severe acute respiratory syndrome (sars) coronavirus 2 (sars-cov-2), has thus far killed over 3,000 people and infected over 80,000 in china and elsewhere in the world, resulting in catastrophe for humans. similar to its homologous virus, sars-cov, which caused sars in thousands of people in 2003, sars-cov-2 might also be transmitted from the bats and causes similar symptoms through a similar mechanism. however, covid-19 has lower severity and mortality than sars but is much more transmissive and affects more elderly individuals than youth and more men than women. in response to the rapidly increasing number of publications on the emerging disease, this article attempts to provide a timely and comprehensive review of the swiftly developing research subject. we will cover the basics about the epidemiology, etiology, virology, diagnosis, treatment, prognosis, and prevention of the disease. although many questions still require answers, we hope that this review helps in the understanding and eradication of the threatening disease. the spring festival on january 25, 2020 has become an unprecedented and unforgettable memory to all chinese who were urged to stay indoors for all the holiday and for many weeks after due to the outbreak of a novel viral disease. the virus is highly homologous to the coronavirus (cov) that caused an outbreak of severe acute respiratory syndrome (sars) in 2003; thus, it was named sars-cov-2 by the world health organization (who) on february 11, 2020, and the associated disease was named cov disease-19 (covid-19) [1] . the epidemic started in wuhan, china, and quickly spread throughout the entire country and to near 50 others all over the world. as of march 2, 2020, the virus has resulted in over 80,000 confirmed cases of covid-19, with more than 40,000 patients discharged and over 3,000 patients who died. who warns that covid-19 is "public enemy number 1" and potentially more powerful than terrorism [2] . according to pubmed (https://www.ncbi.nlm. nih.gov/pubmed/), in less than two months, over 200 papers have been published on covid-19 including its virology, epidemiology, etiology, diagnosis, and treatment since the first report on january 7, 2020 that determined the sequence of the virus isolated from multiple patients [3] . this review attempts to summarize the research progress in the new and swiftly developing subject area. whenever possible, we will try to compare covid-19 with sars and another cov-caused disease, middle east respiratory syndrome (mers, an outbreak in 2012). we will also discuss what we have learned so far regarding the prevention and prognosis of the disease as well as some remaining yet urgent questions. covs have been traditionally considered nonlethal pathogens to humans, mainly causing approximately 15% of common colds [4] . however, in this century, we have encountered highly pathogenic human covs twice, i.e., sars-cov and mers-cov, which caused an outbreak originally in china in 2003 ivyspring international publisher and saudi arabia in 2012, respectively, and soon spread to many other countries with horrible morbidity and mortality [5] . therefore, the current covid-19 is the third cov outbreak in the recorded history of humans. as shown in fig. 1 , clusters of pneumonia that had unknown origins were first reported from wuhan on december 31, 2019 to the china national health commission [6] . seven days later the sequence of the cov was released [7] . on january 15, 2020 the first fatal case from wuhan was reported [6] . meanwhile, the epidemic rapidly spread to the neighboring cities, provinces, and countries. on january 20, the infection of health-care providers was reported, suggesting that human-to-human transmission was possible [8] . on january 23, the city of wuhan was locked down with all its public transportation stopped. on january 24 the first clinical study on the disease reported that, out of 41 patients with confirmed cases, only 21 had direct contact with the wuhan seafood market that was considered the starting site of the infection from an unknown animal source [6] . on january 30, who declared the outbreak a global health emergency. by the time of this report, the disease has already spread throughout china and near 50 other countries all over the world (fig. 2) . as the situation is rapidly evolving, the final scope and severity of the outbreak remain to be determined. on february 11, 2020, a multi-center study on 8,866 patients including 4,021 confirmed covid-19 patients presented a more updated illustration of the epidemic as follows (https://mp.weixin.qq.com/s/ ulbi-hx_rhpxa1qha2bhda). • sars-cov-2 infected people of all ages, but mainly at the age of 30-65. almost half (47.7%) of the infected individuals were over 50 years old, very few were under 20, and only 14 infected individuals were under the age of 10. • sars-cov-2 infected more men (0.31/100,000) than women (0.27/100,000). • covid-19 expanded in clusters mainly in and around hubei. • covid-19 took an average of 5 (2-9) days from onset to diagnosis. the average incubation period was 4.8 (3.0-7.2) days. the average time from onset to death was 9.5 (4.8-13) days. • the basic reproductive number (r0) was 3.77 (95% ci: 3.51-4.05), and the adjusted r0 was 2.23-4.82. • the number of infected people increased exponentially before 23 jan. 2020, matching the time of massive transportation before the spring festival in china. • the mortality of patients with confirmed cases was 1.44% (95% ci: 1.10-1.86%), and the adjusted mortality of all the patients was 3.06% (95% ci: 2.02-4.59%). • three major risk factors for covid-19 were sex (male), age (≥60), and severe pneumonia. covs are a subfamily of large and enveloped viruses containing a single strand of sense rna. they can be divided into four genera, i.e., alpha, beta, gamma, and delta, of which alpha-and beta-covs are known to infect humans [11] . the envelope spike (s) glycoprotein binds to its cellular receptors angiotensin-converting enzyme 2 (ace2) and dipeptidyl peptidase 4 (dpp4) for sars-cov and mers-cov, respectively, and then membrane fusion occurs [12] . the viral rna genome is released into the cytoplasm; after replication of the viral genome, genomic rna accompanied by envelope glycoproteins and nucleocapsid proteins forms virion-containing vesicles, which then fuse with the plasma membrane to release the virus [13] . the first genomic sequence of sars-cov-2 was reported on january 10, 2020 [3]. sars-cov-2 was found to be a new type of beta-cov with more than 99.98% genetic identity among 10 sequenced samples collected from the original site of the outbreak, the huanan seafood market in wuhan. sars-cov-2 is genetically more similar to sars-cov than to mers-cov [14] [15] [16] . through transmission electron microscopy, sars-cov-2 particles were found in ultrathin sections of human airway epithelium [17] . human ace2 was found to be a receptor for sars-cov-2 as well as sars-cov [16, 18, 19] . however, the s protein of sars-cov-2 binds to human ace2 more weakly than that of sars-cov, which is coincident with the fact that sars-cov-2 causes less severe infection in patients than sars-cov [14] . sars-cov-2 can also form a novel short protein encoded by orf3b and a secreted protein encoded by orf8. the orf3b of sars-cov-2 may play a role in the viral pathogenicity and inhibit the expression of ifnβ; however, orf8 does not contain any known functional domain or motif [20] . on february 18, 2020, zhou, et al., reported the cryo-em structure of the full-length human ace2 at 2.9 å resolution in complex with the amino acid transporter b 0 at1 [21] . they found that the complex, which had open and closed conformations, was assembled as a dimer and the ace2-b 0 at1 complex can bind two s proteins, which provides evidence for cov recognition and infection. b 0 at1 may become a therapeutic target for drug screening to suppress sars-cov-2 infection. it has been known that both sars-cov and mers-cov originated from bats and were transmitted to humans via civet cats and camels, respectively. through a phylogenetic comparison of sars-cov-2 with other covs, bats were considered the native host of sars-cov-2 as the new virus is 96% identical to two sars-like covs from bats called bat-sl-covzx45 and bat-sl-covzx21 [14] [15] [16] 19] . however, what intermediate host helped the virus cross the species barrier to infect humans remains unknown, and the transmission route is yet to be elucidated. ji, et al., proposed snakes as a carrier of the virus from bats to humans which involved homologous recombination within the s protein [22] . according to a study, researchers in guangzhou, china, suggested that pangolins -long-snouted, anteating mammals often used in traditional chinese medicine -are the potential intermediate host of sars-cov-2 based on 99% genetic homology in a cov discovered in pangolins and sars-cov-2 [23] . however, 1% difference spread all over two genomes is still a big difference; thus, conclusive results for concrete evidence are awaited (fig. 3) . the physicochemical properties of sars-cov-2 are largely not yet known. sars-cov and mers-cov can survive in vitro for 48 hours in a dry environment and up to 5 days under 20 °c and 40%-50% humidity [24] [25] [26] . sars-cov-2 may possess similar properties. it has been reported that sars-cov-2 is sensitive to ultraviolet rays and heat at 56 °c for 30 minutes; ether, 75% ethanol, chlorine-containing disinfectant, peracetic acid, chloroform, and other fatty solvents, but not chlorhexidine, can effectively inactivate the virus [27] . the entire human population generally lacks immunity to sars-cov-2 and hence is susceptible to the novel virus. currently, no detailed study has been reported regarding the immunological response to sars-cov-2. thus, we can only refer to previous studies on other covs, especially sars-cov and mers-cov (fig. 4) . in general, after a virus invades the host, it is first recognized by the host innate immune system through pattern recognition receptors (prrs) including c-type lectin-like receptors, toll-like receptor (tlr), nod-like receptor (nlr), and rig-ilike receptor (rlr) [28] . through different pathways, the virus induces the expression of inflammatory factors, maturation of dendritic cells, and synthesis of type i interferons (ifns) which limit the spreading of the virus and accelerate macrophage phagocytosis of viral antigens [28] . however, the n protein of sars-cov can help the virus escape from the immune responses [29] . soon, the adaptive immune response joins the fight against the virus. t lymphocytes including cd4 + and cd8 + t cells play an important role in the defense. cd4 + t cells stimulate b cells to produce virus-specific antibodies, and cd8 + t cells directly kill virus-infected cells. t helper cells produce proinflammatory cytokines to help the defending cells. however, cov can inhibit t cell functions by inducing apoptosis of t cells. the humoral immunity including complements such as c3a and c5a and antibodies is also essential in combating the viral infection [30, 31] . for example, antibodies isolated from a recovered patient neutralized mers-cov [32] . on the other hand, an overreaction of the immune system generates a large number of free radicals locally that can cause severe damages to the lungs and other organs, and, in the worst scenario, multi-organ failure and even death [33] . the sars-cov-2 infection, featured by clustering onset, is more likely to affect elderly people with comorbidities and pregnant women [8] . it is common that for people who are exposed to a large number of viruses or whose immune functions are compromised, they have higher chance to be infected than others. the estimated mean incubation period of sars-cov-2 is 1-14 days, mostly 3-7 days based on a study of the first 425 cases in wuhan [36] . however, a study on 1,099 cases demonstrates that the incubation period was 3 days on average and ranged from 0 to 24 days [8] . a more recent study, as described above, demonstrates that the incubation period was 4.8 (3.0-7.2) days based on the demography of 8,866 cases [37] . it is very important for health authorities to adjust the effective quarantine time based on the most accurate incubation period, thus preventing infected but symptomless people from transmitting the virus to others [38] . as a common practice, individuals exposed to, or infected by, the virus are usually required to be quarantined for 14 days. should the quarantine time be extended to 24 days? fever is often the major and initial symptom of covid-19, which can be accompanied by no symptom or other symptoms such as dry cough, shortness of breath, muscle ache, dizziness, headache, sore throat, rhinorrhea, chest pain, diarrhea, nausea, and vomiting. some patients experienced dyspnea and/or hypoxemia one week after the onset of the disease [8] . in severe cases, patients quickly progressed to develop acute respiratory syndrome, septic shock, metabolic acidosis, and coagulopathy. patients with fever and/or respiratory symptoms and acute fever, even without pulmonary imaging abnormalities, should be screened for the virus for early diagnosis [39] [40] [41] . a demographic study in late december of 2019 showed that the percentages of the symptoms were 98% for fever, 76% for dry cough, 55% for dyspnea, and 3% for diarrhea; 8% of the patients required ventilation support [42] . similar findings were reported in two recent studies of a family cluster and a cluster caused by transmission from an asymptomatic individual [43, 44] . comparably, a demographic study in 2012 showed that mers-cov patients also had fever (98%), dry cough (47%), and dyspnea (55%) as their main symptoms. however, 80% of them required ventilation support, much more than covid-19 patients and consistent with the higher lethality of mers than of covid-19. diarrhea (26%) and sore throat (21%) were also observed with mers patients. in sars patients, it has been demonstrated that fever (99%-100%), dry cough (29%-75%), dyspnea (40%-42%), diarrhea (20-25%), and sore throat (13-25%) were the major symptoms and ventilation support was required for approximately 14%-20% of the patients [45] . by february 14, the mortality of covid-19 was 2% when the confirmed cases reached 66,576 globally. comparably, the mortality of sars by november 2002 was 10% of 8,096 confirmed cases [46] . for mers, based on a demographic study in june 2012, the mortality was 37% of 2,494 confirmed cases [47] . an earlier study reported that the r0 of sars-cov-2 was as high as 6.47 with a 95% confidence interval (ci) of 5.71-7.23 [48] , whereas the r0 of sars-cov only ranged from 2 to 4 [49] . a comparison of sars-cov-2 with mers-cov and sara-cov regarding their symptoms, mortality, and r0 is presented in table 1 . the above figures suggest that sars-cov-2 has a higher ability to spread than mers-cov and sars-cov, but it is less lethal than the latter two [6] . thus, it is much more challenging to control the epidemic of sars-cov-2 than those of mers-cov and sars-cov. clustered onset often happens in the same family or from the same gathering or vehicle such as a cruise ship. patients often have a history of travel or residence in wuhan or other affected areas or contact with infected individuals or patients in the recent two weeks before the onset [50] . however, it has been reported that people can carry the virus without symptoms longer than two weeks and cured patients discharged from hospitals can carry the virus again [51] , which sends out an alarm to increase the time for quarantine. patients have normal or reduced number of peripheral white blood cells (especially lymphocytes) at the early stage. for example, lymphopenia with white blood cell count < 4×10 9 /l including lymphocyte count < 1×10 9 /l, and elevated aspartate aminotransferase levels and viremia were found in 1,099 covid-19 patients [8] . the levels of liver and muscle enzymes and myoglobin were increased in the blood of some patients, and c-reactive protein and erythrocyte sedimentation were increased in the blood of most patients [52] . in patients with severe cases, the level of d-dimer, a fibrin degradation product present in the blood, was elevated, and lymphocyte count was progressively reduced [34] . abnormalities in chest radiography are found in most covid-19 patients and featured by bilateral patchy shadows or ground glass opacity in the lungs. patients often develop an atypical pneumonia, acute lung injury, and acute respiratory distress syndrome (ards) [34] . when ards happens, uncontrolled inflammation, fluid accumulation, and progressive fibrosis severely compromise the gas exchange. dysfunction of type-i and type-ii pneumocytes decreases the surfactant level and increases surface tension, thus reducing the ability of the lungs to expand and heightening the risk of lung collapse [53, 54] . therefore, the worst chest radiographic findings often parallel the most severe extent of the disease [55] . on february 18, 2020, the first pathological analysis of covid-19 demonstrated the desquamation of pneumocytes, hyaline membrane formation, and interstitial lymphocyte infiltration, and multinucleated syncytial cells in the lungs of a patient who died of the disease, consistent with the pathology of viral infection and ards [56] and similar to that of sars and mers patients [57, 58] . the detection of sars-cov-2 rna via reversetranscriptase polymerase chain reaction (rt-pcr) was used as the major criteria for the diagnosis of covid-19. however, due to the high false-negative rate, which may accelerate the epidemic, clinical manifestations started to be used for diagnosis (which no longer solely relied on rt-pcr) in china on february 13, 2020. a similar situation also occurred with the diagnosis of sars [59] . therefore, a combination of disease history, clinical manifestations, laboratory tests, and radiological findings is essential and imperative for making an effective diagnosis. on february 14, 2020, the feng zhang group described a protocol of using the crispr-based sherlock technique to detect sars-cov-2, which detects synthetic sars-cov-2 rna fragments at 20 × 10 -18 mol/l to 200 × 10 -18 mol/l (10-100 copies per microliter of input) using a dipstick in less than an hour without requiring elaborate instrumentation [60] . hopefully, the new technique can dramatically enhance the sensitivity and convenience if verified in clinical samples. due to the lack of experience with the novel cov, physicians can mainly provide supportive care to covid-19 patients, while attempting a variety of therapies that have been used or proposed before for the treatment of other covs such as sars-cov and mers-cov and other viral diseases ( table 2) . these therapies include current and potential treatments with antiviral drugs, immunosuppressants, steroids, plasma from recovered patients, chinese medicine, and psychological support. even plasma from recovered patients was proposed to be used for treatment [61] . pharmaceutical companies are racing to develop antibodies and vaccines against the virus [62] . sars-cov-2 mainly attacks the lungs in the beginning and probably also attacks, to a lesser degree, other organs that express ace2, such as the gastrointestinal system and the kidneys. nevertheless, respiratory dysfunction and failure are the major threat to the patients and the major cause of death. thus, respiratory support is critical to relieve the symptoms and save lives and includes general oxygen therapy, high-flow oxygen, noninvasive ventilation, and invasive mechanical ventilation depending on the severity of the disease. patients with severe respiratory symptoms have to be supported by extracorporeal membrane oxygenation (ecmo), a modified cardiopulmonary bypass technique used for the treatment of life-threatening cardiac or respiratory failure. in addition, the maintenance of electrolyte balance, the prevention and treatment of secondary infection and septic shock, and the protection of the functions of the vital organs are also essential for sars-cov-2 patients [7] . it has been known that a cytokine storm results from an overreaction of the immune system in sars and mers patients [33] . cytokine storm is a form of systemic inflammatory response featured by the release of a series of cytokines including tnfα, il-1β, il-2, il-6, ifnα, ifnβ, ifnγ, and mcp-1. these cytokines induce immune cells to release a vast number of free radicals which are the major cause of ards and multiple organ failure [67] . immunosuppression is essential in the treatment of cytokine storms, especially in severe patients. corticosteroids and tocilizumab, an anti-il6 monoclonal antibody, have been used to treat cytokine storm [68] . other immunosuppression treatments for cytokine storm include the modulation of t cell-directed immune response; the blockade of ifn-γ, il-1, and tnf; jak inhibition [69] ; blinatumomab [70] ; suppressor of cytokine signaling 4 [71] ; and hdac inhibitors [72] . steroids, as immunosuppressants, were widely used in the treatment of sars to reduce the severity of inflammatory damage [65] . however, steroids at high dosages were not beneficial to severe lung injury in sars and covid-19 patients [59, 73] . instead, they may cause severe side effects, especially avascular osteonecrosis, dramatically affecting the prognosis [74] . nevertheless, short courses of corticosteroids at low-to-moderate doses have been recommended to be used prudently for critically ill covid-19 patients [75] . at the time of writing, no effective antiviral therapy has been confirmed. however, intravenous administration with remdesivir, a nucleotide analog, has been found to be efficacious in an american patient with covid-19 [64] . remdesivir is a novel antiviral drug developed by gilead initially for the treatment of diseases caused by ebola and marlburg viruses [76] . later, remdesivir also demonstrated possible inhibition of other single stranded rna viruses including mers and sars viruses [77, 78] . based on these, gilead has provided the compound to china to conduct a pair of trials on sars-cov-2infected individuals [79] , and the results are highly anticipated. in addition, baricitinb, interferon-α, lopinavir/ ritonavir, and ribavirin have been suggested as potential therapies for patients with acute respiratory symptoms [80, 81] . diarrhea, nausea, vomiting, liver damage, and other adverse reactions can occur following combined therapy with lopinavir/ritonavir [80] . the interaction of these treatments with other drugs used in the patients should be monitored carefully. the collection of the blood from patients who recovered from a contagious disease to treat other patients suffering from the same disease or to protect healthy individuals from catching the disease has a long history [82] . indeed, recovered patients often have a relatively high level of antibodies against the pathogen in their blood. antibodies are an immunoglobulin (ig) produced by b lymphocytes to fight pathogens and other foreign objects and they recognize unique molecules in the pathogens and neutralize them directly [83] . based on this, plasma was collected from the blood of a group of patients who recovered from covid-19 and was injected into 10 seriously ill patients. their symptoms improved within 24 hours, accompanied by reduced inflammation and viral loads and improved oxygen saturation in the blood. however, verification and clarification are necessary to propose the method for large-scale use before specific therapies are not yet developed. in addition, given the therapeutic effects, some disadvantages associated with the plasma should be considered carefully. for example, antibodies can overstimulate the immune response and cause cytokine release syndrome, which is potentially a life-threatening toxicity [84] . the concentration of antibodies in the blood is usually low, and the demand for the plasma is large to treat critically ill patients. it is difficult to develop and produce specific antibodies rapidly enough to fight against a global epidemic [62] . thus, it is more critical and practical to isolate b cells from recovered patients and identify the genetic codes encoding effective antibodies or screen for effective antibodies against essential proteins of the virus. this way, we can readily scale up the production of the antibodies. tcm has been used to treat a variety of diseases in china for thousands of years. however, its effects largely rely on a combination of multiple components in a formula that varies depending on the diagnosis of a disease based on the theories of tcm. most of the effective components remain unknown or are vague as it is difficult to extract and verify such components or their optimal combinations. currently, due to the lack of effective and specific therapy for covid-19, tcm has become one of the major alternative treatments for patients with light to moderate symptoms or for those who have recovered from severe stages [85] . for example, shu feng jie du capsules and lian hua qing wen capsules were found to be effective for covid-19 treatment [86] . top cure rates in the treatment of covid-19 patients were observed in several provinces in china that used tcm in 87% of their patients, including gansu (63.7%), ningxia (50%), and hunan (50%), whereas hubei province, which used tcm in only approximately 30% of its covid-19 patients, had the lowest cure rate (13%) [87] . however, this is quite a rough comparison as many other impact factors such as the number and severity of the patients should be included in the evaluation. on february 18, 2020, boli zhang and coworkers published a study to compare western medicine (wm) treatment alone with combined treatment of wm and tcm [88] . they found that the times needed for body temperature recovery, symptom disappearance, and hospitalization were remarkably shorter in the wm+tcm group than in the wm only group. most impressively, the rate for symptomatic worsening (from light to severe) was remarkably lower for the wm+tcm group than for the wm only group (7.4% versus 46.2%) and the mortality was lower in the wm+tcm group than wm only group (8.8% versus 39%). nevertheless, the efficacy and safety of tcm still await more well-controlled trials at larger scales and in more centers. it would also be intriguing to characterize the mechanism of actions and clarify the effective components of tcm treatments or their combinations if possible. patients with suspected or confirmed covid-19 mostly experience great fear of the highly contagious and even fatal disease, and quarantined people also experience boredom, loneliness, and anger. furthermore, symptoms of the infection such as fever, hypoxia, and cough as well as adverse effects of the treatments such as insomnia caused by corticosteroids can lead to more anxiety and mental distress. in the early phase of the sars outbreak, a range of psychiatric morbidities including persistent depression, anxiety, panic attacks, psychomotor excitement, psychotic symptoms, delirium, and even suicidality were reported [89, 90] . mandatory contact tracing and quarantine, as a part of the public health responses to the covid-19 outbreak, can make people more anxious and guilty about the effects of the contagion, quarantine, and stigma on their families and friends [66] . thus, mental health care should be provided to covid-19 patients, suspected individuals, and people in contact with them as well as the general public who are in need. the psychological support should include the establishment of multidisciplinary mental health teams, clear communications with regular and accurate updates about the sars-cov-2 outbreak and treatment plans and the use of professional electronic devices and applications to avoid close contact with each other [66] . effective vaccines are essential for interrupting the chain of transmission from animal reservoirs and infected humans to susceptible hosts and are often complementary to antiviral treatment in the control of epidemics caused by emerging viruses. efforts have been made to develop s protein-based vaccines to generate long-term and potent neutralizing antibodies and/or protective immunity against sars-cov [81, 91] . live-attenuated vaccines have been evaluated in animal models for sars [92] . however, the in vivo efficacy of these vaccine candidates in elderly individuals and lethal-challenge models and their protection against zoonotic virus infection have yet to be determined before a clinical study is initiated. this is probably because sars died down 17 years ago and no new case has been reported since. in contrast, sporadic cases and clusters of mers continue to occur in the middle east and spread to other regions owing to the persistence of zoonotic sources in endemic areas. vaccination strategies have been developed for mers by using inactivated virus, dna plasmids, viral vectors, nanoparticles, virus-like particles and recombinant protein subunits and some have been evaluated in animal models [93] . the development of a safe and effective vaccine against sars-cov-2 for non-immune individuals is an urgent and critical task for controlling the ongoing epidemic. however, it is challenging to overcome the difficulty because of the long period of time (averaged 18 months) needed for vaccine development and the dynamic variations of covs. as a novel disease, covid-19 has just started to manifest its full clinical course throughout thousands of patients. in most cases, patients can recover gradually without sequelae. however, similar to sars and mers, covid-19 is also associated with high morbidity and mortality in patients with severe cases. therefore, building a prognosis model for the disease is essential for health-care agencies to prioritize their services, especially in resourceconstrained areas. based on clinical studies reported thus far, the following factors may affect or be associated with the prognosis of covid-19 patients (table 3) : • age: age was the most important factor for the prognosis of sars [99] , which is also true for covid-19. covid-19 mainly happened at the age of 30-65 with 47.7% of those patients being over 50 in a study of 8,866 cases as described above [37] . patients who required intensive care were more likely to have underlying comorbidities and complications and were significantly older than those who did not (at the median age of 66 versus 51) [34] , suggesting age as a prognostic factor for the outcome of covid-19 patients. • sex: sars-cov-2 has infected more men than women (0.31/100,000 versus 0.27/100,000), as described above [37] . • comorbidities and complications: patients with covid-19 who require intensive care are more likely to suffer from acute cardiac injury and arrhythmia [34] . cardiac events were also the main reason for death in sars patients [55, 65, 99] . it has been reported that sars-cov-2 can also bind to ace2-positive cholangiocytes, which might lead to liver dysfunctions in covid-19 patients [100] . it is worth noting that age and underlying disease are strongly correlated and might interfere with each other [55] . • abnormal laboratory findings: the c-reactive protein (crp) level in blood reflects the severity of inflammation or tissue injury and has been proposed to be a potential prognostic factor for disease, response to therapy, and ultimate recovery [101] . the correlation of crp level to the severity and prognosis of covid-19 has also been proposed [101] . in addition, elevated lactate dehydrogenase (ldh), aspartate aminotransferase (ast), alanine aminotransferase (alt), and creatine kinase (ck) may also help predict the outcome. these enzymes are expressed extensively in multiple organs, especially in the heart and liver, and are released during tissue damage [102, 103] . thus, they are traditional markers for heart or liver dysfunctions. • major clinical symptoms: chest radiography and temporal progression of clinical symptoms should be considered together with the other issues for the prediction of outcomes and complications of covid-19. • use of steroids: as described above, steroids are immunosuppressant commonly used as an adjunctive therapy for infectious diseases to reduce the severity of inflammatory damage [104] . since a high dosage of corticosteroids was widely used in severe sars patients, many survivors suffered from avascular osteonecrosis with life-long disability and poor life quality [105] . thus, if needed, steroids should be used at low dosage and for a short time in covid-19 patients. • mental stress: as described above, during the covid-19 outbreak many patients have suffered from extraordinary stress as they often endured long periods of quarantine and extreme uncertainty and witnessed the death of close family members and fellow patients. it is imperative to provide psychological counseling and long-term support to help these patients recover from the stress and return to normal life [66] . according to demographic studies so far, covid-19 seems to have different epidemiological features from sars. in addition to replicating in the lower respiratory tract, sars-cov-2 can efficiently replicate in the upper respiratory tract and causes mild or no symptoms in the early phase of infection, similar to other covs that cause common colds [106] . therefore, infected patients at the early phase or incubation period can produce a large amount of virus during daily activities, causing great difficulty for the control of the epidemic. however, the transmission of sars-cov was considered to occur when the patients are severely ill, while most transmission did not happen at the early phase [107] . thus, the current outbreak of covid-19 is much more severe and difficult to control than the outbreak of sars. great efforts are currently underway in china including the lockdown of wuhan and surrounding cities and continuous quarantine of almost the entire population in hopes of interrupting the transmission of sars-cov-2. although these actions have been dramatically damaging the economy and other sectors of the country, the number of new patients is declining, indicating the slowdown of the epidemic. the most optimistic estimate is that the outbreak will end by march and the downswing phase will last for 3-4 months [108] . however, some other experts are not that optimistic. paul hunter, et al., estimated that covid-19, which seems substantially more infectious than sars, will not end in 2020 [109] . ira longini, et al., established a model to predict the outcome of the epidemic and suggested that sars-cov-2 could infect two-thirds of the global population [110] . a canadian group reported that sars-cov-2 was detected in both mid-turbinate and throat swabs of patients who recovered and left the hospital 2 weeks earlier [111] , which indicates that the newly identified virus could become a cyclical episode similar to influenza. however, promising signs have occurred in china based on the declining number of new cases, indicating the current strategies might have been working. ebola was originally predicted to cause up to a million cases with half a million deaths. however, via strict quarantine and isolation, the disease has eventually been put under control [112, 113] . it is possible, similar to sars-cov, that sars-cov-2 might become weaker in infectivity and eventually die down or become a less pathogenic virus co-existent with humans. a comparison of the epidemic of covid-19 with that of sars and mers is provided below (fig. 5 ). sars-cov-2 is highly transmittable through coughing or sneezing, and possibly also through direct contact with materials contaminated by the virus [12] . the virus was also found in feces, which raises a new possibility of feces-to-mouth transmission [114] . a recent study on 138 cases reported that 41% of the cases were possibly caused by nosocomial infections, including 17 patients with other prior diseases and 40 health-care providers [115] . thus, great precaution should be used to protect humans, especially health-care providers, social workers, family members, colleagues, and even bystanders in contact with patients or infected people. the first line of defense that could be used to lower the risk of infection is through wearing face masks; both the use of surgical masks and n95 respirator masks (series # 1860s) helps control the spread of viruses [116] . surgical face masks prevent liquid droplets from a potentially infected individual from traveling through the air or sticking onto surfaces of materials, where they could be passed on to others [117] . however, only n95 (series # 1860s) masks can protect against the inhalation of virions as small as 10 to 80 nm, with only 5% of the virions being able to penetrate completely; sars-cov-2 is similar to sars-cov in size and both are approximately 85 nm [117] . since particles can penetrate even five surgical masks stacked together, health-care providers in direct contact with patients must wear n95 (series # 1860s) masks but not surgical masks [118] . in addition to masks, health-care providers should wear fitted isolation gowns in order to further reduce contact with viruses. viruses can also infect an individual through the eyes. on january 22, 2020, a doctor was infected with sars-cov-2 although he wore an n95 mask; the virus might have entered his body through his inflammatory eyes [119] . thus, health-care providers should also wear transparent face shields or goggles while working with patients. for the general public in affected or potentially affected areas, it is highly suggested that everybody wash their hands with disinfectant soaps more often than usual, try to stay indoors for self-quarantine and limit contact with potentially infected individuals. three feet is considered an appropriate distance for people to stay away from a patient [120] . these actions are effective methods to lower the risk of infection as well as prevent the spread of the virus. although sars-cov-2 came as a new virus to the human world, its high homology to sars-cov as reported on 7 january 2020 [3] should have caused high alert to china based on her deep memory of the sars outbreak in 2003. however, not until 19 january 2020 did the director of the center of disease control of wuhan comfort the citizens by saying that the novel virus has low contagiousness and limited reproductivity from human to human and that it is not a problem to prevent and contain the disease. this message remarkably relaxed the alarm of the public, especially when the entire country was preparing for the spring festival, and the critical time was missed to contain the disease at its minimal scale in wuhan. the disease control agencies in china may take this hard lesson and make critical improvements in the future. for example, these agencies should be (1) more careful when making public announcements as every word counts to citizens and can change their attitude and decisions; (2) more sensitive and reactive to unusual information from clinics rather than waiting for formal reports from doctors or officials; (3) more restrictive to contain a potential epidemic at its early stage rather than attempting to comfort the public; and (4) more often to issue targeted and effective drills to increase the public's awareness about epidemic diseases and to test and improve the response system of the society periodically. the outbreak of covid-19 caused by the novel virus sars-cov-2 started in the end of december 2019. in less than two months, it has spread all over china and near 50 other countries globally at the time of this writing. since the virus is very similar to sars-cov and the symptoms are also similar between covid-19 and sars, the outbreak of covid-19 has created a sense of sars recurring. however, there are some remarkable differences between covid-19 and sars, which are essential for containing the epidemic and treating the patients. • covid-19 affects more elderly individuals than youth and more men than women, and the severity and death rate are also higher in elderly individual than in youth. • sars has higher mortality than covid-19 (10.91% versus 1.44%). • covid-19 patients transmit the virus even when they are symptomless whereas sars patients do so usually when they are severely ill, which causes much greater difficulty to contain the spread of covid-19 than sars. this partially explains why sars-cov-2 spread much faster and broader than sars-cov. • the regular rna assay for sars-cov-2 can be negative in some covid-19 patients. on the other hand, cured patients can be positive for the virus again. these findings dramatically increase the risk of virus spreading. given such rapid progress in research on covid-19, several critical issues remain to be solved, as follows: • where did sars-cov-2 come from? although 96% genetic homolog was found between sars-cov-2 and two bat sars-like covs, we still cannot conclude that sars-cov-2 is from bats. • what animal was the intermediate species to transmit the virus from the original host, say bats, to humans? without knowing answers to #1 and 2, we cannot efficiently cut the transmission, and the outbreak can relapse at any time. • although molecular modeling and biochemical assays have demonstrated that sars-cov-2 binds to ace2, how exactly does the virus enter the airway cells and cause subsequent pathological changes? does the virus also bind ace2-expressing cells in other organs [121] ? without clear answers to these questions, we cannot achieve fast and accurate diagnosis and effective treatment. • how long will the epidemic last? how is the virus genetically evolving during transmission among humans? will it become a pandemic worldwide, die down like sars or relapse periodically like the flu? it is essential but may take some time to search for answers to the above and many other questions. however, with whatever expense it may demand, we have no other choice but to stop the epidemic as soon as possible and bring our life back to normal. the covid-19 epidemic a: who 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quantitative assessment of the efficacy of surgical and n95 masks to filter influenza virus in patients with acute influenza infection do n95 respirators provide 95% protection level against airborne viruses, and how adequate are surgical masks? protecting healthcare staff from severe acute respiratory syndrome: filtration capacity of multiple surgical masks 2019-ncov transmission through the ocular surface must not be ignored cdc: guideline for isolation precautions: preventing transmission of infectious agents in healthcare settings ace2 expression in kidney and testis may cause kidney and testis damage after 2019-ncov infection y.y. and r.x. conceived and designed the manuscript. y.y., p.l., s.y., e.l. and r.x. wrote the manuscript. r.x gave the final approval of the manuscript. r.x. is a founder of imstem biotechnology, inc., a stem cell company. the other authors declare no competing financial interests. key: cord-279255-v861kk0i authors: dhama, kuldeep; khan, sharun; tiwari, ruchi; sircar, shubhankar; bhat, sudipta; malik, yashpal singh; singh, karam pal; chaicumpa, wanpen; bonilla-aldana, d. katterine; rodriguez-morales, alfonso j. title: coronavirus disease 2019–covid-19 date: 2020-06-24 journal: clin microbiol rev doi: 10.1128/cmr.00028-20 sha: doc_id: 279255 cord_uid: v861kk0i in recent decades, several new diseases have emerged in different geographical areas, with pathogens including ebola virus, zika virus, nipah virus, and coronaviruses (covs). recently, a new type of viral infection emerged in wuhan city, china, and initial genomic sequencing data of this virus do not match with previously sequenced covs, suggesting a novel cov strain (2019-ncov), which has now been termed severe acute respiratory syndrome cov-2 (sars-cov-2). although coronavirus disease 2019 (covid-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. compared to diseases caused by previously known human covs, covid-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. compared to other emerging viruses, such as ebola virus, avian h7n9, sars-cov, and middle east respiratory syndrome coronavirus (mers-cov), sars-cov-2 has shown relatively low pathogenicity and moderate transmissibility. codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. early diagnosis by real-time pcr and next-generation sequencing has facilitated the identification of the pathogen at an early stage. since no antiviral drug or vaccine exists to treat or prevent sars-cov-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating sars-cov, mers-cov, and other emerging viral diseases. in this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus. o ver the past 2 decades, coronaviruses (covs) have been associated with significant disease outbreaks in east asia and the middle east. the severe acute respiratory syndrome (sars) and the middle east respiratory syndrome (mers) began to emerge in 2002 and 2012, respectively. recently, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), causing coronavirus disease 2019 (covid19) , emerged in late 2019, and it has posed a global health threat, causing an ongoing pandemic in many countries and territories (1) . health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel cov (originally named 2019-ncov), which was first identified in wuhan city, hubei province, china, on 12 december 2019. on 11 february 2020, the world health organization (who) announced the official designation for the current cov-associated disease to be covid-19, caused by sars-cov-2. the primary cluster of patients was found to be connected with the huanan south china seafood market in wuhan (2) . covs belong to the family coronaviridae (subfamily coronavirinae), the members of which infect a broad range of hosts, producing symptoms and diseases ranging from the common cold to severe and ultimately fatal illnesses, such as sars, mers, and, presently, covid-19. sars-cov-2 is considered one of the seven members of the cov family that infect humans (3) , and it belongs to the same lineage of covs that causes sars; however, this novel virus is genetically distinct. until 2020, six covs were known to infect humans, including human cov 229e (hcov-229e), hcov-nl63, hcov-oc43, hcov-hku1, sars-cov, and mers-cov. although sars-cov and mers-cov have resulted in outbreaks with high mortality, others remain associated with mild upper-respiratory-tract illnesses (4) . newly evolved covs pose a high threat to global public health. the current emergence of covid-19 is the third cov outbreak in humans over the past 2 decades (5) . it is no coincidence that fan et al. predicted potential sars-or mers-like cov outbreaks in china following pathogen transmission from bats (6) . covid-19 emerged in china and spread rapidly throughout the country and, subsequently, to other countries. due to the severity of this outbreak and the potential of spreading on an international scale, the who declared a global health emergency on 31 january 2020; subsequently, on 11 march 2020, they declared it a pandemic situation. at present, we are not in a position to effectively treat covid-19, since neither approved vaccines nor specific antiviral drugs for treating human cov infections are available (7) (8) (9) . most nations are currently making efforts to prevent the further spreading of this potentially deadly virus by implementing preventive and control strategies. in domestic animals, infections with covs are associated with a broad spectrum of furthermore, it acts as a critical factor for tissue tropism and the determination of host range (45) . notably, s protein is one of the vital immunodominant proteins of covs capable of inducing host immune responses (45) . the ectodomains in all covs s proteins have similar domain organizations, divided into two subunits, s1 and s2 (43) . the first one, s1, helps in host receptor binding, while the second one, s2, accounts for fusion. the former (s1) is further divided into two subdomains, namely, the n-terminal domain (ntd) and c-terminal domain (ctd). both of these subdomains act as receptorbinding domains, interacting efficiently with various host receptors (45) . the s1 ctd contains the receptor-binding motif (rbm). in each coronavirus spike protein, the trimeric s1 locates itself on top of the trimeric s2 stalk (45) . recently, structural analyses of the s proteins of covid-19 have revealed 27 amino acid substitutions within a 1,273-amino-acid stretch (16) . six substitutions are located in the rbd (amino acids 357 to 528), while four substitutions are in the rbm at the ctd of the s1 domain (16) . of note, no amino acid change is seen in the rbm, which binds directly to the angiotensinconverting enzyme-2 (ace2) receptor in sars-cov (16, 46) . at present, the main emphasis is knowing how many differences would be required to change the host tropism. sequence comparison revealed 17 nonsynonymous changes between the early sequence of sars-cov-2 and the later isolates of sars-cov. the changes were found scattered over the genome of the virus, with nine substitutions in orf1ab, orf8 (4 substitutions), the spike gene (3 substitutions) , and orf7a (single substitution) (4) . notably, the same nonsynonymous changes were found in a familial cluster, indicating that the viral evolution happened during person-to-person transmission (4, 47) . such adaptive evolution events are frequent and constitute a constantly ongoing process once the virus spreads among new hosts (47) . even though no functional changes occur in the virus associated with this adaptive evolution, close monitoring of the viral mutations that occur during subsequent human-to-human transmission is warranted. the m protein is the most abundant viral protein present in the virion particle, giving a definite shape to the viral envelope (48) . it binds to the nucleocapsid and acts as a central organizer of coronavirus assembly (49) . coronavirus m proteins are highly diverse in amino acid contents but maintain overall structural similarity within different genera (50) . the m protein has three transmembrane domains, flanked by a short amino terminus outside the virion and a long carboxy terminus inside the virion (50) . overall, the viral scaffold is maintained by m-m interaction. of note, the m protein of sars-cov-2 does not have an amino acid substitution compared to that of sars-cov (16) . the coronavirus e protein is the most enigmatic and smallest of the major structural proteins (51) . it plays a multifunctional role in the pathogenesis, assembly, and release of the virus (52) . it is a small integral membrane polypeptide that acts as a viroporin (ion channel) (53) . the inactivation or absence of this protein is related to the altered virulence of coronaviruses due to changes in morphology and tropism (54) . the e protein consists of three domains, namely, a short hydrophilic amino terminal, a large hydrophobic transmembrane domain, and an efficient c-terminal domain (51) . the sars-cov-2 e protein reveals a similar amino acid constitution without any substitution (16) . the n protein of coronavirus is multipurpose. among several functions, it plays a role in complex formation with the viral genome, facilitates m protein interaction needed during virion assembly, and enhances the transcription efficiency of the virus (55, 56) . it contains three highly conserved and distinct domains, namely, an ntd, an rna-binding domain or a linker region (lkr), and a ctd (57) . the ntd binds with the 3= end of the viral genome, perhaps via electrostatic interactions, and is highly diverged both in length and sequence (58) . the charged lkr is serine and arginine rich and is also known as the sr (serine and arginine) domain (59) . the lkr is capable of direct interaction with in vitro rna interaction and is responsible for cell signaling (60, 61) . it also modulates the antiviral response of the host by working as an antagonist for interferon (ifn) and rna interference (62) . compared to that of sars-cov, the n protein of sars-cov-2 possess five amino acid mutations, where two are in the intrinsically dispersed region (idr; positions 25 and 26) , one each in the ntd (position 103), lkr (position 217), and ctd (position 334) (16) . besides the important structural proteins, the sars-cov-2 genome contains 15 nsps, nsp1 to nsp10 and nsp12 to nsp16, and 8 accessory proteins (3a, 3b, p6, 7a, 7b, 8b, 9b, and orf14) (16) . all these proteins play a specific role in viral replication (27) . unlike the accessory proteins of sars-cov, sars-cov-2 does not contain 8a protein and has a longer 8b and shorter 3b protein (16) . the nsp7, nsp13, envelope, matrix, and p6 and 8b accessory proteins have not been detected with any amino acid substitutions compared to the sequences of other coronaviruses (16) . the virus structure of sars-cov-2 is depicted in fig. 2 . sequence percent similarity analysis. we assessed the nucleotide percent similarity using the megalign software program, where the similarity between the novel sars-cov-2 isolates was in the range of 99.4% to 100%. among the other serbecovirus cov sequences, the novel sars-cov-2 sequences revealed the highest similarity to bat-sl-cov, with nucleotide percent identity ranges between 88.12 and 89.65%. meanwhile, earlier reported sars-covs showed 70.6 to 74.9% similarity to sars-cov-2 at the nucleotide level. further, the nucleotide percent similarity was 55.4%, 45.5% to 47.9%, 46 .2% to 46.6%, and 45.0% to 46.3% to the other four subgenera, namely, hibecovirus, nobecovirus, merbecovirus, and embecovirus, respectively. the percent similarity index of current outbreak isolates indicates a close relationship between sars-cov-2 isolates and bat-sl-cov, indicating a common origin. however, particular pieces of evidence based on further complete genomic analysis of current isolates are necessary to draw any conclusions, although it was ascertained that the current novel sars-cov-2 isolates belong to the subgenus sarbecovirus in the diverse range of betacoronaviruses. their possible ancestor was hypothesized to be from bat cov strains, wherein bats might have played a crucial role in harboring this class of viruses. splitstree phylogeny analysis. in the unrooted phylogenetic tree of different betacoronaviruses based on the s protein, virus sequences from different subgenera grouped into separate clusters. sars-cov-2 sequences from wuhan and other countries exhibited a close relationship and appeared in a single cluster (fig. 1 ). the covs from the subgenus sarbecovirus appeared jointly in splitstree and divided into three subclusters, namely, sars-cov-2, bat-sars-like-cov (bat-sl-cov), and sars-cov (fig. 1) . in the case of other subgenera, like merbecovirus, all of the sequences grouped clinical microbiology reviews than italy. a john hopkins university web platform has provided daily updates on the basic epidemiology of the covid-19 outbreak (https://gisanddata.maps.arcgis.com/ apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6) (238) . covid-19 has also been confirmed on a cruise ship, named diamond princess, quarantined in japanese waters (port of yokohama), as well as on other cruise ships around the world (239) (fig. 3) . the significant events of the sars-cov-2/covid-19 virus outbreak occurring since 8 december 2019 are presented as a timeline in fig. 5 . at the beginning, china experienced the majority of the burden associated with covid-19 in the form of disease morbidity and mortality (65), but over time the covid-19 menace moved to europe, particularly italy and spain, and now the united states has the highest number of confirmed cases and deaths. the covid-19 outbreak has also been associated with severe economic impacts globally due to the sudden interruption of global trade and supply chains that forced multinational companies to make decisions that led to significant economic losses (66) . the recent increase in the number of confirmed critically ill patients with covid-19 has already surpassed the intensive care supplies, limiting intensive care services to only a small portion of critically ill patients (67) . this might also have contributed to the increased case fatality rate observed in the covid-19 outbreak. the novel coronavirus was identified within 1 month (28 days) of the outbreak. this is impressively fast compared to the time taken to identify sars-cov reported in foshan, guangdong province, china (125 days) (68) . immediately after the confirmation of viral etiology, the chinese virologists rapidly released the genomic sequence of sars-cov-2, which played a crucial role in controlling the spread of this newly emerged novel coronavirus to other parts of the world (69) . the possible origin of sars-cov-2 and the first mode of disease transmission are not yet identified (70) . analysis of the initial cluster of infections suggests that the infected individuals had a common exposure point, a seafood market in wuhan, hubei province, china (fig. 6 ). the restaurants of this market are well-known for providing different types of wild animals for human consumption (71) . the huanan south china seafood market also sells live animals, such as poultry, bats, snakes, and marmots (72) . this might be the point where zoonotic (animal-to-human) transmission occurred (71) . although sars-cov-2 is alleged to have originated from an animal host (zoonotic origin) with further humanto-human transmission (fig. 6 ), the likelihood of foodborne transmission should be ruled out with further investigations, since it is a latent possibility (1). additionally, other clinical microbiology reviews potential and expected routes would be associated with transmission, as in other respiratory viruses, by direct contact, such as shaking contaminated hands, or by direct contact with contaminated surfaces (fig. 6) . still, whether blood transfusion and organ transplantation (276) , as well as transplacental and perinatal routes, are possible routes for sars-cov-2 transmission needs to be determined (fig. 6 ). from experience with several outbreaks associated with known emerging viruses, higher pathogenicity of a virus is often associated with lower transmissibility. compared to emerging viruses like ebola virus, avian h7n9, sars-cov, and mers-cov, sars-cov-2 has relatively lower pathogenicity and moderate transmissibility (15) . the risk of death among individuals infected with covid-19 was calculated using the infection fatality risk (ifr). the ifr was found to be in the range of 0.3% to 0.6%, which is comparable to that of a previous asian influenza pandemic (1957 to 1958) (73, 277) . notably, the reanalysis of the covid-19 pandemic curve from the initial cluster of cases pointed to considerable human-to-human transmission. it is opined that the exposure history of sars-cov-2 at the wuhan seafood market originated from humanto-human transmission rather than animal-to-human transmission (74) ; however, in light of the zoonotic spillover in covid-19, is too early to fully endorse this idea (1). following the initial infection, human-to-human transmission has been observed with a preliminary reproduction number (r 0 ) estimate of 1.4 to 2.5 (70, 75) , and recently it is estimated to be 2.24 to 3.58 (76) . in another study, the average reproductive number of covid-19 was found to be 3.28, which is significantly higher than the initial who estimate of 1.4 to 2.5 (77) . it is too early to obtain the exact r 0 value, since there is a possibility of bias due to insufficient data. the higher r 0 value is indicative of the more significant potential of sars-cov-2 transmission in a susceptible population. this is not the first time where the culinary practices of china have been blamed for the origin of novel coronavirus infection in humans. previously, the animals present in the liveanimal market were identified to be the intermediate hosts of the sars outbreak in china (78) . several wildlife species were found to harbor potentially evolving coronavirus strains that can overcome the species barrier (79) . one of the main principles of chinese food culture is that live-slaughtered animals are considered more nutritious (5) . after 4 months of struggle that lasted from december 2019 to march 2020, the covid-19 situation now seems under control in china. the wet animal markets have reopened, and people have started buying bats, dogs, cats, birds, scorpions, badgers, rabbits, pangolins (scaly anteaters), minks, soup from palm civet, ostriches, hamsters, snapping turtles, ducks, fish, siamese crocodiles, and other animal meats without any fear of covid-19. the chinese government is encouraging people to feel they can return to normalcy. however, this could be a risk, as it has been mentioned in advisories that people should avoid contact with live-dead animals as much as possible, as sars-cov-2 has shown zoonotic spillover. additionally, we cannot rule out the possibility of new mutations in the same virus being closely related to contact with both animals and humans at the market (284) . in january 2020, china imposed a temporary ban on the sale of live-dead animals in wet markets. however, now hundreds of such wet markets have been reopened without optimizing standard food safety and sanitation practices (286) . with china being the most populated country in the world and due to its domestic and international food exportation policies, the whole world is now facing the menace of covid-19, including china itself. wet markets of live-dead animals do not maintain strict food hygienic practices. fresh blood splashes are present everywhere, on the floor and tabletops, and such food customs could encourage many pathogens to adapt, mutate, and jump the species barrier. as a result, the whole world is suffering from novel sars-cov-2, with more than 4,170,424 cases and 287,399 deaths across the globe. there is an urgent need for a rational international campaign against the unhealthy food practices of china to encourage the sellers to increase hygienic food practices or close the crude live-dead animal wet markets. there is a need to modify food policies at national and international levels to avoid further life threats and clinical microbiology reviews economic consequences from any emerging or reemerging pandemic due to close animal-human interaction (285) . even though individuals of all ages and sexes are susceptible to covid-19, older people with an underlying chronic disease are more likely to become severely infected (80) . recently, individuals with asymptomatic infection were also found to act as a source of infection to susceptible individuals (81) . both the asymptomatic and symptomatic patients secrete similar viral loads, which indicates that the transmission capacity of asymptomatic or minimally symptomatic patients is very high. thus, sars-cov-2 transmission can happen early in the course of infection (82) . atypical clinical manifestations have also been reported in covid-19 in which the only reporting symptom was fatigue. such patients may lack respiratory signs, such as fever, cough, and sputum (83) . hence, the clinicians must be on the look-out for the possible occurrence of atypical clinical manifestations to avoid the possibility of missed diagnosis. the early transmission ability of sars-cov-2 was found to be similar to or slightly higher than that of sars-cov, reflecting that it could be controlled despite moderate to high transmissibility (84) . increasing reports of sars-cov-2 in sewage and wastewater warrants the need for further investigation due to the possibility of fecal-oral transmission. sars-cov-2 present in environmental compartments such as soil and water will finally end up in the wastewater and sewage sludge of treatment plants (328) . therefore, we have to reevaluate the current wastewater and sewage sludge treatment procedures and introduce advanced techniques that are specific and effective against sars-cov-2. since there is active shedding of sars-cov-2 in the stool, the prevalence of infections in a large population can be studied using wastewater-based epidemiology. recently, reverse transcription-quantitative pcr (rt-qpcr) was used to enumerate the copies of sars-cov-2 rna concentrated from wastewater collected from a wastewater treatment plant (327) . the calculated viral rna copy numbers determine the number of infected individuals. the increasing reports of virus shedding via the fecal route warrants the introduction of negative fecal viral nucleic acid test results as one of the additional discharge criteria in laboratory-confirmed cases of covid-19 (326) . the covid-19 pandemic does not have any novel factors, other than the genetically unique pathogen and a further possible reservoir. the cause and the likely future outcome are just repetitions of our previous interactions with fatal coronaviruses. the only difference is the time of occurrence and the genetic distinctness of the pathogen involved. mutations on the rbd of covs facilitated their capability of infecting newer hosts, thereby expanding their reach to all corners of the world (85) . this is a potential threat to the health of both animals and humans. advanced studies using bayesian phylogeographic reconstruction identified the most probable origin of sars-cov-2 as the bat sars-like coronavirus, circulating in the rhinolophus bat family (86) . phylogenetic analysis of 10 whole-genome sequences of sars-cov-2 showed that they are related to two covs of bat origin, namely, bat-sl-covzc45 and bat-sl-covzxc21, which were reported during 2018 in china (17) . it was reported that sars-cov-2 had been confirmed to use ace2 as an entry receptor while exhibiting an rbd similar to that of sars-cov (17, 87, 254, 255) . several countries have provided recommendations to their people traveling to china (88, 89) . compared to the previous coronavirus outbreaks caused by sars-cov and mers-cov, the efficiency of sars-cov-2 human-to-human transmission was thought to be less. this assumption was based on the finding that health workers were affected less than they were in previous outbreaks of fatal coronaviruses (2) . superspreading events are considered the main culprit for the extensive transmission of sars and mers (90, 91) . almost half of the mers-cov cases reported in saudi arabia are of secondary origin that occurred through contact with infected asymptomatic or symptomatic individuals through human-tohuman transmission (92) . the occurrence of superspreading events in the covid-19 outbreak cannot be ruled out until its possibility is evaluated. like sars and mers, covid-19 can also infect the lower respiratory tract, with milder symptoms (27) . the basic reproduction number of covid-19 has been found to be in the range of 2.8 to 3.3 based on real-time reports and 3.2 to 3.9 based on predicted infected cases (84) . coronavirus infection in humans is commonly associated with mild to severe respiratory diseases, with high fever, severe inflammation, cough, and internal organ dysfunction that can even lead to death (92) . most of the identified coronaviruses cause the common cold in humans. however, this changed when sars-cov was identified, paving the way for severe forms of the disease in humans (22) . our previous experience with the outbreaks of other coronaviruses, like sars and mers, suggests that the mode of transmission in covid-19 as mainly human-to-human transmission via direct contact, droplets, and fomites (25) . recent studies have demonstrated that the virus could remain viable for hours in aerosols and up to days on surfaces; thus, aerosol and fomite contamination could play potent roles in the transmission of sars-cov-2 (257) . the immune response against coronavirus is vital to control and get rid of the infection. however, maladjusted immune responses may contribute to the immunopathology of the disease, resulting in impairment of pulmonary gas exchange. understanding the interaction between covs and host innate immune systems could enlighten our understanding of the lung inflammation associated with this infection (24) . sars is a viral respiratory disease caused by a formerly unrecognized animal cov that originated from the wet markets in southern china after adapting to the human host, thereby enabling transmission between humans (90) . the sars outbreak reported in 2002 to 2003 had 8,098 confirmed cases with 774 total deaths (9.6%) (93) . the outbreak severely affected the asia pacific region, especially mainland china (94) . even though the case fatality rate (cfr) of sars-cov-2 (covid-19) is lower than that of sars-cov, there exists a severe concern linked to this outbreak due to its epidemiological similarity to influenza viruses (95, 279) . this can fail the public health system, resulting in a pandemic (96) . mers is another respiratory disease that was first reported in saudi arabia during the year 2012. the disease was found to have a cfr of around 35% (97) . the analysis of available data sets suggests that the incubation period of sars-cov-2, sars-cov, and mers-cov is in almost the same range. the longest predicted incubation time of sars-cov-2 is 14 days. hence, suspected individuals are isolated for 14 days to avoid the risk of further spread (98) . even though a high similarity has been reported between the genome sequence of the new coronavirus (sars-cov-2) and sars-like covs, the comparative analysis recognized a furin-like cleavage site in the sars-cov-2 s protein that is missing from other sars-like covs (99) . the furin-like cleavage site is expected to play a role in the life cycle of the virus and disease pathogenicity and might even act as a therapeutic target for furin inhibitors. the highly contagious nature of sars-cov-2 compared to that of its predecessors might be the result of a stabilizing mutation that occurred in the endosome-associated-protein-like domain of nsp2 protein. similarly, the destabilizing mutation near the phosphatase domain of nsp3 proteins in sars-cov-2 could indicate a potential mechanism that differentiates it from other covs (100) . even though the cfr reported for covid-19 is meager compared to those of the previous sars and mers outbreaks, it has caused more deaths than sars and mers combined (101) . possibly related to the viral pathogenesis is the recent finding of an 832-nucleotide (nt) deletion in orf8, which appears to reduce the replicative fitness of the virus and leads to attenuated phenotypes of sars-cov-2 (256) . coronavirus is the most prominent example of a virus that has crossed the species barrier twice from wild animals to humans during sars and mers outbreaks (79, 102) . the possibility of crossing the species barrier for the third time has also been suspected in the case of sars-cov-2 (covid19) . bats are recognized as a possible natural reservoir host of both sars-cov and mers-cov infection. in contrast, the possible intermediary host is the palm civet for sars-cov and the dromedary camel for mers-cov infection (102) . bats are considered the ancestral hosts for both sars and mers (103) . bats are also considered the reservoir host of human coronaviruses like clinical microbiology reviews hcov-229e and hcov-nl63 (104) . in the case of covid-19, there are two possibilities for primary transmission: it can be transmitted either through intermediate hosts, similar to that of sars and mers, or directly from bats (103) . the emergence paradigm put forward in the sars outbreak suggests that sars-cov originated from bats (reservoir host) and later jumped to civets (intermediate host) and incorporated changes within the receptor-binding domain (rbd) to improve binding to civet ace2. this civetadapted virus, during their subsequent exposure to humans at live markets, promoted further adaptations that resulted in the epidemic strain (104) . transmission can also occur directly from the reservoir host to humans without rbd adaptations. the bat coronavirus that is currently in circulation maintains specific "poised" spike proteins that facilitate human infection without the requirement of any mutations or adaptations (105) . altogether, different species of bats carry a massive number of coronaviruses around the world (106) . the high plasticity in receptor usage, along with the feasibility of adaptive mutation and recombination, may result in frequent interspecies transmission of coronavirus from bats to animals and humans (106) . the pathogenesis of most bat coronaviruses is unknown, as most of these viruses are not isolated and studied (4) . hedgehog coronavirus hku31, a betacoronavirus, has been identified from amur hedgehogs in china. studies show that hedgehogs are the reservoir of betacoronavirus, and there is evidence of recombination (107) . the current scientific evidence available on mers infection suggests that the significant reservoir host, as well as the animal source of mers infection in humans, is the dromedary camels (97) . the infected dromedary camels may not show any visible signs of infection, making it challenging to identify animals actively excreting mers-cov that has the potential to infect humans. however, they may shed mers-cov through milk, urine, feces, and nasal and eye discharge and can also be found in the raw organs (108) . in a study conducted to evaluate the susceptibility of animal species to mers-cov infection, llamas and pigs were found to be susceptible, indicating the possibility of mers-cov circulation in animal species other than dromedary camels (109) . following the outbreak of sars in china, sars-cov-like viruses were isolated from himalayan palm civets (paguma larvata) and raccoon dogs (nyctereutes procyonoides) found in a live-animal market in guangdong, china. the animal isolates obtained from the live-animal market retained a 29-nucleotide sequence that was not present in most of the human isolates (78) . these findings were critical in identifying the possibility of interspecies transmission in sars-cov. the higher diversity and prevalence of bat coronaviruses in this region compared to those in previous reports indicate a host/ pathogen coevolution. sars-like coronaviruses also have been found circulating in the chinese horseshoe bat (rhinolophus sinicus) populations. the in vitro and in vivo studies carried out on the isolated virus confirmed that there is a potential risk for the reemergence of sars-cov infection from the viruses that are currently circulating in the bat population (105) . the disease caused by sars-cov-2 is also named severe specific contagious pneumonia (sscp), wuhan pneumonia, and, recently, covid-19 (110) . compared to sars-cov, sars-cov-2 has less severe pathogenesis but has superior transmission capability, as evidenced by the rapidly increasing number of covid-19 cases (111) . the incubation period of sars-cov-2 in familial clusters was found to be 3 to 6 days (112) . the mean incubation period of covid-19 was found to be 6.4 days, ranging from 2.1 to 11.1 days (113) . among an early affected group of 425 patients, 59 years was the median age, of which more males were affected (114) . similar to sars and mers, the severity of this ncov is high in age groups above 50 years (2, 115) . symptoms of covid-19 include fever, cough, myalgia or fatigue, and, less commonly, headache, hemoptysis, and diarrhea (116, 282) . compared to the sars-cov-2-infected patients in wuhan during the initial stages of the outbreak, only mild symptoms were noticed in those patients that are infected by human-to-human transmission (14) . the initial trends suggested that the mortality associated with covid-19 was less than that of previous outbreaks of sars (101) . the updates obtained from countries like china, japan, thailand, and south korea indicated that the covid-19 patients had relatively mild manifestations compared to those with sars and mers (4). regardless of the coronavirus type, immune cells, like mast cells, that are present in the submucosa of the respiratory tract and nasal cavity are considered the primary barrier against this virus (92) . advanced in-depth analysis of the genome has identified 380 amino acid substitutions between the amino acid sequences of sars-cov-2 and the sars/sarslike coronaviruses. these differences in the amino acid sequences might have contributed to the difference in the pathogenic divergence of sars-cov-2 (16) . further research is required to evaluate the possible differences in tropism, pathogenesis, and transmission of this novel agent associated with this change in the amino acid sequence. with the current outbreak of covid-19, there is an expectancy of a significant increase in the number of published studies about this emerging coronavirus, as occurred with sars and mers (117) . sars-cov-2 invades the lung parenchyma, resulting in severe interstitial inflammation of the lungs. this is evident on computed tomography (ct) images as ground-glass opacity in the lungs. this lesion initially involves a single lobe but later expands to multiple lung lobes (118) . the histological assessment of lung biopsy samples obtained from covid-19-infected patients revealed diffuse alveolar damage, cellular fibromyxoid exudates, hyaline membrane formation, and desquamation of pneumocytes, indicative of acute respiratory distress syndrome (119) . it was also found that the sars-cov-2infected patients often have lymphocytopenia with or without leukocyte abnormalities. the degree of lymphocytopenia gives an idea about disease prognosis, as it is found to be positively correlated with disease severity (118) . pregnant women are considered to have a higher risk of getting infected by covid-19. the coronaviruses can cause adverse outcomes for the fetus, such as intrauterine growth restriction, spontaneous abortion, preterm delivery, and perinatal death. nevertheless, the possibility of intrauterine maternal-fetal transmission (vertical transmission) of covs is low and was not seen during either the sars-or mers-cov outbreak (120) . however, there has been concern regarding the impact of sars-cov-2/covid-19 on pregnancy. researchers have mentioned the probability of in utero transmission of novel sars-cov-2 from covid-19-infected mothers to their neonates in china based upon the rise in igm and igg antibody levels and cytokine values in the blood obtained from newborn infants immediately postbirth; however, rt-pcr failed to confirm the presence of sars-cov-2 genetic material in the infants (283) . recent studies show that at least in some cases, preterm delivery and its consequences are associated with the virus. nonetheless, some cases have raised doubts for the likelihood of vertical transmission (240) (241) (242) (243) . covid-19 infection was associated with pneumonia, and some developed acute respiratory distress syndrome (ards). the blood biochemistry indexes, such as albumin, lactate dehydrogenase, c-reactive protein, lymphocytes (percent), and neutrophils (percent) give an idea about the disease severity in covid-19 infection (121) . during covid-19, patients may present leukocytosis, leukopenia with lymphopenia (244), hypoalbuminemia, and an increase of lactate dehydrogenase, aspartate transaminase, alanine aminotransferase, bilirubin, and, especially, d-dimer (244) . middle-aged and elderly patients with primary chronic diseases, especially high blood pressure and diabetes, were found to be more susceptible to respiratory failure and, therefore, had poorer prognoses. providing respiratory support at early stages improved the disease prognosis and facilitated recovery (18) . the ards in covid-19 is due to the occurrence of cytokine storms that results in exaggerated immune response, immune regulatory network imbalance, and, finally, multiple-organ failure (122) . in addition to the exaggerated inflammatory response seen in patients with covid-19 pneumonia, the bile duct epithelial cell-derived hepatocytes upregulate ace2 expression in liver tissue by compensatory proliferation that might result in hepatic tissue injury (123) . coronavirus can cause disease in several species of domestic and wild animals, as well as humans (23) . the different animal species that are infected with cov include horses, camels, cattle, swine, dogs, cats, rodents, birds, ferrets, minks, bats, rabbits, snakes, and various other wild animals (20, 30, 79, 93, 124, 125, 287) . coronavirus infection is linked to different kinds of clinical manifestations, varying from enteritis in cows and pigs, upper respiratory disease in chickens, and fatal respiratory infections in humans (30) . among the cov genera, alphacoronavirus and betacoronavirus infect mammals, while gammacoronavirus and deltacoronavirus mainly infect birds, fishes, and, sometimes, mammals (27, 29, 106) . several novel coronaviruses that come under the genus deltacoronavirus have been discovered in the past from birds, like wigeon coronavirus hku20, bulbul coronavirus hku11, munia coronavirus hku13, white-eye coronavirus hku16, night-heron coronavirus hku19, and common moorhen coronavirus hku21, as well as from pigs (porcine coronavirus hku15) (6, 29) . transmissible gastroenteritis virus (tgev), porcine epidemic diarrhea virus (pedv), and porcine hemagglutinating encephalomyelitis virus (phev) are some of the coronaviruses of swine. among them, tgev and pedv are responsible for causing severe gastroenteritis in young piglets with noteworthy morbidity and mortality. infection with phev also causes enteric infection but can cause encephalitis due to its ability to infect the nervous system (30) . bovine coronaviruses (bocovs) are known to infect several domestic and wild ruminants (126) . bocov inflicts neonatal calf diarrhea in adult cattle, leading to bloody diarrhea (winter dysentery) and respiratory disease complex (shipping fever) in cattle of all age groups (126) . bocov-like viruses have been noted in humans, suggesting its zoonotic potential as well (127) . feline enteric and feline infectious peritonitis (fip) viruses are the two major feline covs (128) , where feline covs can affect the gastrointestinal tract, abdominal cavity (peritonitis), respiratory tract, and central nervous system (128) . canines are also affected by covs that fall under different genera, namely, canine enteric coronavirus in alphacoronavirus and canine respiratory coronavirus in betacoronavirus, affecting the enteric and respiratory tract, respectively (129, 130) . ibv, under gammacoronavirus, causes diseases of respiratory, urinary, and reproductive systems, with substantial economic losses in chickens (131, 132) . in small laboratory animals, mouse hepatitis virus, rat sialodacryoadenitis coronavirus, and guinea pig and rabbit coronaviruses are the major covs associated with disease manifestations like enteritis, hepatitis, and respiratory infections (10, 133) . swine acute diarrhea syndrome coronavirus (sads-cov) was first identified in suckling piglets having severe enteritis and belongs to the genus alphacoronavirus (106) . the outbreak was associated with considerable scale mortality of piglets (24,693 deaths) across four farms in china (134) . the virus isolated from the piglets was almost identical to and had 95% genomic similarity with horseshoe bat (rhinolophus species) coronavirus hku2, suggesting a bat origin of the pig virus (106, 134, 135) . it is also imperative to note that the sads-cov outbreak started in guangdong province, near the location of the sars pandemic origin (134) . before this outbreak, pigs were not known to be infected with bat-origin coronaviruses. this indicates that the bat-origin coronavirus jumped to pig by breaking the species barrier. the next step of this jump might not end well, since pigs are considered the mixing vessel for influenza a viruses due to their ability to be infected by both human and avian influenza a viruses (136) . similarly, they may act as the mixing vessel for coronaviruses, since they are in frequent contact with both humans and multiple wildlife species. additionally, pigs are also found to be susceptible to infection with human sars-cov and mers-cov, making this scenario a nightmare (109, 137) . it is only a matter of time before another zoonotic coronavirus results in an epidemic by jumping the so-called species barrier (287) . the host spectrum of coronavirus increased when a novel coronavirus, namely, sw1, was recognized in the liver tissue of a captive beluga whale (delphinapterus leucas) (138) . in recent decades, several novel coronaviruses were identified from different animal species. bats can harbor these viruses without manifesting any clinical disease but are persistently infected (30) . they are the only mammals with the capacity for self-powered flight, which enables them to migrate long distances, unlike land mammals. bats are distributed worldwide and also account for about a fifth of all mammalian species (6) . this makes them the ideal reservoir host for many viral agents and also the source of novel coronaviruses that have yet to be identified. it has become a necessity to study the diversity of coronavirus in the bat population to prevent future outbreaks that could jeopardize livestock and public health. the repeated outbreaks caused by bat-origin coronaviruses calls for the development of efficient molecular surveillance strategies for studying betacoronavirus among animals (12) , especially in the rhinolophus bat family (86) . chinese bats have high commercial value, since they are used in traditional chinese medicine (tcm). therefore, the handling of bats for trading purposes poses a considerable risk of transmitting zoonotic cov epidemics (139) . due to the possible role played by farm and wild animals in sars-cov-2 infection, the who, in their novel coronavirus (covid-19) situation report, recommended the avoidance of unprotected contact with both farm and wild animals (25) . the live-animal markets, like the one in guangdong, china, provides a setting for animal coronaviruses to amplify and to be transmitted to new hosts, like humans (78) . such markets can be considered a critical place for the origin of novel zoonotic diseases and have enormous public health significance in the event of an outbreak. bats are the reservoirs for several viruses; hence, the role of bats in the present outbreak cannot be ruled out (140) . in a qualitative study conducted for evaluating the zoonotic risk factors among rural communities of southern china, the frequent human-animal interactions along with the low levels of environmental biosecurity were identified as significant risks for the emergence of zoonotic disease in local communities (141, 142) . the comprehensive sequence analysis of the sars-cov-2 rna genome identified that the cov from wuhan is a recombinant virus of the bat coronavirus and another coronavirus of unknown origin. the recombination was found to have happened within the viral spike glycoprotein, which recognizes the cell surface receptor. further analysis of the genome based on codon usage identified the snake as the most probable animal reservoir of sars-cov-2 (143) . contrary to these findings, another genome analysis proposed that the genome of sars-cov-2 is 96% identical to bat coronavirus, reflecting its origin from bats (63) . the involvement of bat-derived materials in causing the current outbreak cannot be ruled out. high risk is involved in the production of bat-derived materials for tcm practices involving the handling of wild bats. the use of bats for tcm practices will remain a severe risk for the occurrence of zoonotic coronavirus epidemics in the future (139) . furthermore, the pangolins are an endangered species of animals that harbor a wide variety of viruses, including coronaviruses (144) . the coronavirus isolated from malayan pangolins (manis javanica) showed a very high amino acid identity with covid-19 at e (100%), m (98.2%), n (96.7%), and s genes (90.4%). the rbd of s protein in cov isolated from pangolin was almost identical (one amino acid difference) to that of sars-cov-2. a comparison of the genomes suggests recombination between pangolin-cov-like viruses with the bat-cov-ratg13-like virus. all this suggests the potential of pangolins to act as the intermediate host of sars-cov-2 (145) . human-wildlife interactions, which are increasing in the context of climate change (142) , are further considered high risk and responsible for the emergence of sars-cov. covid-19 is also suspected of having a similar mode of origin. hence, to prevent the occurrence of another zoonotic spillover (1), exhaustive coordinated efforts are needed to identify the high-risk pathogens harbored by wild animal populations, conducting surveillance among the people who are susceptible to zoonotic spillover events (12) , and to improve the biosecurity measures associated with the wildlife trade (146) . the serological surveillance studies conducted in people living in proximity to bat caves had earlier identified the serological confirmation of sars-related covs in humans. people clinical microbiology reviews living at the wildlife-human interface, mainly in rural china, are regularly exposed to sars-related covs (147) . these findings will not have any significance until a significant outbreak occurs due to a virus-like sars-cov-2. there is a steady increase in the reports of covid-19 in companion and wild animals around the world. further studies are required to evaluate the potential of animals (especially companion animals) to serve as an efficient reservoir host that can further alter the dynamics of human-to-human transmission (330) . to date, two pet dogs (hong kong) and four pet cats (one each from belgium and hong kong, two from the united states) have tested positive for sars-cov-2 (335) . the world organization for animal health (oie) has confirmed the diagnosis of covid-19 in both dogs and cats due to human-to-animal transmission (331) . the similarity observed in the gene sequence of sars-cov-2 from an infected pet owner and his dog further confirms the occurrence of human-to-animal transmission (333) . even though asymptomatic, feline species should be considered a potential transmission route from animals to humans (326) . however, currently, there are no reports of sars-cov-2 transmission from felines to human beings. based on the current evidence, we can conclude that cats are susceptible to sars-cov-2 and can get infected by human beings. however, evidence of cat-to-human transmission is lacking and requires further studies (332) . rather than waiting for firmer evidence on animal-to-human transmission, necessary preventive measures are advised, as well as following social distancing practices among companion animals of different households (331) . one of the leading veterinary diagnostic companies, idexx, has conducted large-scale testing for covid-19 in specimens collected from dogs and cats. however, none of the tests turned out to be positive (334) . in a study conducted to investigate the potential of different animal species to act as the intermediate host of sars-cov-2, it was found that both ferrets and cats can be infected via experimental inoculation of the virus. in addition, infected cats efficiently transmitted the disease to naive cats (329) . sars-cov-2 infection and subsequent transmission in ferrets were found to recapitulate the clinical aspects of covid-19 in humans. the infected ferrets also shed virus via multiple routes, such as saliva, nasal washes, feces, and urine, postinfection, making them an ideal animal model for studying disease transmission (337) . experimental inoculation was also done in other animal species and found that the dogs have low susceptibility, while the chickens, ducks, and pigs are not at all susceptible to sars-cov-2 (329) . similarly, the national veterinary services laboratories of the usda have reported covid-19 in tigers and lions that exhibited respiratory signs like dry cough and wheezing. the zoo animals are suspected to have been infected by an asymptomatic zookeeper (335) . the total number of covid-19-positive cases in human beings is increasing at a high rate, thereby creating ideal conditions for viral spillover to other species, such as pigs. the evidence obtained from sars-cov suggests that pigs can get infected with sars-cov-2 (336). however, experimental inoculation with sars-cov-2 failed to infect pigs (329) . further studies are required to identify the possible animal reservoirs of sars-cov-2 and the seasonal variation in the circulation of these viruses in the animal population. research collaboration between human and animal health sectors is becoming a necessity to evaluate and identify the possible risk factors of transmission between animals and humans. such cooperation will help to devise efficient strategies for the management of emerging zoonotic diseases (12) . rna tests can confirm the diagnosis of sars-cov-2 (covid-19) cases with real-time rt-pcr or next-generation sequencing (148, 149, 245, 246) . at present, nucleic acid detection techniques, like rt-pcr, are considered an effective method for confirming the diagnosis in clinical cases of covid-19 (148) . several companies across the world are currently focusing on developing and marketing sars-cov-2-specific nucleic acid detection kits. multiple laboratories are also developing their own in-house rt-pcr. one of them is the sars-cov-2 nucleic acid detection kit produced by shuoshi biotechnology (double fluorescence pcr method) (150) . up to 30 march 2020, the u.s. food and drug administration (fda) had granted 22 in vitro diagnostics emergency use authorizations (euas), including for the rt-pcr diagnostic panel for the universal detection of sars-like betacoronaviruses and specific detection of sars-cov-2, developed by the u.s. cdc (table 1) (258, 259) . recently, 95 full-length genomic sequences of saras-cov-2 strains available in the national center for biotechnology information and gisaid databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260) . all the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. overall variation was found to be low in orf regions, with 13 variation sites recognized in 1a, 1b, s, 3a, m, 8, and n regions. mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (orf8) and nt 8782 (orf1a) positions, respectively. owing to such selective mutations, a few specific regions of sars-cov-2 should not be considered for designing primers and probes. the sars-cov-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering sars-cov-2 (260) . nucleic acids of sars-cov-2 can be detected from samples (64) such as bronchoalveolar lavage fluid, sputum, nasal swabs, fiber bronchoscope brush biopsy specimen, pharyngeal swabs, feces, blood, and urine, with different levels of diagnostic performance (table 2) (80, 245, 246) . the viral loads of sars-cov-2 were measured using n-gene-specific quantitative rt-pcr in throat swab and sputum samples collected from covid-19-infected individuals. the results indicated that the viral load peaked at around 5 to 6 days following the onset of symptoms, and it ranged from 10 4 to 10 7 copies/ml during this time (151) . in another study, the viral load was found to be higher in the nasal swabs than the throat swabs obtained from covid-19 symptomatic patients (82) . although initially it was thought that viral load would be associated with poor outcomes, some case reports have shown asymptomatic individuals with high viral loads (247) . recently, the viral load in nasal and throat swabs of 17 symptomatic patients was determined, and higher viral loads were recorded soon after the onset of symptoms, particularly in the nose compared to the throat. the pattern of viral nucleic the results of the studies related to sars-cov-2 viral loads reflect active replication of this virus in the upper respiratory tract and prolonged viral shedding after symptoms disappear, including via stool. thus, the current case definition needs to be updated along with a reassessment of the strategies to be adopted for restraining the sars-cov-2 outbreak spread (248) . in some cases, the viral load studies of sars-cov-2 have also been useful to recommend precautionary measures when handling specific samples, e.g., feces. in a recent survey from 17 confirmed cases of sars-cov-2 infection with available data (representing days 0 to 13 after onset), stool samples from nine cases (53%; days 0 to 11 after onset) were positive on rt-pcr analysis. although the viral loads were lower than those of respiratory samples (range, 550 copies per ml to 1.21 ϫ 10 5 copies per ml), this has essential biosafety implications (151) . the samples from 18 sars-cov-2-positive patients in singapore who had traveled from wuhan to singapore showed the presence of viral rna in stool and whole blood but not in urine by real-time rt-pcr (288) . further, novel sars-cov-2 infections have been detected in a variety of clinical specimens, like bronchoalveolar lavage fluid, sputum, nasal swabs, fibrobronchoscope brush biopsy specimens, pharyngeal swabs, feces, and blood (246) . the presence of sars-cov-2 in fecal samples has posed grave public health concerns. in addition to the direct transmission mainly occurring via droplets of sneezing and coughing, other routes, such as fecal excretion and environmental and fomite contamination, are contributing to sars-cov-2 transmission and spread (249) (250) (251) (252) . fecal excretion has also been documented for sars-cov and mers-cov, along with the potential to stay viable in situations aiding fecal-oral transmission. thus, sars-cov-2 has every possibility to be transmitted through this mode. fecal-oral transmission of sars-cov-2, particularly in regions having low standards of hygiene and poor sanitation, may have grave consequences with regard to the high spread of this virus. ethanol and disinfectants containing chlorine or bleach are effective against coronaviruses (249) (250) (251) (252) . appropriate precautions need to be followed strictly while handling the stools of patients infected with sars-cov-2. biowaste materials and sewage from hospitals must be adequately disinfected, treated, and disposed of properly. the significance of frequent and good hand hygiene and sanitation practices needs to be given due emphasis (249) (250) (251) (252) . future explorative research needs to be conducted with regard to the fecal-oral transmission of sars-cov-2, along with focusing on environmental investigations to find out if this virus could stay viable in situations and atmospheres facilitating such potent routes of transmission. the correlation of fecal concentrations of viral rna with disease severity needs to be determined, along with assessing the gastrointestinal symptoms and the possibility of fecal sars-cov-2 rna detection during the covid-19 incubation period or convalescence phases of the disease (249) (250) (251) (252) . the lower respiratory tract sampling techniques, like bronchoalveolar lavage fluid aspirate, are considered the ideal clinical materials, rather than the throat swab, due to their higher positive rate on the nucleic acid test (148) . the diagnosis of covid-19 can be made by using upper-respiratory-tract specimens collected using nasopharyngeal and oropharyngeal swabs. however, these techniques are associated with unnecessary risks to health care workers due to close contact with patients (152) . similarly, a single patient with a high viral load was reported to contaminate an entire endoscopy room by shedding the virus, which may remain viable for at least 3 days and is considered a great risk for uninfected patients and health care workers (289) . recently, it was found that the anal swabs gave more positive results than oral swabs in the later stages of infection (153) . hence, clinicians have to be cautious while discharging any covid-19infected patient based on negative oral swab test results due to the possibility of fecal-oral transmission. even though the viral loads in stool samples were found to be less than those of respiratory samples, strict precautionary measures have to be followed while handling stool samples of covid-19 suspected or infected patients (151) . children infected with sars-cov-2 experience only a mild form of illness and recover immediately after treatment. it was recently found that stool samples of sars-cov-2-infected children that gave negative throat swab results were positive within ten days of negative results. this could result in the fecal-oral transmission of sars-cov-2 infections, especially in children (290) . hence, to prevent the fecal-oral transmission of sars-cov-2, infected covid-19 patients should only be considered negative when they test negative for sars-cov-2 in the stool sample. a suspected case of covid-19 infection is said to be confirmed if the respiratory tract aspirate or blood samples test positive for sars-cov-2 nucleic acid using rt-pcr or by the identification of sars-cov-2 genetic sequence in respiratory tract aspirate or blood samples (80) . the patient will be confirmed as cured when two subsequent oral swab results are negative (153) . recently, the live virus was detected in the selfcollected saliva of patients infected with covid-19. these findings were confirmative of using saliva as a noninvasive specimen for the diagnosis of covid-19 infection in suspected individuals (152) . it has also been observed that the initial screening of covid-19 patients infected with rt-pcr may give negative results even if they have chest ct findings that are suggestive of infection. hence, for the accurate diagnosis of covid-19, a combination of repeated swab tests using rt-pcr and ct scanning is required to prevent the possibility of false-negative results during disease screening (154) . rt-pcr is the most widely used test for diagnosing covid-19. however, it has some significant limitations from the clinical perspective, since it will not give any clarity regarding disease progression. droplet digital pcr (ddpcr) can be used for the quantification of viral load in the samples obtained from lower respiratory tracts. hence, based on the viral load, we can quickly evaluate the progression of infection (291) . in addition to all of the above findings, sequencing and phylogenetics are critical in the correct identification and confirmation of the causative viral agent and useful to establish relationships with previous isolates and sequences, as well as to know, especially during an epidemic, the nucleotide and amino acid mutations and the molecular divergence. the rapid development and implementation of diagnostic tests against emerging novel diseases like covid-19 pose significant challenges due to the lack of resources and logistical limitations associated with an outbreak (155) . sars-cov-2 infection can also be confirmed by isolation and culturing. the human airway epithelial cell culture was found to be useful in isolating sars-cov-2 (3). the efficient control of an outbreak depends on the rapid diagnosis of the disease. recently, in response to the covid-19 outbreak, 1-step quantitative realtime reverse transcription-pcr assays were developed that detect the orf1b and n regions of the sars-cov-2 genome (156) . that assay was found to achieve the rapid detection of sars-cov-2. nucleic acid-based assays offer high accuracy in the diagnosis of sars-cov-2, but the current rate of spread limits its use due to the lack of diagnostic assay kits. this will further result in the extensive transmission of covid-19, since only a portion of suspected cases can be diagnosed. in such situations, conventional serological assays, like enzyme-linked immunosorbent assay (elisa), that are specific to covid-19 igm and igg antibodies can be used as a high-throughput alternative (149) . at present, there is no diagnostic kit available for detecting the sars-cov-2 antibody (150) . the specific antibody profiles of covid-19 patients were analyzed, and it was found that the igm level lasted more than 1 month, indicating a prolonged stage of virus replication in sars-cov-2-infected patients. the igg levels were found to increase only in the later stages of the disease. these findings indicate that the specific antibody profiles of sars-cov-2 and sars-cov were similar (325) . these findings can be utilized for the development of specific diagnostic tests against covid-19 and can be used for rapid screening. even though diagnostic test kits are already available that can detect the genetic sequences of sars-cov-2 (95), their availability is a concern, as the number of covid-19 cases is skyrocketing (155, 157) . a major problem associated with this diagnostic kit is that it works only when the test subject has an active infection, limiting its use to the earlier stages of infection. several laboratories around the world are currently developing antibody-based diagnostic tests against sars-cov-2 (157). chest ct is an ideal diagnostic tool for identifying viral pneumonia. the sensitivity of chest ct is far superior to that of x-ray screening. the chest ct findings associated with covid-19-infected patients include characteristic patchy infiltration that later progresses to ground-glass opacities (158) . early manifestations of covid-19 pneumonia might not be evident in x-ray chest radiography. in such situations, a chest ct examination can be performed, as it is considered highly specific for covid-19 pneumonia (118) . those patients having covid-19 pneumonia will exhibit the typical ground-glass opacity in their chest ct images (154) . the patients infected with covid-19 had elevated plasma angiotensin 2 levels. the level of angiotensin 2 was found to be linearly associated with viral load and lung injury, indicating its potential as a diagnostic biomarker (121) . the chest ct imaging abnormalities associated with covid-19 pneumonia have also been observed even in asymptomatic patients. these abnormalities progress from the initial focal unilateral to diffuse bilateral ground-glass opacities and will further progress to or coexist with lung consolidation changes within 1 to 3 weeks (159). the role played by radiologists in the current scenario is very important. radiologists can help in the early diagnosis of lung abnormalities associated with covid-19 pneumonia. they can also help in the evaluation of disease severity, identifying its progression to acute respiratory distress syndrome and the presence of secondary bacterial infections (160) . even though chest ct is considered an essential diagnostic tool for covid-19, the extensive use of ct for screening purposes in the suspected individuals might be associated with a disproportionate risk-benefit ratio due to increased radiation exposure as well as increased risk of cross-infection. hence, the use of ct for early diagnosis of sars-cov-2 infection in high-risk groups should be done with great caution (292) . more recently, other advanced diagnostics have been designed and developed for the detection of sars-cov-2 (345, 347, (350) (351) (352) . a reverse transcriptional loopmediated isothermal amplification (rt-lamp), namely, ilaco, has been developed for rapid and colorimetric detection of this virus (354) . rt-lamp serves as a simple, rapid, and sensitive diagnostic method that does not require sophisticated equipment or skilled personnel (349) . an interactive web-based dashboard for tracking sars-cov-2 in a real-time mode has been designed (238) . a smartphone-integrated home-based point-of-care testing (poct) tool, a paper-based poct combined with lamp, is a useful point-of-care diagnostic (353) . an abbott id now covid-19 molecular poct-based test, using isothermal nucleic acid amplification technology, has been designed as a pointof-care test for very rapid detection of sars-cov-2 in just 5 min (344) . a crispr-based sherlock (specific high-sensitivity enzymatic reporter unlocking) diagnostic for rapid detection of sars-cov-2 without the requirement of specialized instrumentation has been reported to be very useful in the clinical diagnosis of covid-19 (360) . a crispr-cas12-based lateral flow assay also has been developed for rapid detection of sars-cov-2 (346) . artificial intelligence, by means of a three-dimensional deep-learning model, has been developed for sensitive and specific diagnosis of covid-19 via ct images (332) . tracking and mapping of the rising incidence rates, disease outbreaks, community spread, clustered transmission events, hot spots, and superspreader potential of sars-cov-2/covid warrant full exploitation of real-time disease mapping by employing geographical information systems (gis), such as the gis software kosmo 3.1, web-based real-time tools and dashboards, apps, and advances in information technology (356-359). researchers have also developed a few prediction tools/models, such as the prediction model risk of bias assessment tool (probast) and critical appraisal and data extraction for systematic reviews of prediction modeling studies (charms), which could aid in assessing the possibility of getting infection and estimating the prognosis in patients; however, such models may suffer from bias issues and, hence, cannot be considered completely trustworthy, which necessitates the development of new and reliable predictors (360) . recently emerged viruses, such as zika, ebola, and nipah viruses, and their grave threats to humans have begun a race in exploring the designing and developing of advanced vaccines, prophylactics, therapeutics, and drug regimens to counter emerging viruses (161) (162) (163) 280) . several attempts are being made to design and develop vaccines for cov infection, mostly by targeting the spike glycoprotein. nevertheless, owing to extensive diversity in antigenic variants, cross-protection rendered by the vaccines is significantly limited, even within the strains of a phylogenetic subcluster (104) . due to the lack of effective antiviral therapy and vaccines in the present scenario, we need to depend solely on implementing effective infection control measures to lessen the risk of possible nosocomial transmission (68) . recently, the receptor for sars-cov-2 was established as the human angiotensin-converting enzyme 2 (hace2), and the virus was found to enter the host cell mainly through endocytosis. it was also found that the major components that have a critical role in viral entry include pikfyve, tpc2, and cathepsin l. these findings are critical, since the components described above might act as candidates for vaccines or therapeutic drugs against sars-cov-2 (293) . the majority of the treatment options and strategies that are being evaluated for sars-cov-2 (covid-19) have been taken from our previous experiences in treating sars-cov, mers-cov, and other emerging viral diseases. several therapeutic and preventive strategies, including vaccines, immunotherapeutics, and antiviral drugs, have been exploited against the previous cov outbreaks (sars-cov and mers-cov) (8, 104, (164) (165) (166) (167) . these valuable options have already been evaluated for their potency, efficacy, and safety, along with several other types of current research that will fuel our search for ideal therapeutic agents against covid-19 (7, 9, 19, 21, 36) . the primary cause of the unavailability of approved and commercial vaccines, drugs, and therapeutics to counter the earlier sars-cov and mers-cov seems to owe to the lesser attention of the biomedicine and pharmaceutical companies, as these two covs did not cause much havoc, global threat, and panic like those posed by the sars-cov-2 pandemic (19) . moreover, for such outbreak situations, the requirement for vaccines and therapeutics/drugs exists only for a limited period, until the outbreak is controlled. the proportion of the human population infected with sars-cov and mers-cov was also much lower across the globe, failing to attract drug and vaccine manufacturers and clinical microbiology reviews producers. therefore, by the time an effective drug or vaccine is designed against such disease outbreaks, the virus would have been controlled by adopting appropriate and strict prevention and control measures, and patients for clinical trials will not be available. the newly developed drugs cannot be marketed due to the lack of end users. the s protein plays a significant role in the induction of protective immunity against sars-cov by mediating t-cell responses and neutralizing antibody production (168) . in the past few decades, we have seen several attempts to develop a vaccine against human coronaviruses by using s protein as the target (168, 169) . however, the developed vaccines have minimal application, even among closely related strains of the virus, due to a lack of cross-protection. that is mainly because of the extensive diversity existing among the different antigenic variants of the virus (104) . the contributions of the structural proteins, like spike (s), matrix (m), small envelope (e), and nucleocapsid (n) proteins, of sars-cov to induce protective immunity has been evaluated by expressing them in a recombinant parainfluenza virus type 3 vector (bhpiv3). of note, the result was conclusive that the expression of m, e, or n proteins without the presence of s protein would not confer any noticeable protection, with the absence of detectable serum sars-cov-neutralizing antibodies (170) . antigenic determinant sites present over s and n structural proteins of sars-cov-2 can be explored as suitable vaccine candidates (294) . in the asian population, s, e, m, and n proteins of sars-cov-2 are being targeted for developing subunit vaccines against covid-19 (295) . the identification of the immunodominant region among the subunits and domains of s protein is critical for developing an effective vaccine against the coronavirus. the c-terminal domain of the s1 subunit is considered the immunodominant region of the porcine deltacoronavirus s protein (171) . similarly, further investigations are needed to determine the immunodominant regions of sars-cov-2 for facilitating vaccine development. however, our previous attempts to develop a universal vaccine that is effective for both sars-cov and mers-cov based on t-cell epitope similarity pointed out the possibility of cross-reactivity among coronaviruses (172) . that can be made possible by selected potential vaccine targets that are common to both viruses. sars-cov-2 has been reported to be closely related to sars-cov (173, 174) . hence, knowledge and understanding of s protein-based vaccine development in sars-cov will help to identify potential s protein vaccine candidates in sars-cov-2. therefore, vaccine strategies based on the whole s protein, s protein subunits, or specific potential epitopes of s protein appear to be the most promising vaccine candidates against coronaviruses. the rbd of the s1 subunit of s protein has a superior capacity to induce neutralizing antibodies. this property of the rbd can be utilized for designing potential sars-cov vaccines either by using rbd-containing recombinant proteins or recombinant vectors that encode rbd (175) . hence, the superior genetic similarity existing between sars-cov-2 and sars-cov can be utilized to repurpose vaccines that have proven in vitro efficacy against sars-cov to be utilized for sars-cov-2. the possibility of cross-protection in covid-19 was evaluated by comparing the s protein sequences of sars-cov-2 with that of sars-cov. the comparative analysis confirmed that the variable residues were found concentrated on the s1 subunit of s protein, an important vaccine target of the virus (150) . hence, the possibility of sars-cov-specific neutralizing antibodies providing cross-protection to covid-19 might be lower. further genetic analysis is required between sars-cov-2 and different strains of sars-cov and sarslike (sl) covs to evaluate the possibility of repurposed vaccines against covid-19. this strategy will be helpful in the scenario of an outbreak, since much time can be saved, because preliminary evaluation, including in vitro studies, already would be completed for such vaccine candidates. multiepitope subunit vaccines can be considered a promising preventive strategy against the ongoing covid-19 pandemic. in silico and advanced immunoinformatic tools can be used to develop multiepitope subunit vaccines. the vaccines that are engineered by this technique can be further evaluated using docking studies and, if found effective, then can be further evaluated in animal models (365) . identifying epitopes that have the potential to become a vaccine candidate is critical to developing an effective vaccine against covid-19. the immunoinformatics approach has been used for recognizing essential epitopes of cytotoxic t lymphocytes and b cells from the surface glycoprotein of sars-cov-2. recently, a few epitopes have been recognized from the sars-cov-2 surface glycoprotein. the selected epitopes explored targeting molecular dynamic simulations, evaluating their interaction with corresponding major histocompatibility complex class i molecules. they potentially induce immune responses (176) . the recombinant vaccine can be designed by using rabies virus (rv) as a viral vector. rv can be made to express mers-cov s1 protein on its surface so that an immune response is induced against mers-cov. the rv vector-based vaccines against mers-cov can induce faster antibody response as well as higher degrees of cellular immunity than the gram-positive enhancer matrix (gem) particle vector-based vaccine. however, the latter can induce a very high antibody response at lower doses (167) . hence, the degree of humoral and cellular immune responses produced by such vaccines depends upon the vector used. dual vaccines have been getting more popular recently. among them, the rabies virus-based vectored vaccine platform is used to develop vaccines against emerging infectious diseases. the dual vaccine developed from inactivated rabies virus particles that express the mers-cov s1 domain of s protein was found to induce immune responses for both mers-cov and rabies virus. the vaccinated mice were found to be completely protected from challenge with mers-cov (169) . the intranasal administration of the recombinant adenovirus-based vaccine in balb/c mice was found to induce long-lasting neutralizing immunity against mers spike pseudotyped virus, characterized by the induction of systemic igg, secretory iga, and lung-resident memory t-cell responses (177) . immunoinformatics methods have been employed for the genomewide screening of potential vaccine targets among the different immunogens of mers-cov (178) . the n protein and the potential b-cell epitopes of mers-cov e protein have been suggested as immunoprotective targets inducing both t-cell and neutralizing antibody responses (178, 179) . the collaborative effort of the researchers of rocky mountain laboratories and oxford university is designing a chimpanzee adenovirus-vectored vaccine to counter covid-19 (180) . the coalition for epidemic preparedness innovations (cepi) has initiated three programs to design sars-cov-2 vaccines (181) . cepi has a collaborative project with inovio for designing a mers-cov dna vaccine that could potentiate effective immunity. cepi and the university of queensland are designing a molecular clamp vaccine platform for mers-cov and other pathogens, which could assist in the easier identification of antigens by the immune system (181) . cepi has also funded moderna to develop a vaccine for covid-19 in partnership with the vaccine research center (vrc) of the national institute of allergy and infectious diseases (niaid), part of the national institutes of health (nih) (182) . by employing mrna vaccine platform technology, a vaccine candidate expressing sars-cov-2 spike protein is likely to go through clinical testing in the coming months (180 (298) . the process of vaccine development usually takes approximately ten years, in the case of inactivated or live attenuated vaccines, since it involves the generation of long-term efficacy data. however, this was brought down to 5 years during the ebola emergency for viral vector vaccines. in the urgency associated with the covid-19 outbreaks, we expect a vaccine by the end of this year (343) . the development of an effective vaccine against covid-19 with high speed and precision is the combined result of advancements in computational biology, gene synthesis, protein engineering, and the invention of advanced manufacturing platforms (342) . the recurring nature of the coronavirus outbreaks calls for the development of a pan-coronavirus vaccine that can produce cross-reactive antibodies. however, the success of such a vaccine relies greatly on its ability to provide protection not only against present versions of the virus but also the ones that are likely to emerge in the future. this can be achieved by identifying antibodies that can recognize relatively conserved epitopes that are maintained as such even after the occurrence of considerable variations (362) . even though several vaccine clinical trials are being conducted around the world, pregnant women have been completely excluded from these studies. pregnant women are highly vulnerable to emerging diseases such as covid-19 due to alterations in the immune system and other physiological systems that are associated with pregnancy. therefore, in the event of successful vaccine development, pregnant women will not get access to the vaccines (361) . hence, it is recommended that pregnant women be included in the ongoing vaccine trials, since successful vaccination in pregnancy will protect the mother, fetus, and newborn. the heterologous immune effects induced by bacillus calmette guérin (bcg) vaccination is a promising strategy for controlling the covid-19 pandemic and requires further investigations. bcg is a widely used vaccine against tuberculosis in high-risk regions. it is derived from a live attenuated strain of mycobacterium bovis. at present, three new clinical trials have been registered to evaluate the protective role of bcg vaccination against sars-cov-2 (363) . recently, a cohort study was conducted to evaluate the impact of childhood bcg vaccination in covid-19 pcr positivity rates. however, childhood bcg vaccination was found to be associated with a rate of covid-19-positive test results similar to that of the nonvaccinated group (364) . further studies are required to analyze whether bcg vaccination in childhood can induce protective effects against covid-19 in adulthood. population genetic studies conducted on 103 genomes identified that the sars-cov-2 virus has evolved into two major types, l and s. among the two types, l type is expected to be the most prevalent (ϳ70%), followed by the s type (ϳ30%) (366) . this finding has a significant impact on our race to develop an ideal vaccine, since the vaccine candidate has to target both strains to be considered effective. at present, the genetic differences between the l and s types are very small and may not affect the immune response. however, we can expect further genetic variations in the coming days that could lead to the emergence of new strains (367) . there is no currently licensed specific antiviral treatment for mers-and sars-cov infections, and the main focus in clinical settings remains on lessening clinical signs and providing supportive care (183) (184) (185) (186) . effective drugs to manage covid-19 patients include remdesivir, lopinavir/ritonavir alone or in a blend with interferon beta, convalescent plasma, and monoclonal antibodies (mabs); however, efficacy and safety issues of these drugs require additional clinical trials (187, 281) . a controlled trial of ritonavirboosted lopinavir and interferon alpha 2b treatment was performed on covid-19 hospitalized patients (chictr2000029308) (188) . in addition, the use of hydroxychloroquine and tocilizumab for their potential role in modulating inflammatory responses in the lungs and antiviral effect has been proposed and discussed in many research articles. still, no fool-proof clinical trials have been published (194, 196, 197, (261) (262) (263) (264) (265) (266) (267) (268) (269) (270) (271) (272) . recently, a clinical trial conducted on adult patients suffering from severe covid-19 revealed no benefit of lopinavir-ritonavir treatment over standard care (273) . the efforts to control sars-cov-2 infection utilize defined strategies as followed against mers and sars, along with adopting and strengthening a few precautionary measures owing to the unknown nature of this novel virus (36, 189) . presently, the main course of treatment for severely affected sars-cov-2 patients admitted to hospitals includes mechanical ventilation, intensive care unit (icu) admittance, and symptomatic and supportive therapies. additionally, rna synthesis inhibitors (lamivudine and tenofovir disoproxil fumarate), remdesivir, neuraminidase inhibitors, peptide (ek1), antiinflammatory drugs, abidol, and chinese traditional medicine (lianhuaqingwen and shufengjiedu capsules) could aid in covid-19 treatment. however, further clinical trials are being carried out concerning their safety and efficacy (7) . it might require months to a year(s) to design and develop effective drugs, therapeutics, and vaccines against covid-19, with adequate evaluation and approval from regulatory bodies and moving to the bulk production of many millions of doses at commercial levels to meet the timely demand of mass populations across the globe (9) . continuous efforts are also warranted to identify and assess viable drugs and immunotherapeutic regimens that revealed proven potency in combating other viral agents similar to sars-cov-2. covid-19 patients showing severe signs are treated symptomatically along with oxygen therapy. in such cases where the patients progress toward respiratory failure and become refractory to oxygen therapy, mechanical ventilation is necessitated. the covid-19-induced septic shock can be managed by providing adequate hemodynamic support (299) . several classes of drugs are currently being evaluated for their potential therapeutic action against sars-cov-2. therapeutic agents that have anti-sars-cov-2 activity can be broadly classified into three categories: drugs that block virus entry into the host cell, drugs that block viral replication as well as its survival within the host cell, and drugs that attenuate the exaggerated host immune response (300) . an inflammatory cytokine storm is commonly seen in critically ill covid-19 patients. hence, they may benefit from the use of timely anti-inflammation treatment. anti-inflammatory therapy using drugs like glucocorticoids, cytokine inhibitors, jak inhibitors, and chloroquine/hydroxychloroquine should be done only after analyzing the risk/benefit ratio in covid-19 patients (301). there have not been any studies concerning the application of nonsteroidal anti-inflammatory drugs (nsaid) to covid-19-infected patients. however, reasonable pieces of evidence are available that link nsaid uses with the occurrence of respiratory and cardiovascular adverse effects. hence, as a cautionary approach, it is better to recommend the use of nsaids as the first-line option for managing covid-19 symptoms (302) . the use of corticosteroids in covid-19 patients is still a matter of controversy and requires further systematic clinical studies. the guidelines that were put forward to manage critically ill adults suggest the use of systemic corticosteroids in mechanically ventilated adults with ards (303) . the generalized use of corticosteroids is not indicated in covid-19, since there are some concerns associated with the use of corticosteroids in viral pneumonia. stem cell therapy using mesenchymal stem cells (mscs) is another hopeful strategy that can be used in clinical cases of covid-19 owing to its potential immunomodulatory capacity. it may have a beneficial role in attenuating the cytokine storm that is observed in severe cases of sars-cov-2 infection, thereby reducing mortality. among the different types of mscs, expanded umbilical cord mscs can be considered a potential therapeutic agent that requires further validation for managing critically ill covid-19 patients (304) . repurposed broad-spectrum antiviral drugs having proven uses against other viral pathogens can be employed for sars-cov-2-infected patients. these possess benefits of easy accessibility and recognized pharmacokinetic and pharmacodynamic activities, stability, doses, and side effects (9) . repurposed drugs have been studied for treating cov infections, like lopinavir/ritonavir, and interferon-1␤ revealed in vitro anti-mers-cov action. the in vivo experiment carried out in the nonhuman primate model of clinical microbiology reviews common marmosets treated with lopinavir/ritonavir and interferon beta showed superior protective results in treated animals than in the untreated ones (190) . a combination of these drugs is being evaluated to treat mers in humans (miracle trial) (191) . these two protease inhibitors (lopinavir and ritonavir), in combination with ribavirin, gave encouraging clinical outcomes in sars patients, suggesting their therapeutic values (165) . however, in the current scenario, due to the lack of specific therapeutic agents against sars-cov-2, hospitalized patients confirmed for the disease are given supportive care, like oxygen and fluid therapy, along with antibiotic therapy for managing secondary bacterial infections (192) . patients with novel coronavirus or covid-19 pneumonia who are mechanically ventilated often require sedatives, analgesics, and even muscle relaxation drugs to prevent ventilator-related lung injury associated with human-machine incoordination (122) . the result obtained from a clinical study of four patients infected with covid-19 claimed that combination therapy using lopinavir/ritonavir, arbidol, and shufeng jiedu capsules (traditional chinese medicine) was found to be effective in managing covid-19 pneumonia (193) . it is difficult to evaluate the therapeutic potential of a drug or a combination of drugs for managing a disease based on such a limited sample size. before choosing the ideal therapeutic agent for the management of covid-19, randomized clinical control studies should be performed with a sufficient study population. several classes of routinely used antiviral drugs, like oseltamivir (neuraminidase inhibitor), acyclovir, ganciclovir, and ribavirin, do not have any effect on covid-19 and, hence, are not recommended (187) . oseltamivir, a neuraminidase inhibitor, has been explored in chinese hospitals for treating suspected covid-19 cases, although proven efficacy against sars-cov-2 is still lacking for this drug (7) . the in vitro antiviral potential of fad-approved drugs, viz., ribavirin, penciclovir, nitazoxanide, nafamostat, and chloroquine, tested in comparison to remdesivir and favipiravir (broad-spectrum antiviral drugs) revealed remdesivir and chloroquine to be highly effective against sars-cov-2 infection in vitro (194) . ribavirin, penciclovir, and favipiravir might not possess noteworthy in vivo antiviral actions for sars-cov-2, since higher concentrations of these nucleoside analogs are needed in vitro to lessen the viral infection. both remdesivir and chloroquine are being used in humans to treat other diseases, and such safer drugs can be explored for assessing their effectiveness in covid-19 patients. several therapeutic agents, such as lopinavir/ritonavir, chloroquine, and hydroxychloroquine, have been proposed for the clinical management of covid-19 (299) . a molecular docking study, conducted in the rna-dependent rna polymerase (rdrp) of sars-cov-2 using different commercially available antipolymerase drugs, identified that drugs such as ribavirin, remdesivir, galidesivir, tenofovir, and sofosbuvir bind rdrp tightly, indicating their vast potential to be used against covid-19 (305). a broadspectrum antiviral drug that was developed in the united states, tilorone dihydrochloride (tilorone), was previously found to possess potent antiviral activity against mers, marburg, ebola, and chikungunya viruses (306) . even though it had broad-spectrum activity, it was neglected for an extended period. tilorone is another antiviral drug that might have activity against sars-cov-2. remdesivir, a novel nucleotide analog prodrug, was developed for treating ebola virus disease (evd), and it was also found to inhibit the replication of sars-cov and mers-cov in primary human airway epithelial cell culture systems (195) . recently, in vitro study has proven that remdesivir has better antiviral activity than lopinavir and ritonavir. further, in vivo studies conducted in mice also identified that treatment with remdesivir improved pulmonary function and reduced viral loads and lung pathology both in prophylactic and therapeutic regimens compared to lopinavir/ritonavir-ifn-␥ treatment in mers-cov infection (8) . remdesivir also inhibits a diverse range of coronaviruses, including circulating human cov, zoonotic bat cov, and prepandemic zoonotic cov (195) . remdesivir is also considered the only therapeutic drug that significantly reduces pulmonary pathology (8) . all these findings indicate that remde-sivir has to be further evaluated for its efficacy in the treatment of covid-19 infection in humans. the broad-spectrum activity exhibited by remdesivir will help control the spread of disease in the event of a new coronavirus outbreak. chloroquine is an antimalarial drug known to possess antiviral activity due to its ability to block virus-cell fusion by raising the endosomal ph necessary for fusion. it also interferes with virus-receptor binding by interfering with the terminal glycosylation of sars-cov cellular receptors, such as ace2 (196) . in a recent multicenter clinical trial that was conducted in china, chloroquine phosphate was found to exhibit both efficacy and safety in the therapeutic management of sars-cov-2-associated pneumonia (197) . this drug is already included in the treatment guidelines issued by the national health commission of the people's republic of china. the preliminary clinical trials using hydroxychloroquine, another aminoquinoline drug, gave promising results. the covid-19 patients received 600 mg of hydroxychloroquine daily along with azithromycin as a single-arm protocol. this protocol was found to be associated with a noteworthy reduction in viral load. finally, it resulted in a complete cure (271) ; however, the study comprised a small population and, hence, the possibility of misinterpretation could arise. however, in another case study, the authors raised concerns over the efficacy of hydroxychloroquine-azithromycin in the treatment of covid-19 patients, since no observable effect was seen when they were used. in some cases, the treatment was discontinued due to the prolongation of the qt interval (307) . hence, further randomized clinical trials are required before concluding this matter. recently, another fda-approved drug, ivermectin, was reported to inhibit the in vitro replication of sars-cov-2. the findings from this study indicate that a single treatment of this drug was able to induce an ϳ5,000-fold reduction in the viral rna at 48 h in cell culture. (308) . one of the main disadvantages that limit the clinical utility of ivermectin is its potential to cause cytotoxicity. however, altering the vehicles used in the formulations, the pharmacokinetic properties can be modified, thereby having significant control over the systemic concentration of ivermectin (338) . based on the pharmacokinetic simulation, it was also found that ivermectin may have limited therapeutic utility in managing covid-19, since the inhibitory concentration that has to be achieved for effective anti-sars-cov-2 activity is far higher than the maximum plasma concentration achieved by administering the approved dose (340) . however, ivermectin, being a host-directed agent, exhibits antiviral activity by targeting a critical cellular process of the mammalian cell. therefore, the administration of ivermectin, even at lower doses, will reduce the viral load at a minor level. this slight decrease will provide a great advantage to the immune system for mounting a large-scale antiviral response against sars-cov-2 (341). further, a combination of ivermectin and hydroxychloroquine might have a synergistic effect, since ivermectin reduces viral replication, while hydroxychloroquine inhibits the entry of the virus in the host cell (339) . further, in vivo studies and randomized clinical control trials are required to understand the mechanism as well as the clinical utility of this promising drug. nafamostat is a potent inhibitor of mers-cov that acts by preventing membrane fusion. nevertheless, it does not have any sort of inhibitory action against sars-cov-2 infection (194) . recently, several newly synthesized halogenated triazole compounds were evaluated, using fluorescence resonance energy transfer (fret)-based helicase assays, for their ability to inhibit helicase activity. among the evaluated compounds, 4-(cyclopent-1-en-3-ylamino)-5-[2-(4-iodophenyl) hydrazinyl]-4h-1,2,4-triazole-3-thiol and 4-(cyclopent-1-en-3-ylamino)-5-[2-(4-chlorophenyl) hydrazinyl]-4h-1,2,4-triazole-3-thiol were found to be the most potent. these compounds were used for in silico studies, and molecular docking was accomplished into the active binding site of mers-cov helicase nsp13 (21) . further studies are required for evaluating the therapeutic potential of these newly identified compounds in the management of covid-19 infection. monoclonal antibodies (mabs) may be helpful in the intervention of disease in clinical microbiology reviews cov-exposed individuals. patients recovering from sars showed robust neutralizing antibodies against this cov infection (164) . a set of mabs aimed at the mers-cov s protein-specific domains, comprising six specific epitope groups interacting with receptor-binding, membrane fusion, and sialic acid-binding sites, make up crucial entry tasks of s protein (198, 199) . passive immunization employing weaker and strongly neutralizing antibodies provided considerable protection in mice against a mers-cov lethal challenge. such antibodies may play a crucial role in enhancing protective humoral responses against the emerging covs by aiming appropriate epitopes and functions of the s protein. the cross-neutralization ability of sars-cov rbd-specific neutralizing mabs considerably relies on the resemblance between their rbds; therefore, sars-cov rbd-specific antibodies could cross-neutralized sl covs, i.e., bat-sl-cov strain wiv1 (rbd with eight amino acid differences from sars-cov) but not bat-sl-cov strain shc014 (24 amino acid differences) (200) . appropriate rbd-specific mabs can be recognized by a relative analysis of rbd of sars-cov-2 to that of sars-cov, and cross-neutralizing sars-cov rbd-specific mabs could be explored for their effectiveness against covid-19 and further need to be assessed clinically. the u.s. biotechnology company regeneron is attempting to recognize potent and specific mabs to combat covid-19. an ideal therapeutic option suggested for sars-cov-2 (covid-19) is the combination therapy comprised of mabs and the drug remdesivir (covid-19) (201) . the sars-cov-specific human mab cr3022 is found to bind with sars-cov-2 rbd, indicating its potential as a therapeutic agent in the management of covid-19. it can be used alone or in combination with other effective neutralizing antibodies for the treatment and prevention of covid-19 (202) . furthermore, sars-cov-specific neutralizing antibodies, like m396 and cr3014, failed to bind the s protein of sars-cov-2, indicating that a particular level of similarity is mandatory between the rbds of sars-cov and sars-cov-2 for the cross-reactivity to occur. further assessment is necessary before confirming the effectiveness of such combination therapy. in addition, to prevent further community and nosocomial spread of covid-19, the postprocedure risk management program should not be neglected (309) . development of broad-spectrum inhibitors against the human coronaviral pathogens will help to facilitate clinical trials on the effectiveness of such inhibitors against endemic and emerging coronaviruses (203) . a promising animal study revealed the protective effect of passive immunotherapy with immune serum from mers-immune camels on mice infected with mers-cov (204) . passive immunotherapy using convalescent plasma is another strategy that can be used for treating covid-19-infected, critically ill patients (205) . the exploration of fully human antibodies (human single-chain antibodies; huscfvs) or humanized nanobodies (single-domain antibodies; sdab, vh/vhh) could aid in blocking virus replication, as these agents can traverse the virus-infected cell membranes (transbodies) and can interfere with the biological characteristics of the replicating virus proteins. such examples include transbodies to the influenza virus, hepatitis c virus, ebola virus, and dengue virus (206) . producing similar transbodies against intracellular proteins of coronaviruses, such as papain-like proteases (plpro), cysteinelike protease (3clpro), or other nsps, which are essential for replication and transcription of the virus, might formulate a practical move forward for a safer and potent passive immunization approach for virus-exposed persons and rendering therapy to infected patients. in a case study on five grimly sick patients having symptoms of severe pneumonia due to covid-19, convalescent plasma administration was found to be helpful in patients recovering successfully. the convalescent plasma containing a sars-cov-2specific elisa (serum) antibody titer higher than 1:1,000 and neutralizing antibody titer more significant than 40 was collected from the recovered patients and used for plasma transfusion twice in a volume of 200 to 250 ml on the day of collection (310) . at present, treatment for sepsis and ards mainly involves antimicrobial therapy, source control, and supportive care. hence, the use of therapeutic plasma exchange can be considered an option in managing such severe conditions. further randomized trials can be designed to investigate its efficacy (311) . potent therapeutics to combat sars-cov-2 infection include virus binding molecules, molecules or inhibitors targeting particular enzymes implicated in replication and transcription process of the virus, helicase inhibitors, vital viral proteases and proteins, protease inhibitors of host cells, endocytosis inhibitors, short interfering rna (sirna), neutralizing antibodies, mabs against the host receptor, mabs interfering with the s1 rbd, antiviral peptide aimed at s2, and natural drugs/medicines (7, 166, 186) . the s protein acts as the critical target for developing cov antivirals, like inhibitors of s protein and s cleavage, neutralizing antibodies, rbd-ace2 blockers, sirnas, blockers of the fusion core, and proteases (168) . all of these therapeutic approaches have revealed both in vitro and in vivo anti-cov potential. although in vitro research carried out with these therapeutics showed efficacy, most need appropriate support from randomized animal or human trials. therefore, they might be of limited applicability and require trials against sars-cov-2 to gain practical usefulness. the binding of sars-cov-2 with ace2 leads to the exacerbation of pneumonia as a consequence of the imbalance in the reninangiotensin system (ras). the virus-induced pulmonary inflammatory responses may be reduced by the administration of ace inhibitors (acei) and angiotensin type-1 receptor (at1r) (207) . several investigations have suggested the use of small-molecule inhibitors for the potential control of sars-cov infections. drugs of the fda-approved compound library were screened to identify four small-molecule inhibitors of mers-cov (chlorpromazine, chloroquine, loperamide, and lopinavir) that inhibited viral replication. these compounds also hinder sars-cov and human covs (208) . therapeutic strategies involving the use of specific antibodies or compounds that neutralize cytokines and their receptors will help to restrain the host inflammatory responses. such drugs acting specifically in the respiratory tract will help to reduce virus-triggered immune pathologies in covid-19 (209) . the later stages of coronavirus-induced inflammatory cascades are characterized by the release of proinflammatory interleukin-1 (il-1) family members, such as il-1 and il-33. hence, there exists a possibility that the inflammation associated with coronavirus can be inhibited by utilizing anti-inflammatory cytokines that belong to the il-1 family (92) . it has also been suggested that the actin protein is the host factor that is involved in cell entry and pathogenesis of sars-cov-2. hence, those drugs that modulate the biological activity of this protein, like ibuprofen, might have some therapeutic application in managing the disease (174). the plasma angiotensin 2 level was found to be markedly elevated in covid-19 infection and was correlated with viral load and lung injury. hence, drugs that block angiotensin receptors may have potential for treating covid-19 infection (121) . a scientist from germany, named rolf hilgenfeld, has been working on the identification of drugs for the treatment of coronaviral infection since the time of the first sars outbreak (19) . the sars-cov s2 subunit has a significant function in mediating virus fusion that provides entry into the host cell. heptad repeat 1 (hr1) and heptad repeat 2 (hr2) can interact and form a six-helix bundle that brings the viral and cellular membranes in close proximity, facilitating its fusion. the sequence alignment study conducted between covid-19 and sars-cov identified that the s2 subunits are highly conserved in these covs. the hr1 and hr2 domains showed 92.6% and 100% overall identity, respectively (210) . from these findings, we can confirm the significance of covid-19 hr1 and hr2 and their vital role in host cell entry. hence, fusion inhibitors target the hr1 domain of s protein, thereby preventing viral fusion and entry into the host cell. this is another potential therapeutic strategy that can be used in the management of covid-19. other than the specific therapy directed against covid-19, general treatments play a vital role in the enhancement of host immune responses against the viral agent. inadequate nutrition is linked to the weakening of the host immune response, clinical microbiology reviews making the individual more susceptible. the role played by nutrition in disease susceptibility should be measured by evaluating the nutritional status of patients with covid-19 (205) . for evaluating the potential of vaccines and therapeutics against covs, including sars-cov, mers-covs, and the presently emerging sars-cov-2, suitable animal models that can mimic the clinical disease are needed (211, 212) . various animal models were assessed for sars-and mers-covs, such as mice, guinea pigs, golden syrian hamsters, ferrets, rabbits, nonhuman primates like rhesus macaques and marmosets, and cats (185, (213) (214) (215) (216) (217) (218) . the specificity of the virus to hace2 (receptor of sars-cov) was found to be a significant barrier in developing animal models. consequently, a sars-cov transgenic mouse model has been developed by inserting the hace2 gene into the mouse genome (219) . the inability of mers-cov to replicate in the respiratory tracts of animals (mice, hamsters, and ferrets) is another limiting factor. however, with genetic engineering, a 288-330 ϩ/ϩ mers-cov genetically modified mouse model was developed and now is in use for the assessment of novel drugs and vaccines against mers-cov (220). in the past, small animals (mice or hamsters) have been targeted for being closer to a humanized structure, such as mouse dpp4 altered with human dpp4 (hdpp4), hdpp4-transduced mice, and hdpp4-tg mice (transgenic for expressing hdpp4) for mers-cov infection (221) . the crispr-cas9 gene-editing tool has been used for inserting genomic alterations in mice, making them susceptible to mers-cov infection (222) . efforts are under way to recognize suitable animal models for sars-cov2/covid-19, identify the receptor affinity of this virus, study pathology in experimental animal models, and explore virus-specific immune responses and protection studies, which together would increase the pace of efforts being made for developing potent vaccines and drugs to counter this emerging virus. cell lines, such as monkey epithelial cell lines (llc-mk2 and vero-b4), goat lung cells, alpaca kidney cells, dromedary umbilical cord cells, and advanced ex vivo three-dimensional tracheobronchial tissue, have been explored to study human covs (mers-cov) (223, 224) . vero and huh-7 cells (human liver cancer cells) have been used for isolating sars-cov-2 (194) . recently, an experimental study with rhesus monkeys as animal models revealed the absence of any viral loads in nasopharyngeal and anal swabs, and no viral replication was recorded in the primary tissues at a time interval of 5 days post-reinfection in reexposed monkeys (274) . the subsequent virological, radiological, and pathological observations indicated that the monkeys with reexposure had no recurrence of covid-19, like the sars-cov-2-infected monkeys without rechallenge. these findings suggest that primary infection with sars-cov-2 could protect from later exposures to the virus, which could help in defining disease prognosis and crucial inferences for designing and developing potent vaccines against covid-19 (274). in contrast to their response to the 2002 sars outbreak, china has shown immense political openness in reporting the covid-19 outbreak promptly. they have also performed rapid sequencing of covid-19 at multiple levels and shared the findings globally within days of identifying the novel virus (225) . the move made by china opened a new chapter in global health security and diplomacy. even though complete lockdown was declared following the covid-19 outbreak in wuhan, the large-scale movement of people has resulted in a radiating spread of infections in the surrounding provinces as well as to several other countries. large-scale screening programs might help us to control the spread of this virus. however, this is both challenging as well as time-consuming due to the present extent of infection (226) . the current scenario demands effective implementation of vigorous prevention and control strategies owing to the prospect of covid-19 for nosocomial infections (68) . follow-ups of infected patients by telephone on day 7 and day 14 are advised to avoid any further unintentional spread or nosocomial transmission (312) . the availability of public data sets provided by independent analytical teams will act as robust evidence that would guide us in designing interventions against the covid-19 outbreak. newspaper reports and social media can be used to analyze and reconstruct the progression of an outbreak. they can help us to obtain detailed patient-level data in the early stages of an outbreak (227) . immediate travel restrictions imposed by several countries might have contributed significantly to preventing the spread of sars-cov-2 globally (89, 228) . following the outbreak, a temporary ban was imposed on the wildlife trade, keeping in mind the possible role played by wild animal species in the origin of sars-cov-2/covid-19 (147) . making a permanent and bold decision on the trade of wild animal species is necessary to prevent the possibility of virus spread and initiation of an outbreak due to zoonotic spillover (1) . personal protective equipment (ppe), like face masks, will help to prevent the spread of respiratory infections like covid-19. face masks not only protect from infectious aerosols but also prevent the transmission of disease to other susceptible individuals while traveling through public transport systems (313) . another critical practice that can reduce the transmission of respiratory diseases is the maintenance of hand hygiene. however, the efficacy of this practice in reducing the transmission of respiratory viruses like sars-cov-2 is much dependent upon the size of droplets produced. hand hygiene will reduce disease transmission only if the virus is transmitted through the formation of large droplets (314) . hence, it is better not to overemphasize that hand hygiene will prevent the transmission of sars-cov-2, since it may produce a false sense of safety among the general public that further contributes to the spread of covid-19. even though airborne spread has not been reported in sars-cov-2 infection, transmission can occur through droplets and fomites, especially when there is close, unprotected contact between infected and susceptible individuals. hence, hand hygiene is equally as important as the use of appropriate ppe, like face masks, to break the transmission cycle of the virus; both hand hygiene and face masks help to lessen the risk of covid-19 transmission (315) . medical staff are in the group of individuals most at risk of getting covid-19 infection. this is because they are exposed directly to infected patients. hence, proper training must be given to all hospital staff on methods of prevention and protection so that they become competent enough to protect themselves and others from this deadly disease (316) . as a preventive measure, health care workers caring for infected patients should take extreme precautions against both contact and airborne transmission. they should use ppe such as face masks (n95 or ffp3), eye protection (goggles), gowns, and gloves to nullify the risk of infection (299) . the human-to-human transmission reported in sars-cov-2 infection occurs mainly through droplet or direct contact. due to this finding, frontline health care workers should follow stringent infection control and preventive measures, such as the use of ppe, to prevent infection (110) . the mental health of the medical/health workers who are involved in the covid-19 outbreak is of great importance, because the strain on their mental well-being will affect their attention, concentration, and decision-making capacity. hence, for control of the covid-19 outbreak, rapid steps should be taken to protect the mental health of medical workers (229) . since the living mammals sold in the wet market are suspected to be the intermediate host of sars-cov-2, there is a need for strengthening the regulatory mechanism for wild animal trade (13) . the total number of covid-19 confirmed cases is on a continuous rise and the cure rate is relatively low, making disease control very difficult to achieve. the chinese government is making continuous efforts to contain the disease by taking emergency control and prevention measures. they have already built a hospital for patients affected by this virus and are currently building several more for accommodating the continuously increasing infected population (230) . the effective control of sars-cov-2/covid-19 requires high-level interventions like intensive contact tracing, as well as the quarantine of people with suspected infection and the isolation of infected individuals. the implementation of rigorous control and preventive measures together might control the r 0 number and reduce the transmission risk (228) . clinical microbiology reviews considering the zoonotic links associated with sars-cov-2, the one health approach may play a vital role in the prevention and control measures being followed to restrain this pandemic virus (317) (318) (319) . the substantial importation of covid-19 presymptomatic cases from wuhan has resulted in independent, self-sustaining outbreaks across major cities both within the country and across the globe. the majority of chinese cities are now facing localized outbreaks of covid-19 (231) . hence, deploying efficient public health interventions might help to cut the spread of this virus globally. the occurrence of covid-19 infection on several cruise ships gave us a preliminary idea regarding the transmission pattern of the disease. cruise ships act as a closed environment and provide an ideal setting for the occurrence of respiratory disease outbreaks. such a situation poses a significant threat to travelers, since people from different countries are on board, which favors the introduction of the pathogen (320). although nearly 30 cruise ships from different countries have been found harboring covid-19 infection, the major cruise ships that were involved in the covid-19 outbreaks are the diamond princess, grand princess, celebrity apex, and ruby princess. the number of confirmed covid-19 cases around the world is on the rise. the success of preventive measures put forward by every country is mainly dependent upon their ability to anticipate the approaching waves of patients. this will help to properly prepare the health care workers and increase the intensive care unit (icu) capacity (321) . instead of entirely relying on lockdown protocols, countries should focus mainly on alternative intervention strategies, such as large-scale testing, contract tracing, and localized quarantine of suspected cases for limiting the spread of this pandemic virus. such intervention strategies will be useful either at the beginning of the pandemic or after lockdown relaxation (322) . lockdown should be imposed only to slow down disease progression among the population so that the health care system is not overloaded. the reproduction number (r 0 ) of covid-19 infection was earlier estimated to be in the range of 1.4 to 2.5 (70); recently, it was estimated to be 2.24 to 3.58 (76) . compared to its coronavirus predecessors, covid-19 has an r 0 value that is greater than that of mers (r 0 ͻ 1) (108) but less than that of sars (r 0 value of 2 to 5) (93) . still, to prevent further spread of disease at mass gatherings, functions remain canceled in the affected cities, and persons are asked to work from home (232) . hence, it is a relief that the current outbreak of covid-19 infection can be brought under control with the adoption of strategic preventive and control measures along with the early isolation of subsequent cases in the coming days. studies also report that since air traffic between china and african countries increased many times over in the decade after the sars outbreak, african countries need to be vigilant to prevent the spread of novel coronavirus in africa (225) . due to fear of virus spread, wuhan city was completely shut down (233) . the immediate control of the ongoing covid-19 outbreaks appears a mammoth task, especially for developing countries, due to their inability to allocate quarantine stations that could screen infected individuals' movements (234) . such underdeveloped countries should divert their resources and energy to enforcing the primary level of preventive measures, like controlling the entry of individuals from china or countries where the disease has flared up, isolating the infected individuals, and quarantining individuals with suspected infection. most of the sub-saharan african countries have a fragile health system that can be crippled in the event of an outbreak. effective management of covid-19 would be difficult for low-income countries due to their inability to respond rapidly due to the lack of an efficient health care system (65) . controlling the imported cases is critical in preventing the spread of covid-19 to other countries that have not reported the disease until now. the possibility of an imported case of covid-19 leading to sustained human-to-human transmission was estimated to be 0.41. this can be reduced to a value of 0.012 by decreasing the mean time from the onset of symptoms to hospitalization and can only be made possible by using intense disease surveillance systems (235) . the silent importations of infected individuals (before the manifestation of clinical signs) also contributed significantly to the spread of disease across the major cities of the world. even though the travel ban was implemented in wuhan (89) , infected persons who traveled out of the city just before the imposition of the ban might have remained undetected and resulted in local outbreaks (236) . emerging novel diseases like covid-19 are difficult to contain within the country of origin, since globalization has led to a world without borders. hence, international collaboration plays a vital role in preventing the further spread of this virus across the globe (237) . we also predict the possibility of another outbreak, as predicted by fan et al. (6) . indeed, the present outbreak caused by sars-cov-2 (covid-19) was expected. similar to previous outbreaks, the current outbreak also will be contained shortly. however, the real issue is how we are planning to counter the next zoonotic cov epidemic that is likely to occur within the next 5 to 10 years or even sooner (fig. 7) . several years after the global sars epidemic, the current sars-cov-2/covid-19 pandemic has served as a reminder of how novel pathogens can rapidly emerge and spread through the human population and eventually cause severe public health crises. further research should be conducted to establish animal models for sars-cov-2 to investigate replication, transmission dynamics, and pathogenesis in humans. this may help develop and evaluate potential therapeutic strategies against zoonotic cov epidemics. present trends suggest the occurrence of future outbreaks of covs due to changes in the climate, and ecological conditions may be associated with humananimal contact. live-animal markets, such as the huanan south china seafood market, represent ideal conditions for interspecies contact of wildlife with domestic birds, pigs, and mammals, which substantially increases the probability of interspecies transmission of cov infections and could result in high risks to humans due to adaptive genetic recombination in these viruses (323) (324) (325) . the covid-19-associated symptoms are fever, cough, expectoration, headache, and myalgia or fatigue. individuals with asymptomatic and atypical clinical manifestations were also identified recently, further adding to the complexity of disease transmission dynamics. atypical clinical manifestations may only express symptoms such as fatigue instead of respiratory signs such as fever, cough, and sputum. in such cases, the clinician must be vigilant for the possible occurrence of asymptomatic and atypical clinical manifestations to avoid the possibility of missed diagnoses. the present outbreak caused by sars-cov-2 was, indeed, expected. similar to clinical microbiology reviews previous outbreaks, the current pandemic also will be contained shortly. however, the real question is, how are we planning to counter the next zoonotic cov epidemic that is likely to occur within the next 5 to 10 years or perhaps sooner? our knowledge of most of the bat covs is scarce, as these viruses have not been isolated and studied, and extensive studies on such viruses are typically only conducted when they are associated with specific disease outbreaks. the next step following the control of the covid-19 outbreak in china should be focused on screening, identification, isolation, and characterization of covs present in wildlife species of china, particularly in bats. both in vitro and in vivo studies (using suitable animal models) should be conducted to evaluate the risk of future epidemics. presently, licensed antiviral drugs or vaccines against sars-cov, mers-cov, and sars-cov-2 are lacking. however, 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origin and continuing evolution of sars-cov-2 covid-19: the race for a vaccine all authors substantially contributed to the conception, design, analysis, and interpretation of data and checking and approving the final version of the manuscript, and we agree to be accountable for its contents.this compilation is a review article written, analyzed, and designed by its authors and required no substantial funding to be developed.all authors declare that there are no existing commercial or financial relationships that could, in any way, lead to a potential conflict of interest. with 25 years of research and teaching experience in the areas of microbiology, immunology, virology, public health, medicine, and biomedicine as an eminent researcher, he has developed several diagnostics, vaccines, immunomodulatory modules, and hypotheses to counter infectious diseases of animals, poultry, and public health concerns. he has to his credit 600 publications, 6 books, and 65 book chapters. dr. dhama has been recognized as an extremely productive researcher in the journal nature. he has been honored with 50 best paper awards and other recognitions. he is an naas (national academy of agricultural science, india) associate and has worked as nodal officer, wto, and member, wildlife health specialist group (iucn). he is actively serving as editor-in-chief, co-eic, editor, and member, editorial board, of nearly 20 scientific journals. his google scholar h-index is 47 and scopus h-index is 31. sharun khan, m.v.sc., is currently working as a researcher in the stem cell laboratory, division of surgery, icar-indian veterinary research institute, izatnagar, india. his area of interest is regenerative medicine with a focus on understanding cell biology and molecular pathways involved in the maintenance and differentiation of stem cells originating from different tissues. he has particular interest and knowledge in the fields of veterinary medicine, pharmacology, infectious diseases of animals, wildlife diseases, diagnosis and therapy of animal diseases, nutrition, and biomedicine. with excellent academic records, he has received awards and recognitions (fellowships and scholarships) and participated in national and international workshops, training programs, and courses. he has a keen interest in learning excellent scientific writing skills and has published 30 papers, including in international journals of repute. he is highly enthusiastic about gaining knowledge of advancements in educational and scientific research areas.ruchi tiwari is currently working as assistant professor in the department of veterinary microbiology, college of veterinary sciences, duvasu, mathura, india. she is currently pursuing her ph.d. (hons) degree from duvasu. with an excellent academic record and 10 years of research and teaching experience, she has expertise in the field of diagnosis, prevention, and control of important livestock/poultry diseases/pathogens having public health significance, along with particular reference to veterinary microbiology, immunology, ethnoveterinary medicine, alternative and complementary therapies, and bacteriophage therapy. dr. tiwari has published 150 research/review articles and 5 book chapters. she has been honored with the young scientist award, best paper awards (10) key: cord-314311-xbpb9nfi authors: ge, huipeng; wang, xiufen; yuan, xiangning; xiao, gong; wang, chengzhi; deng, tianci; yuan, qiongjing; xiao, xiangcheng title: the epidemiology and clinical information about covid-19 date: 2020-04-14 journal: eur j clin microbiol infect dis doi: 10.1007/s10096-020-03874-z sha: doc_id: 314311 cord_uid: xbpb9nfi in december 2019, pneumonia of unknown cause occurred in wuhan, hubei province, china. on 7 january 2020, a novel coronavirus, named as severe acute respiratory syndrome coronavirus-2 (sars-cov-2), was identified in the throat swab sample of one patient. the world health organization (who) announced the epidemic disease caused by sars-cov-2 as coronavirus disease 2019 (covid-19). currently, covid-19 has spread widely around the world, affecting more than seventy countries. china, with a huge burden of this disease, has taken strong measures to control the spread and improve the curative rate of covid-19. in this review, we summarized the epidemiological characteristics, clinical features, diagnosis, treatment, and prognosis of covid-19. a comprehensive understanding will help to control the disease. at the end of 2019, several cases of pneumonia with unknown etiology emerged in wuhan, hubei province, china [1] [2] [3] . the pneumonia spread quickly to other provinces of china and overseas. at early stage, it was reported that most patients had the contact history with huanan seafood market [1] [2] [3] . after that, more and more patients had fever and cough symptoms. on 7 january 2020, a novel coronavirus was identified in the throat swab sample of one patient by the chinese center for disease control and prevention (cdc), and was subsequently named as 2019ncov by world health organization (who) [1, 2] . as the situation got worse, the who declared the outbreak as the public health emergency of international concern (pheic) [4] . on 11 february 2020, the international committee on taxonomy of viruses renamed the virus as severe acute respiratory syndrome coronaviruse-2(sars-cov-2) [5] . and who announced the epidemic disease caused by sars-cov-2 as coronavirus disease 2019 (covid-19) [6] . this is the third coronavirus pneumonia in the past 20 years around the world. in november 2002, a novel betacoronavirus called severe acute respiratory syndrome coronavirus (sars-cov) emerged in guangdong, china, and resulted in more than 8000 infections and 774 deaths in 37 countries. in 2012, middle east respiratory syndrome coronavirus (mers-cov), which was first detected in saudi arabia, affected 2494 individuals and caused 858 fatalities [7, 8] . after the outbreak of covid-19, the chinese government has initiated a level-1 public health response to prevent the spread of the disease on 26 january 2020 [9] . as of 24:00 on 3 march 2020 (beijing time), the sars-cov-2 has resulted in 80,270 laboratory and clinical confirmed cases in the mainland of china, and 2981 patient deaths [10] . currently, there are many studies of sars-cov-2 and covid-19. this review makes a comprehensive introduction about this disease, including the genome structure and receptor of sars-cov-2, epidemiology, clinical features, diagnosis, treatment, and prognosis of covid-19. we hope our work can provide more information in understanding this disease, and more research findings are needed to help to limit spread of the disease and to invent vaccine and specific drugs. huipeng ge and xiufen wang contributed equally to this work. about two thirds of the overall genome, encoding 16 nonstructural proteins (nsps), while the remaining one-third encodes accessory proteins and structural proteins [12, 16] . as shown in fig. 1 , there are some slight differences in the reported genome structure, mainly in accessory proteins [7, 12, 15, [17] [18] [19] . for example, the significant difference of two accessory proteins (orf3b and orf8) on the gene sequence between sars-cov-2 and sars-cov was reported by several studies [12, 16] . using the different genome sequences as comparison can partly account for the results. as for the novel proteins of sars-cov-2, whether involving in pathogenesis of the virus or not is unclear. inspired by the pathogenesis of sars-cov, the sars-cov-2 was presumed to infect the human cells by spike glycoprotein binding to its cellular receptor, angiotensinconverting enzyme 2 (ace2). in fact, current evidence supports this idea. as for the spike protein of sars-cov-2, it contains two regions, s1 subunit and s2 subunit, which consists of 1253 amino acids [20] . the amino acid identity of spike protein between sars-cov-2 and sars-cov was about 75% [21, 22] . generally, s1 domain is linked to receptor binding; s2 domain is linked to cell membrane fusion. similar to sars-cov, s1 contains the n-terminal domain (ntd) and a receptor-binding domain (rbd) which contains core domain and external subdomain (esd). s2 contains three functional domains, fusion peptide (fp), and heptad repeat (hr) 1 and 2 (fig. 1) . whether sars-cov-2 can combine with host cells or not is determined by the affinity between the viral rbd and ace2 of human cells [22] . once rbd binds to the receptor, the s2 changes conformation to facilitate the membrane fusion by three functional domains. although sars-cov is not the closest to sars-cov-2 at the wholegenome level, the rbd of sars-cov-2 is closer to that of [7, 12, 15, [17] [18] [19] . orf = open reading frame (orange). structural proteins including s, e, m, n (blue) (s = spike, e = envelope, m = membrane, n = nucleocapsid). accessory proteins including 3, 3a, 3b, 6, 7, 8, 9a, 9b, 10b, 13, 14 (purple). sp = signal peptide. s1 = subunit 1. s2 = subunit 2. ntd = n-terminal domain. rbd = receptor binding domain. esd = external subdomain. fp = fusion peptide. hr1 = heptad repeat 1. hr2 = heptad repeat 2. tm = transmembrane domain. cp = cytoplasmic domain. the length of genes is not drawn in scale sars-cov, and 72-74.9% amino acid sequences of rbd in both are identical [7, 19, 23] . several critical residues in sars-cov-2 rbd have good interactions with human ace2. most residues of rbd interacting with ace2 are fully conserved [22, 24] . as for function domains of s2, there is no difference between sars-cov-2 and sars-cov except some non-critical amino acids in hr1 region [22] . another strong piece of evidence supporting ace2 as a receptor of cells is that hr1 and hr2 domain of sars-cov-2 can fuse with each other to form 6-hb following sars-cov's fusion mechanism [25] . despite this, several studies speculated sars-cov-2 has less affinity with ace2 than sars-cov [20, 21, 26] . on the contrary, chen et al. [23] reported sars-cov-2 provided a stronger interaction with ace2 than sars-cov by structure analysis of the receptor binding of sars-cov-2. by elucidating cryo-em structure of sars-cov-2 spike protein, wrapp et al. [27] also found that compared with sars-cov, sars-cov-2 bound to ace2 with 10-to 20fold higher affinity. in order to identify the suppose of entering cellular by ace2, peng et al. [28] found that sars-cov-2 was able to use ace2 protein of many kinds of cells, including human cells, as an entry receptor in the ace2-expressing cells, but not cells without ace2. it also could not use aminopeptidase n and dipeptidyl peptidase which are other coronaviruses' receptors. in most recent studies, the results provided direct evidence to support ace2 as the receptor. yan et al. [29] reported the ace2-b 0 at1 (a neutral amino acid transporter) complex can combine with two spike proteins by structural modeling in a structure analysis of fulllength human ace2, and the extracellular peptidase domain (pd) of ace2 has the direct interaction with polar residues of rbd [29, 30] . overall, there is sufficient evidence to support that sars-cov-2 infects cells by using the human ace2. as the cryo-em structure of spike protein and human ace2 were revealed successfully, we have more opportunity to clarify the detailed process of entering cells [27, 29, 30] . in early studies, 49-66% patients had the contact history of huanan seafood market, where various kinds of living wild animals were on sale, including poultry, bats, and marmots [1, 2, 31] . it is currently speculated that the outbreak of covid-19 in wuhan is associated with wild animals. according to who, the environmental samples taken from huanan seafood market were tested positive for sars-cov-2 [21] , but the specific animals associated with the virus have not been identified. based on previous evidence, the bats, the host of more than 30 coronaviruses [32] , may be the origin of covid-19. the bats are the natural reservoir of sars-cov and mers-cov, and spread to human through the palm civets and dromedary camels, respectively [8] . the ratg13, which is a short rna-dependent rna polymerase (rdrp) region from a bat coronavirus, was closest to sars-cov-2 with 96.2-98.7% identity in whole-genome sequence [11, 15, 16, 28] . the other two bat-derived sars-like coronaviruses, bat-sl-covzxc21 and bat-sl-covzc45, were closer to sars-cov-2 than sars-covand mers-cov, which have approximately 88% nucleotide identity [7, [15] [16] [17] [18] . as for the intermediate hosts of sars-cov-2, recent studies suggested pangolins were the most probable animal. two sub-lineages of sars-cov-2 were found in organs of pangolins obtained from anti-smuggling activities in guangdong and guangxi province of china by metagenomic sequence [33] . xiao et al. [34] reported the sars-cov-2 was derived from the reorganization of pangolin-cov-like virus and a bat-cov-ratg13-like virus. however, the pangolin may not be the only intermediate reservoir, because sars-cov-2 was not originated from pangolin-cov-like virus directly, which was demonstrated by the molecular and phylogenetic analyses in liu's study [35] . to sum up, the bats are the most probable original reservoir based on the current evidence. however, it is notable that wuhan huanan seafood market may not be the only source of sars-cov-2 spreading globally. cohen pointed out wuhan huanan seafood market was not the only origin of sars-cov-2 by analyzing the epidemiology of 41 cases in the earliest study [36] . pangolins may act as one of intermediate hosts. more work is needed to provide more precise information about original reservoir and intermediate hosts of sars-cov-2. table 1 lists some information of studies about the genome sequence identity with sars-cov-2. transmissibility is an important factor of an epidemic [37] . data as reported by 10 am cet on 3 march 2020, sars-cov-2 has been responsible for 90,870 confirmed cases with 3112 (3.4%) deaths around the world [38] . the reported median age of patients was ranged from 41 to 57 years [1, 2, 39] . male made up the majority of patients with the proportion of 50-75% [1] [2] [3] 39] . due to different data sources, the infection rate of medical staff has a huge difference, with 2.1-29% [3, 40] . approximately 25.2-50.5% sars-cov-2infected patients had one or more underlying diseases (table 2) , including hypertension, diabetes, chronic obstructive pulmonary disease, cardiovascular disease, and malignancy [1-3, 39, 41] . the covid-19's median incubation period from exposure to illness onset was 3.0 days in a 1099-case cohort and 4.0 days in a 62-case cohort [39, 41] . it was also reported the longest incubation period was 24 days [41] . the percentage of patients exposed to huanan seafood market varies between 8.7% and 66% [1] [2] [3] 42] . patients with no contact history of huanan seafood market and medical staff infection [18, 21, 43] indicated human-to-human transmission mainly via droplets from coughing or sneezing or direct contact [18, [44] [45] [46] [47] . in addition, several studies reported fecal-mouth pathway may also be a potential way for the transmission of sars-cov-2 [23, 48] , and the sars-cov-2 was also isolated from urine of a patient in a recent new [49] . but it is unclear whether humanto-human transmission can be implemented by the above routes. the basic reproduction number r0, the important property of transmission, is commonly used to estimate the average number of secondary cases generated by an infectious case in a fully susceptible population during the early phase of the outbreak [37, 50] . if the r0 is more than 1, human-tohuman transmission may persist. a range from 1.4 to 6.49 of r0 was estimated by various methods [44, [51] [52] [53] . the different values of estimated r0 can attribute to different data and different modeling methods [53] . liu et al. [53] came to conclusion that the average of estimate r0 was 3.28 with a median of 2.79 by an analysis of 12 studies. so, around 2-3 is indeed a reliable range, suggesting the potential of sustained human-to-human transmission [50, 53] . additionally, so many factors can affect the value of r0, including estimation period, utilized models, and datasets [54] . as various aspects of measures have taken effect, the estimated r0 is mutable. as david said, it is impossible to know what will happen so early in this sars-cov-2 epidemic [37] . the initial r0 estimation for sars-cov was more than 2.0, but the predicted large outbreak did not occur [8, 37] . it is also notable that asymptomatic patients can also be a source of infection [43, 48] . the super communicator is worthy of notice, who can infect more than 100 individuals [52] . the immediate priority is to clarify all potential routes of transmission. after all, superspreading has a huge impact on the epidemic. anyway, it is necessary for us to take effective measures and keep alert to control the epidemic. fortunately, the number of confirmed cases maintains at a lower level in mainland of china with 119 confirmed cases on 3 march 2020 [10] . at this critical period, it is apparently wise to continue taking steps to control the outbreak. the clinical manifestations of sars-cov-2-infected patients ranged from mild non-specific symptoms to severe pneumonia with organ function damage. the common symptoms were fever (77.4-98.6%), cough (59.4-81.8%), fatigue (38.1-69.6%), dyspnea (3.2-55.0%), myalgia (11.1-34.8%), sputum production (28.2-56.5%), and headache (6.5-33.9%) [1-3, 39, 41] (table 2 ). sore throat, rhinorrhea, chest pain, hemoptysis, conjunctival congestion, diarrhea, nausea, and vomiting were less common [1-3, 39, 41] . but one study showed 39.6% of 140 confirmed covid-19 patients had gastrointestinal symptoms [40] , and 10.1% patients presented with gastrointestinal discomfort at onset in wang's study [3] . patients did not necessarily have fever at onset, some patients developed after hospitalization [41] , and some severe patients even did not have fever. sars-cov-2, sars-cov, and mers-cov infections share many similar clinical symptoms [8] , including fever, cough, myalgia, and dyspnea. however, patients with sars and mers have more gastrointestinal involvement (about one-third) than covid-19 patients [55] . and mers has a high incidence of renal failure, which is a typical characteristic not often found in other human coronavirus infections [56, 57] . of confirmed patients, 35.3-82.1%, 5.0-36.2%, and 9.1-33.7% had lymphopenia, thrombocytopenia, and leukopenia, respectively [1-3, 39, 41] ( table 2) . c-reactive protein (crp), erythrocyte sedimentation rate (esr), serum ferritin, and interleukin-6 (il6) elevated prominently in chen's research [2] . many patients also had increased levels of d-dimer, lactate dehydrogenase (ldh), creatine kinase (ck), prolonged prothrombin time, alanine aminotransferase (alt), and aspartate aminotransferase (ast) [1-3, 39, 41, 58] . however, elevated levels of procalcitonin, troponin i, and creatinine were uncommon [1, 39, 41] . the typical imaging features of chest computed tomography (ct) for novel coronavirus pneumonia (ncp) included ground-glass opacity, bilateral patchy shadows, and subsegmental areas of consolidation, sometimes with a rounded morphology and a peripheral lung distribution [1-3, 40, 41, 59] . changes in the disease were accompanied by changes in ct imaging, reflecting the severity of the disease [58] . pan et al. [60] analyzed 21 ncp patients from initial diagnosis until recovery (without severe respiratory distress during a hospital stay), and they found chest ct scan showed that the lung abnormalities were the most severe about 10 days after the initial symptoms onset. overall, the ct manifestations of ncp were diverse and fast-changing [61] . however, a normal chest ct image cannot exclude the diagnosis of sars-cov-2 infection [62] . by obtaining biopsy samples at autopsy of one covid-19 patient [63] , the lung biopsy specimens showed bilateral diffuse alveolar damage with cellular fibromyxoid exudates. bilateral lung tissue indicated pulmonary edema with hyaline membrane formation, reflecting ards. meanwhile, flow cytometric analysis of peripheral blood suggested the reduced counts of peripheral cd4 and cd8 t cells but a hyperactivated status. a report on systemic anatomy at autopsy from the other patient [64] indicated gray white patchy lesions in lungs, gray white viscous fluid overflow in the lung section, and pulmonary fiber bands, reflecting that covid-19 caused an inflammatory response characterized by deep airway and alveolar damage. the pathological results of the first one resembled those seen in sars-cov and mers-cov infection [63] . however, the latter found pulmonary fibrosis and consolidation were less severe than sars, but exudation was more obvious [64] . these findings, with more pathological ards, acute respiratory distress syndrome; crp, c-reactive protein; ldh, lactose dehydrogenase; ck, creatinine kinase; alt, alanine aminotransferase; ast, aspartate aminotransferase; esr, erythrocyte sedimentation rate research, will make a great importance in understanding the pathogenesis and making therapeutic strategy for covid-19. the covid-19 patients around the world were diagnosed based on world health organization interim guidance [65] , and china updated the novel coronavirus pneumonia diagnosis and treatment program (trial version) (in chinese) according to epidemic situation and improved awareness of disease. a laboratory confirmed case with sars-cov-2 infection was defined as a positive result to high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rt-pcr) assay for sars-cov-2 [65, 66] . chest ct, as a diagnostic method for covid-19 with a high sensitivity, is being given more important value for diagnosis [67] . in the fifth trial version of novel coronavirus pneumonia diagnosis and treatment program (in chinese) [68] , clinical diagnosis was proposed for cases in hubei province, who had epidemiology history, the above clinical features along with typical chest ct imaging. and more than 10,000 patients for clinical diagnosis got early treatment [69] . the sixth trial version (in chinese) removed the clinical diagnosis, for reduced suspected cases and improved nucleic acid detection capability [66] . in several clinical studies of confirmed cases, strategies for covid-19 patients included antiviral treatment, empirical antibiotic treatment, corticosteroid, intravenous immunoglobulin therapy, oxygen support (nasal cannula, mask oxygen inhalation, non-invasive ventilation, invasive mechanical ventilation), continuous renal replacement therapy (crrt), and extracorporeal membrane oxygenation (ecmo) [1-3, 39, 41] . due to the absence of clinical evidence, there were no approved drugs for antiviral therapy against sars-cov-2. of three clinical cohort studies, oseltamivir was used for antiviral therapy in 35.8% (393/1099) patients, 89.9% (124/138) patients, and 92.7% (38/41) patients, respectively [1, 2, 41] . another research [2] included 99 covid-19 patients, in which 76.0% patients received antiviral treatment, including oseltamivir, ganciclovir, and lopinavir and ritonavir tablets, and the duration of antiviral treatment was 3-14 days. though oseltamivir had high application rate in the early cohort studies, its drug efficacy on covid-19 was not obvious, and the sixth trial version of novel coronavirus pneumonia diagnosis and treatment program (in chinese) did not recommend it [66] . case report implied that lopinavir and ritonavir therapy may be beneficial for covid-19 cases [70, 71] . remdesivir, a nucleotide analogue rna polymerase inhibitor with broad-spectrum antiviral activity, was demonstrated that it could be against ebola virus in rhesus monkeys [72] . wang et al. [73] found that remdesivir and chloroquine were highly effective in the control of sars-cov-2 infection in vitro. what's more, the first reported covid-19 case of the usa was cured by intravenous remdesivir [58] and other supportive care. more researches from cells, animals, and clinical need to explore the effect of remdesivir on sars-cov-2. other methods of antiviral drug administration may also have some certain function. it was reported that different combinations of interferon alpha inhalation, lopinavir/ritonavir, and arbidol may have some effects [39] . furthermore, combined chinese and western medicine treatment, including lopinavir/ ritonavir, arbidol, and shufeng jiedu capsule (a traditional chinese medicine) may also be beneficial to treatment which deserved further study [74] . as for the corticosteroid therapy for sars-cov-2, current interim guidance from who on clinical management of severe acute respiratory infection, when sars-cov-2 infection is suspected (released jan 28, 2020), suggests not routinely using systemic corticosteroids unless indicated for another reason [65] , and there were contradictory opinions from professors [75, 76] . corticosteroid therapy was used in approximately 20-44.9% covid-19 patients [1-3, 39, 41] . compared with non-severe patients, severe patients got more corticosteroid therapy (44.5% vs. 13.7%) with the median of maximal daily dose up to 30.0 (1.0-40.0) (mg/kg) [41] . according to pathological findings of one covid-19 patient, proper use of corticosteroid together with other support care should be considered for the severe patients to prevent ards development [63] . there are more than 80 running or pending clinical trials on potential treatments for covid-19 in china [77] . studies of recombinant human angiotensin-converting enzyme 2 (rhace2), mesenchymal stem cell, pd-1 blocking antibody, bevacizumab injection, and immunoglobulin of cured patients are registered in the website of clinical trial [78] , and some are recruiting patients. safe and effective clinical trials will find more therapeutic possibilities for covid-19 patients. many patients infected withsars-cov-2, especially for severe patients, had complications (table 2) , including ards, shock, acute renal injury, acute cardiac injury, and secondary infection [1] [2] [3] 41] . the mortality rate of covid-19 ranged from 0 to 14.6% [1-3, 39, 41, 79] . however, yang et al. [42] reported 32 of 52 (61.5%) critically ill adult icu patients had died at 28 days. it is not hard to know the disease severity is an independent predictor of poor prognosis [41, 42] . compared with non-icu patients, the icu patients were older with a greater number of comorbid conditions and had more common symptoms of dyspnea, abdominal pain, and anorexia [3] . meanwhile, it was reported that icu patients had higher plasma cytokine and chemokine levels of il2, il7, il10, gscf, ip10, mcp1, mip1a, and tnfî± [1] . non-survivors had more severe lymphopenia and higher blood cell counts, neutrophil counts, d-dimer and fibrin degradation product than survivors [3, 63] . wang et al. [80] analyzed the first 17 deaths up to 22 january 2020, announced by the china national health commission found that the median days from first symptom to death were 14.0 (range 6-41) days, and seemed to be shorter among old people [80] . in yang's study [42] , the survival time of the non-survivors is likely to be within 1-2 weeks after icu admission. in summary, severe patients or icu patients have a relatively higher mortality [41, 42] . age, comorbidity, some symptoms (dyspnea, abdominal pain, etc.), and more prominent laboratory abnormalities (lymphopenia, elevated d-dimer, etc.) may be risk factors for poor outcome [3, 40, 42, 80] . according to the latest data released at 24:00 on 3 march 2020 (beijing time), the fatality is 3.7% and 4.6% for the mainland of china and wuhan, hubei province, respectively [10] . overall, sars-cov-2 has a relatively lower mortality rate than sars-cov and mers-cov (9.6% and 40.0%, respectively) [55] . covid-19 has spread to 73 countries, territories, or areas around the world, and is responsible for 90,870 patients as of 10 am cet on 3 march 2020. the virus may be related to bats, but wuhan huanan seafood market may not be its sole origin. whatever the case, banning of wildlife sales and removing them from wet markets are beneficial to control the epidemic. except several genes of accessory proteins, sars-cov-2 is almost identical to sars-cov in genome organization. hence, we obtain the fact that ace2 is the receptor of sars-cov-2 entering cells. human to human transmission can be realized mainly by droplets from coughing or sneezing or direct contact. fever and cough are the main symptoms. chest ct examination is an important tool for diagnosis, and confirmed cases are diagnosed by detecting sars-cov-2 of specimens taken from the upper respiratory tract and lower respiratory tract. as for the treatment, there are no specific drugs for the infection, and many therapies, with preliminary good clinical response, are being tested in clinical trials. we hope that increased awareness of the virus and ongoing clinical trials can help to find effective treatment against sars-cov-2. though the fatality of sars-cov-2 is lower than sars-cov and mers-cov, the overall mortality of sars-cov-2 remains to be established in the future, because a large number of confirmed and suspected cases are still in hospital; even worse, the confirmed cases are increasing in other countries, like korea and japan. further study is necessary for us to control this epidemic disease. authors' contribution huipeng ge, xiufen wang: manuscript writing, bibliographic retrieval, making tables and figure. xiangning yuan, gong xiao, chengzhi wang, tianci deng: manuscript writing. qiongjing yuan, xiangcheng xiao: manuscript editing and critical review. conflict of interest all authors declared that they had no conflicts of interest. clinical features of patients infected with 2019 novel coronavirus in wuhan epidemiological and clinical 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2019-ncov lung injury more than 80 clinical trials launch to test coronavirus treatments accessed 2 abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia updated understanding of the outbreak of 2019 novel coronavirus (2019-ncov) in wuhan publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations key: cord-320955-xhp96abg authors: allam, zaheer title: the first 50 days of covid-19: a detailed chronological timeline and extensive review of literature documenting the pandemic date: 2020-07-24 journal: surveying the covid-19 pandemic and its implications doi: 10.1016/b978-0-12-824313-8.00001-2 sha: doc_id: 320955 cord_uid: xhp96abg this chapter surveys the global unfolding of events during the first 50 days of the covid-19 pandemic in china. an extensive review of literature from both academic and popular sources provides a daily overview of the situation covering health, economic, political, and social perspectives and outlines the major course of actions. this chapter surveys, and lays, the chronological timeline of the outbreak, health policy, deaths, recovery, and socioeconomic measures and provides a factual narrative on the unfolding of the pandemic and, while doing so, underlines major milestones and contradictory findings and beliefs on the subject. this supports the perception that data collection varied between research groups, organizations, and national bodies, which later fueled differing viewpoints and policies for combatting the outbreak. the covid-19 pandemic took the world by surprise and unfolded extremely rapidly. it began relatively slower, and only a little is documented on its actual first case, with claims as from november, while others links it to on december 1. besides not knowing when it began, there was also very little known on the many issues about the virus, including its mode of transmission, its incubation time, and the medication the vaccination, among many other elements. even to date, at the time of writing, there still remain some gray areas about the virus including its origin and whether it could have permanent impacts on patients, and whether it is possible for patients to develop immunity, among many other areas that are still being looked into. following these uncertainties, there had been numerous health policies with a number of those being rendered ineffective as more knowledge about the virus is revealed. for instance, at the beginning, the world health organization (who) advised that masks should only be worn by health professionals or patients while in hospital, but later on, after it established that there were possibilities of human-to-human transmission, it became apparent that everyone need to wear a mask while in public to prevent transmitting or contracting the virus. however, while the impacts of the virus in the first 50 days were still relatively smaller, and the spread as per the available information was still slower, there were already 44 confirmed cases reported in china, wuhan region (41 cases), thailand (2 cases), and japan (1 case). from the 41 reported cases in wuhan, 2 people had succumbed to the unknown disease, whereas 12 are said to have recovered and discharged. interestingly, on this pandemic, though it took health official approximately 38 days to identify that they were dealing with a new kind of coronavirus, an artificial intelligence (ai)epowered algorithm developed by bluedot, a canadian startup tech company, provided early warnings that the world might be experiencing a new virus outbreak (bowles, 2020) . the warning came 7 days earlier before the chinese scientist identified the virus (huang et al., 2020) , and 9 days before they notified the who, which then made the official announcement to the world (who, 2020e). this early warning supports that computer predictions could be relied upon in predicting future pandemics before they arise, hence saving allowing for early preparations the challenges of future pandemic. in these first 50 days of the covid-19 pandemic, despite the virus having spread to two more countries outside china, most of the global community were not particularly worried, as the perception was that only those who had come into contact with the wuhan seafood market had the highest probability of being infected. therefore, even with the help of technologies like that of bluedot, the countries that were seen to be at risk of the 2019-ncov outbreak (the temporary name previously given to the virus) were those neighboring china and those directly linked to wuhan via airlines. for this reason, some of the countries that were flagged to be at risk included taiwan, australia, united arab emirates, hong kong, japan, and thailand. this chapter documents the outbreak over the first 50 days through the sections in the following. the earliest date of symptoms for covid-19, according to a study performed by huang et al. (2020) and published in the lancet journal, was december 1, 2019. however, there are other sources (bryner, 2020; davidson, 2020) claiming that individuals with similar symptoms may have presented themselves to hospital as early as november. according to the report, by south china morning post (ma, 2020) , the first person who presented similar cases was a male patient of 55-year old from the province of hubei. however, chinese doctors only came to realize that they were dealing with a new and serious virus late december, when similar symptoms continued to increase every day, and mostly originating from wuhan. according to the article in lancet, the first patient, and whom they insist may be the first case, was reported on december 1, 2019, and whom did not have direct link with the wuhan seafood market that has been associated with the origin of the virus. this finding interestingly matches with ma (2020) who also argues that the november 2019 case was not from wuhan. the story as to the origin of the virus has fueled much political and social divides and is expected to evolve as further efforts are poured into understanding this crisis. the number of new patients voluntarily presenting themselves to hospital continued to increase (bryner, 2020) . hospitals report new one to five cases with similar symptoms on average each day. however, this being a new virus, some sources quoted december 8 as the first day where the first patient in the city of wuhan sought medical help for pneumonia-like symptoms. at this time, the european centre for disease prevention and control (ecdc, 2020c) contended that many dimensions, which were known today, like the need for social distancing, human-to-human infections, lack of vaccine or cure, and many such issues, were unknown, and the precautionary measures taken then were routinely delivered. also, during these early stages of the onset of the virus, there was no clear evidence of how many people were affected. for this reason, information from chinese authorities (wuhan city health committee, 2020) and those of the who (who, 2020a) stated that the december 8, 2019, marked the onset of the first 41 cases that were tested and which were later confirmed positive with covid-19, then known as "2019-ncov." as hospitals continued to receive more patients with unknown "pneumonia-like symptoms," fear of the outbreak is already spreading, especially among the social media (wechat) use within china, more so wuhan (secon, 2020) . li et al. (2020) explained that during the period beginning december 1, 2019, the recurrence of the words "sars" and "shortness of breath" in the social media started to increase, and by december 29, it had peaked. meanwhile, in the hospitals, doctors were observed to concede that there might be a new virus of unknown etymology in wuhan, presenting symptoms of acute respiratory syndrome. the reporting is affirmed by availability of the first four cases officially confirmed. all the four cases were linked to the huanan (southern china) seafood wholesale market, which has been highly linked to have been the source of the virus. while only four cases had been pointed, by this date, bryner (2020) reports that already, over 180 people in wuhan had been infected, but since doctors had not earmarked them as suspected cases noting that there were no suspicion of this "unknown" disease. the 180 cases were only identified after doctors cross-verified records. the suspicion after reporting the four cases was that they were not suffering from sars (severe acute respiratory syndrome), which was still in surveillance since it broke in 2003. with the possibility of an unknown outbreak, at this time, the concern was to establish the transmissibility, severity, and other issues that may be related to this new virus (adhikari et al., 2020) . the situation unfolded rapidly on this day. first, the chinese officially reported to the who of the possibility of a new virus with symptoms of pneumonia, but of unknown etymology. the information to who officials based in china was that this disease had been detected in wuhan, from the hubei province. by the time of this reporting, the ecdc supported that wuhan municipal health commission was already handling 27 pneumonia cases with 7 of those in critical conditions (ecdc, 2020b) . while reporting, the officials did not have the information about how the disease was transmitted, and in some sources (who, 2020e), they have ruled out human-to-human infection. while that is the case, all patients with the said symptoms who had been received so far in hospitals in wuhan were placed under quarantine, as work to establish and identify the type of the virus and its origin began (safi, 2020) . while this marked the first official day that the covid-19 pandemic gained and attracted attention from the international body (who), and the centers for disease control and prevention (cdc), as noted in the previous dates, different cases had been reported. with ambiguity on this, there are contradictory figures from different sources denoting cases with varying dates. but the following 2 part 1 a chronological account of the pandemic: the first 150 days days succeeding the event, reporting has been taken over by international organization and by the who, leading to more coordinated and reliable figures. on january 1, 2020, the wuhan's huanan seafood wholesale market was indefinitely closed following its associated link with the virus outbreak (juan, 2020) . the role and link of the market in this story was not only made by the wuhan municipal officials but also by the uscdc (patel and jernigan, 2020) . while workers in the market, under the watchful eyes of the police, proceeded to close their businesses, health officials were collecting samples from surfaces in the market and sealing them in plastic bags to be analyzed further. the closure included banning of live animals from this market and any other wet markets (who, 2020e). sale of wild animals to restaurants, via online markets or in any other such market, was also banned. besides preventing further spread of the virus, the other intention of the closure of the market was to allow for environmental sanitation and disinfection of the same. there were also some levels of public awareness performed, especially to farmers who reared animals, where emphasis on sanitation was being stressed upon (who, 2020c). outside the market, chinese social media were amassed with different messages pointing to the fact that wuhan, an industrial city of over 11 million people, was experiencing an outbreak of an unknown disease. according to safi (2020) , the fears being spread in those social media platforms were catalyzed by leakage of some medical documents from a hospital in wuhan showing that some people with the virus had been reportedly transferred there. since uncertainties revolved around the virus, panic was building up around the perception that sars backer-emerged. following the spread of this fear, eight individuals accused of spreading rumors were arrested and imprisoned by the public security bureau (tardáguila and chen, 2020) . outside china, its neighbors were starting to take caution. taiwan was reported to immediately take the issue seriously and demanded the screening for any signs of pneumonia-like or flu symptoms for all individuals coming from china. until this date, the number of those reported to have shown the signs of the disease in question still remains unknown, but consensus builds around the number of cases to be 41 (zhao et al., 2020) . after rigorous probes, tests, analysis, and other medical practices, the chinese authorities made a global announcement (huang et al., 2020) that they have successfully identified the virus as a novel coronavirus, similar to the one associated with sars and the middle east respiratory syndrome (mars). prior to this ground breaking discovery, the officials had 2 days earlier, on january 5, ruled out that the virus they were dealing with was either sars or mars, hence concluding that it was indeed a new type of virus. upon its successful identification, it was tentatively named as "2019-ncov." the identification came after chinese scientists successfully isolated the virus from one of the patients quarantined in a hospital in wuhan (huang et al., 2020) . according to an article by singhal (2020), the identified virus had greater than 95% (>95%) homology with the bat coronavirus and was also greater than 70% similarity with the virus responsible for causing sars (sars-cov). as the identification occurred, it was also reported that the samples previously collected from the wuhan market tested positive, thus confirming the fears that the virus could have originated from there. even after identification of the virus, it was still not clear of how it could be transmitted. but the executive director of the who's health emergencies programme, dr. mike ryan, argued that the virus being a respiratory pathogen could possibly be transmitted from human to human (who, 2020e). at this stage, it is reported that approximately 44 people had contracted the disease and were still under quarantine as reported earlier. beyond china, as report by the who (who, 2020a), neighboring countries were stepping up their health precautions. for instance, japan began to institute comprehensive screening of all travelers coming from wuhan, and anyone with signs of fever or flu were placed under quarantine. in the united states, the country's cdc created a 2019-ncov incident management structure that would help the country as it prepares for upcoming cases. on january 9, 2020, chinese officials reported to the who that they have finally identified the virus, and subsequently, the who made the official announcement (who, 2020e) of the same to the world. on january 11, the chinese health officials share unfortunate news that a 61-year-old man who had been admitted in one of the hospitals in wuhan had died. from the report (ravelo and jerving, 2020), the man had other underlying health conditions such as chronic liver disease and abdominal tumors, but the cause of his death was attributed to 2019-ncov. by the time of his death, he was reported to have suffered from issues such as respiratory failure and severe pneumonia, septic shock, and multiple organ failure. he was also observed chapter 1 the first 50 days of covid-19: a detailed chronological timeline to have suffered from severe acid-based metabolism disorder and cirrhosis. his hospital treatment included antiinfection, ventilator-assisted breathing, life support, and other treatments, but with no positive results. his death was marked as the first known death from this new virus. in regard to new cases, health officials did not record any other case except the 44 cases that had been received up to january 3. they also expressed that according to an epidemiological survey (who, 2020e), there was no clear evidence that the disease could be transmitted from human to human. however, they affirmed that all the cases in hospital were of people who had been exposed to the wuhan seafood market. on this day, the first 2019-ncov virus genome sequence was deposited in the genbnk (the nih database that where all public genetic sequences are stored) and shared with virologist.org (an online hub for prepublication of data, where the public can freely access for public healtherelated activities and research) and also uploaded to the platform "global initiative on sharing all influenza data" (gisaid) (ecdc, 2020b), through a collaboration of a number of organizations including the shanghai public health clinic centre, the central hospital of wuhan, huazhong university of science and technology, and wuhan center for disease control and prevention among others. all this happened before the information on discovery of the genome sequence was officially shared with the who. however, the details were to be shared with the who the following day together with other viral sequences that were to be shared with gisaid (holmes, 2020) . in parallel, chinese health officials were considering to temporarily close down the chinese laboratory that was the first to share the coronavirus genome with the world. the laboratory was closed on the following day (hjanuary 12) (pinghui, 2020) . the who was briefed of the availability of the first viral genome sequence of coronavirus, and other five other genomes, which were subsequently deposited in the gisaid platform (holmes, 2020) . a lab in china, which was first to share genome, publicly closed down "for rectification" as ordered in the previous day, but still there was no clarification of what this "rectification" was supposed to mean. in addition, on this closure, as reported by pinghui (2020) , the laboratory was not given notice as to why they were asked to be closed down, even after relentless permission applications to reopen without any success. but it is assumed the "rectification" here is all about the lab releasing their genome sequence publicly before the officials could publish theirs. despite this bad blood between the laboratory and the officials from the shanghai public health clinic centre and other agencies involved in establishing and depositing the viral genome sequencing, the information is said to be critical in assisting scientists from different parts of the globe in the development of the testing and diagnostic kits and also in search for vaccine and cure for the disease. another major happening of the day is the publishing of interim guidelines by the who on issues pertaining to travel advice, testing in laboratories and medical investigations. these targeted to help countries across the globe to prepare for any eventuality that may arise from the ncov spread. the guidelines also targeted to urge the travellers, especially from or in wuhan to practice extra health caution. also, the guidelines insisted on the need for countries not to impose any travel restrictions on the international travelers (schnirring, 2020) . while no new cases were reported in wuhan, or in any other parts of china, beyond its border, thailand confirmed their first case, which was also thought to be the first international 2019-ncov one. this first case was a woman, noted to have frequented local fresh market in wuhan, but did not visit the condemned huanan south china seafood market. the 61-year-old chinese citizen was intercepted at the bangkok airport by the thermal surveillance scanners that detected her high temperature (fever). the identification of this case occurred on january 8, where she was hospitalized immediately and samples were taken from her, but the healthy officials delayed reporting the case until january 13. when the samples were subjected to a number of medical tests such aa the reverse transcriptase polymerase chain reaction test and subjected to genetic sequencing, they came back positive for the 2019-ncov. during the travel, she and five family members were in a tour group of 16 members who traveled directly from wuhan to bangkok. before the tests were done, the woman reported to have had experienced fever, chills, sore throat, and headaches. of all those in her company, no one had shown any similar signs (schnirring, 2020) ; thus, she is the only one who was isolated. with the patient having insisted she did not visit the suspected seafood market in wuhan, the hypothesis of the origin of the virus was put into disarray, and the who insisted that the scope for the investigation of the source of the virus needs to be extended beyond the seafood market to other local markets that are 4 part 1 a chronological account of the pandemic: the first 150 days observed to have also been involved in selling of live animals, including bats, which have been linked with the origin of the virus. another issue that came up from the history of this patient is the incubation period of the virus. according to her, her last visit to the markets was on january 5. therefore, since then, to the time she was detected to have symptoms, a number of days had passed. this also led to further question of the incubation period of the 2019-ncov. following the identification of the first case outside china, a research group (bluedot developed an aibased system to track the virus spread as from december 30, 2019 (bowles, 2020) ) from toronto embarked to map out top destinations that would be at high risk following the airline travel history from wuhan. from the research, those flagged as top destinations included thailand, hong kong, japan, taiwan, australia, and the united arab emirates. following the confirmation in thailand, health officials from the country declared that they were tracing and monitoring over 182 contacts that may have interacted with the woman patient (who, 2020b). from january 13, a number of happenings have been reported. on january 14, for instance, following the first confirmation outside china, wuhan embarked on a concerted effort of screening all passengers traveling out of the city either via the air, the rail, or buses. the screening was performed at the points of departure (airports, railway stations, ferry terminals, and bus stations) through the help of 35 infrared thermometers that were installed in those key points (who, 2020d) . on this day still, the who, after consultation with chinese officials, reported that there were no clear evidences to conclude that the 2019-ncov virus could be transmitted from person to person, but the option could not be excluded (who, 2020e) . but, while that was going on, of the 41 quarantined cases, 2 of the cases were confirmed to be a married couple, thus watering down the argument that the virus could not involve human-to-human transmission. on january 15, a major event happened in wuhan, china, where a 69-year-old man died from the virus (siu et al., 2020) . like the first reported death, this man also had some other underlying health conditions such as myocarditis, abnormal renal function, and multiple organ failure (ravelo and jerving, 2020). outside china, japan confirmed their first case, a man in his 30s who had lived in wuhan and traveled back to japan on january 6. while in wuhan, he reported to have developed a high fever (january 3) (sim, 2020), but it was only days later, in japan that he was confirmed to be coronavirus positive, as reported by the japanese ministry of health, labor and welfare (gan, 2020) . the man, who had not visited the huanan seafood market, was taken in hospital in japan as from january 10 where he stayed up to january 15, where, though he tested positive, he recovered and was dismissed from hospital. on january 16, vietnam isolated two chinese travelers coming from the chinese city, and though they had not been found positive, this was done as a preventive measure following the news of the spread of the virus outside china. in germany, a team of researchers from german centre for infection research (dzif), berlin, are noted to have successfully developed a prototype of the first diagnostic test that could help in identifying the coronavirus. the laboratory assay was approved and published by the who as a guideline for diagnostic detection, and it became the first test kit in the world (drosten, 2020) . a second case was reported in thailand. this time, it was a 74-year-old woman who had traveled from wuhan and arrived at bangkok suvarnabhumi airport on january 13. upon arrival and screening, she was found to have fever and was isolated into a local medical institute where the coronavirus testing was performed and come back positive (the government of the hong kong specia administrative region, 2020). the confirmation of the case was made by the ministry of public health of thailand. following this case, thailand was put on a high alert, since in the following weeks was the beginning of the lunar new year holidays, and during such times, millions of chinese travelers usually travel to the country. the alert involved intensifying surveillance in all the country's (four) airports, especially in respect to flights coming from wuhan. but amid such alerts, the country's top officials insisted that there was no outbreak of the virus (promchertchoo, 2020). in the united states, the uscdc was noted to have dispatched a team of a 100 people to three of its airports in san francisco (sfo), new york (jfk), and los angeles (lax) to complement the existing staff in conducting screening for all individuals entering the country from wuhan, china. the medical team would cooperate with officials from homeland security and customs and border protection (cbp) to ensure total compliance with the screening requirements (uscdc, 2020). in regard to new infections, the medical research council (mrc) centre for global infectious disease analysis (mrc gida) at imperial college argued that it had made some estimations, which showed that cases in wuhan would likely have increased to almost 1700 (imai et al., 2020) . they argued that such numbers could be ascertained if pneumonia or related cases within wuhan and other connected cities within china could be investigated. the calculations were based on flight and population data, following the fact that cases in thailand and japan had already been detected, and there were possibilities that there could be new cases not yet reported in other destinations that had originated from wuhan since the period that the coronavirus was reported. however, despite availability of those estimates, a summary report capturing happenings up to january 17 was published by ecdc (2020a) highlighting that the number of confirmed cases after successful laboratory testing still remained at 44 (41 in wuhan, china, 2 in thailand, and 1 in japan). of these, 2 had died, 12 had been discharged from hospital, and 5 were reported as severe cases. after the confirmation of the 44 cases, health officials to this date had managed to trace, identify, and monitor 763 close contacts. of those, 644 were given a clean bill of health, whereas 119 were still under close medical observation, although none of them had tested positive to the virus (wuhan municipal health commission, 2020). epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (covid-19) during the early outbreak period: a scoping review how canadian ai start-up bluedot spotted coronavirus before anyone else had a clue 2020) 1st known case of coronavirus traced back to november in china first covid-19 case happened in november researchers develop first diagnostic test for novel coronavirus in china cluster of pneumonia cases caused by a novel coronavirus event background covid-19 update: cluster of pneumonia cases associated with novel coronavirus e wuhan, china -2019 china's new sars-like virus has spread to japan, but we still know very little about it clinical features of patients infected with 2019 novel coronavirus in wuhan report 1: estimating the potential total number of novel coronavirus cases in wuhan city wuhan wet market closes amid pneumonia outbreak early transmission dynamics in wuhan, china, of novel coronaviruseinfected pneumonia coronavirus: china's first confirmed covid-19 initial public health response and interim clinical guidance for the 2019 novel coronavirus outbreak d united states chinese laboratory that first shared coronavirus genome with world ordered to close for 'rectification', hindering its covid-19 research wuhan virus: 2 more cases confirmed in thailand covid-19 e a timeline of the coronavirus outbreak 100 days that changed the world china release genetic data on new coronavirus, now deadly part 1 a chronological account of the pandemic: the first 150 days chinese social-media platform wechat saw spikes in the terms 'sars,' 'coronavirus,' and 'shortness of breath japan confirms first case of infection from wuhan coronavirus; vietnam quarantines two tourists a review of coronavirus disease-2019 (covid-19) china says second person dies in wuhan pneumonia outbreak china arrested 8 for spreading 'hoaxes' about what is now known as coronavirus. what happened to them? available at the government of the hong kong specia administrative region. (2020) chp closely monitors additional confirmed public health screening to begin at 3 u.s. airports for 2019 novel coronavirus who. (2020a) emergencies preparedness, response: novel coronavirus e china novel coronavirus e thailand (ex-china) who. (2020c) novel coronavirus (2019-ncov) situation report-4. world health organization. who. (2020d) novel coronavirus (2019-ncov) situation report-1. available at who timeline e covid-19 wuhan municipal health commission on unexplained viral pneumonia wuhan municipal health commission on pneumonia infect by new coronavirus estimating the unreported number of novel coronavirus (2019-ncov) cases in china in the first half of key: cord-298899-lkrmg5qr authors: xie, yewei; wang, zaisheng; liao, huipeng; marley, gifty; wu, dan; tang, weiming title: epidemiologic, clinical, and laboratory findings of the covid-19 in the current pandemic: systematic review and meta-analysis date: 2020-08-31 journal: bmc infect dis doi: 10.1186/s12879-020-05371-2 sha: doc_id: 298899 cord_uid: lkrmg5qr background: the covid-19 pandemic has affected the world deeply, with more than 14,000,000 people infected and nearly 600,000 deaths. this review aimed to summarize the epidemiologic traits, clinical spectrum, ct results and laboratory findings of the covid-19 pandemic. methods: we scoped for relevant literatures published during 1st december 2019 to 16th july 2020 based on three databases using english and chinese languages. we reviewed and analyzed the relevant outcomes. results: the covid-19 pandemic was found to have a higher transmission rate compared to sars and mers and involved 4 stages of evolution. the basic reproduction number (r(0)) is 3.32 (95% ci:3.24–3.39), the incubation period was 5.24 days (95% ci:3.97–6.50, 5 studies) on average, and the average time for symptoms onset varied by countries. common clinical spectrums identified included fever (38.1–39.0 °c), cough and fatigue, with acute respiratory distress syndrome (ards) being the most common complication reported. body temperatures above 39.0 °c, dyspnea, and anorexia were more common symptoms in severe patients. aged over 65 years old, having co-morbidities, and developing complications were the commonest high-risk factors associated with severe conditions. leucopenia and lymphopenia were the most common signs of infection while liver and kidney damage were rare but may cause bad outcomes for patients. the bilateral, multifocal ground-glass opacification (ggo) on peripheral, and the consolidative pulmonary opacity were the most frequent ct results and the tendency of mortality rates differed by region. conclusions: we provided a bird’s-eye view of the covid-19 during the current pandemic, which will help better understanding the key traits of the disease. the findings could be used for disease’s future research, control and prevention. the emergence of covid-19 has made it the first infectious disease pandemic in the twenty-first century. as of 20th july 2020, a total of 14,348,858 people got infected, and 603,691 were confirmed dead in 213 countries, territories, and areas globally [1] . while more than 30 countries had issued the highest level of response, the sars-cov-2 (pathogen of continues to spread in different regions around the world [2] . however, the key information on the virus epidemiology, clinical spectrum, and on the pathogen was delayed in response during the early outbreaks in many countries. to fill the research gaps mentioned above, this review article systematically summarizes global findings on the natural history, clinical spectrum, transmission patterns, laboratory findings, ct results, and risk factors of the covid-19. we searched for publications in epidemiology and clinic domains of the covid-19 broadly. the databases we searched were: chkd v3.1 of the cnki [in chinese], pubmed, and medrxiv, by using such search terms as 'covid-19, sars-cov-2, and 2019 ncov' (see additional file 1). the publication date was restricted from 1st dec 2019 to 16th jul 2020. both english and chinese were applied for the search. only the full-text available human studies were eligible for selection. like the realtime data, other data were obtained from health departments of multiple countries, global ngos, and reputable media sources. the searched records were firstly screened by reading titles and abstracts. then, the rest records were screened again by full-text reading. if there were disagreements initially, the records then submitted to the whole team for further discussions. besides, a prisma diagram was conducted to illustrate the entire flows of the review (fig. 1 ). the data for the quantitative analysis was extracted and managed by using microsoft excel 2010 (microsoft©, redmond, wa, usa). the meta-analysis was performed by the r version 4.02 and rstudio (2020) [3] . the cochrane handbook for systematic reviews of interventions suggested review authors collect missing data from investigators. considered that using the imputation method to tackle the missing data problem could not reduce bias, we only analyse data available to us if we could not collect the missing data from the investigators [4] . the heterogeneity of the included studies was assessed by using i 2 . the p-value was generated by wald-type test and likelihood-ratio test. the overlapping confidence intervals (cis) were displayed by the forest plots (see additional file 4). we categorized and combined the data about epidemiologic traits, clinical spectrums, laboratory, and imageology findings in a narrative. then we further analyze the data about common symptoms, reproduction number, and incubation period through meta-analysis. the quantitative outcomes were combined with the narrative of epidemiological and clinical findings. we collected 11,366 records after removing duplications. after three batches of screening, 127 records were included in this review (see screening details in fig. 1 ). in a china based study involving 55,924 covid-19 patients, the majority of patients were aged 30-69 (77.8%) with only 2.4% of the patients being 18 years and below. the median age of the patients was 51 (ranged 2 days-100 years old) [5] . similarly, in the united states, more than half of patients were aged between 20 and 64 years (65%), with only 5% of patients being under 19 years old. older aged patients were more prone to getting infected compared to the young [6] . by gender, the male to female ratio of confirmed cases was 1.06:1.00 in china [7] . however, in south korea and iceland, the male population had a higher incidence rate than the female population [8, 9] . males had twice the secondary attack rate than females [10] . the covid-19 transmission stages could be categorized into four temporal stages according to the chronological order of case reports. the first stage: people with exposure histories to huanan seafood market (hsm) got infected [11] . forty-one patients were found to be having sars-like symptoms in december 2019, and the hsm was believed to be one of the origins of the virus. however, 13 of the 41 patients reported no prior exposure to the hsm thus indicating that the origin of the virus needed further investigation [12] . the second temporal stage is the transition from community transmissions to the outbreak in wuhan [11] . the virus was mainly spread to multiple communities directly and indirectly by people with hsm exposure histories. the interpersonal transmissions and clustered transmissions formed community transmissions [11] . an earlier study showed that the proportion of patients with hsm exposure histories decreased from 55 to 8.6% within 22 days, indicating when people who did not have exposure histories to the hsm became infected [13, 14] . the third stage: the epidemic in china. at this stage, transmissions began to expand to communities outside wuhan and the hubei province as a whole [11] . on 26th jan 2020, a study involving 62 covid-19 patients outside wuhan found that all the patients had been exposed to wuhan, which demonstrated an established local transmission outside wuhan [15] . the fourth temporal stage is the global pandemic. on 13th jan 2020, the first case outside china was reported in thailand [2] . on 30th jan 2020, the who declared a public health emergency of international concern (pheic) [2] . it subsequently took about 51 days for transmission to escalate from the first reported case to the 10,000th reported case outside china. globally, it took 16 days for the number of reported cases to increase from 10,000th cases to 100,000th cases, 21 days from 100,000th cases to 500, 000th cases, only 6 days from 500,000th cases to 1,000, 000th cases and 13 days from 1,000,000th cases to 2,000, 000th cases [2] . the main transmission route of this virus was by human-to-human spread, since only 1.18% patients among 1099 confirmed patients had history of direct contact with wild animals [16] . the vital transmission routes were through respiratory droplets and contact transmissions. there remains the possibility of aerosol transmission when exposed to high concentrations of aerosols for a long time in a relatively closed environment [17] . mother-to-child transmission has been confirmed, whiles fecal-oral transmission was also considered possible but lacked direct evidence until now [18, 19] . other suspected routes of transmission still needed further clarification. community transmission, nosocomial transmission, household transmission, and transmission in closed environments were four typical transmission patterns of the covid-19. firstly, community transmission was considered to be an important pattern in covid-19 spread [5] . in the netherlands, community transmissions were found in the noord-brabant regions [20, 21] . in north america, community transmissions were reported in winnipeg, canada, and eastern idaho, united states [22, 23] . secondly, the potential risk of transmission among medical personnel and through medical facilities was deemed high and thus extreme attention should be paid. transmissions between patients and health workers were in higher proportions during the sars outbreak, while transmission through medical facilities was higher in proportion during the mers outbreak [24] . in wuhan, the proportion of severely infected medical workers was higher than the national average [7] . in italy, 2629 health workers were reported infected with the covid-19 before 18th march and accounted for 8.3% of the total number of cases nationwide. the number however increased to 8358 by 30th march and represented 9% of the country's total number of cases [25, 26] . in spain, the number of diagnosed cases among medical workers increased to 5969 within 6 days and more than 12% of the country's confirmed cases remained among medical workers until march 30th [25] . update from another source reported an increase in the number of cases from 12 to 14% among spain healthcare workers by 31st march and this was attributed to lack of medical supplies, such as masks and gowns. other reasons accounting for these high infection rates among medical personnel varied according to different country's circumstances. an italy study pointed out hospitals as a potential hotspot for infection. facilities and medical personnel turned into untested vectors and patients [27, 28] . in the us for example, the reasons that turned hospitals into infection hotspots included the overload of covid-19 patients and inappropriate management against the pandemic in hospitals [29] . similar to the us, 200 medical workers got infected in a county hospital in romania due to inadequate hospital management. in egypt, a serious wave of emigration by physicians for years led to patient overload for remaining medical workers and placed them at higher risk of infection through continuous exposure. the emigration wave was purportedly caused by low salary, undesirable working conditions, lack of legal protection, and shortage of medical supplies and equipment [30] . thirdly, household transmission contributed to cluster infections and was the major transmission pattern observed in china. for instance, among 1836 reported cases in guangdong and sichuan provinces, most cluster infections occurred in families (78-85%) [5] . the who in this regard issued a statement that household transmission highly occurred among medical workers' families than health facility infection in china. household transmission was also a significant pattern observed in south korea and the us [2, 29] . the european centre for disease prevention and control (ecdc) had provided guidance for the control of household transmission in european countries [5, 31] . what made household transmission worse was that some groups (age < 18 and > 65) had high risk got infection within households than the general population [32] . so, children and elderly living with medical workers at a higher risk of getting than other populations. fourthly, transmissions in a closed environment besides the home should also be of a keen focus on the prevention and control of this outbreak. a japanese health department reported that a closed environment could promote super-spreading events because the transmission of the sars-cov-2 in a closed environment was the same as large-scale transmission, such as the ski chalet-cluster infection in france and the church-hospital infection clusters in south korea [33] . for example, outbreaks of the covid-19 were observed in multiple prisons in china, the uk, and the us [7, 34, 35] . cluster infections also happened on cruise ships, such as the diamond princess, grand princess, golden princess, ruby princess, phoenix reisen, ms westerdam, and punta arenas [36] . further studies are however required to identify and assess other potential transmission patterns for further prevention, especially since some cases were asymptomatic [37, 38] . in addition, patients who were considered cured and no longer needed quarantine still tested rt-pcr positive after 5 to 13 days [39] . we systematically used the data of the incubation period and the reproduction numbers for meta-analysis (see details of selected studies on additional file 2). the result suggested that the mean incubation period was 5.24 days (95% ci:3.97-6.50, 5 studies), and ranged from 3 to 7.4 days [40] [41] [42] [43] [44] . however, the incubation period in some special cases could be as long as 24 days [16] . the result also illustrated that the basic reproduction number (r 0 ) of sars-cov-2 was 3.32 (95% ci:3.24-3.39, 14 studies) and varied between 0.6-6.47 [37, [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] . this finding suggested that the transmission ability of sars-cov-2 was stronger than sars (3) and mers (≤1) [54, 55] . moreover, the median time from the first symptom to first hospital admission was 7 days with the median duration from illness development to severe symptoms development being: 5-8 days for dyspnea, 8-9 days for ards, 10.5 days for mechanical ventilation and icu admission [6, 18] . for covid-19 related deaths, the duration from the onset of symptoms to death averaged 9 days in china 5 and in italy (median) [56] , and 10 days in south korea (median) [9] . by 14th july 2020, 21 nations had reported over 100,000 covid-19 cases in each of the countries, together contributed to 81.4% of the confirmed cases and 81.3% of death in the world1. the world case fatality rate (cfr) was 4.4% on 14th july; however, it was apparently different by country. one third of these 21 countries had a cfr of over 4.4%. france (17.4%), united kingdom (15.5%), italy (14.4%), and mexico (11.6%) were the top four countries with over 10% cfr while qatar (0.1%) and saudi arabia (1.0%) were the two countries with no more than 1% cfr. most countries experienced an increase of cfr at first, and the number was then gradually becoming stable during the disease outbreak (fig. 2) . however, the cfr was high in iran (13.7% on 27th february) and the united states (7.2% on 4th march) at first, experienced a sharp decrease to 2.5% on 8th march and 1.1% on 20th march, and rebounded to 5.0 and 4.0% on 14th july, respectively. bangladesh was the only country that had high cfr of around 10% at the beginning and then continuously decreased until 1.3% on 14th july. as the pandemic outbreak continued, more surveillance is needed for the cfr of covid-19 [57] . the mortality is higher among elderly, patients requiring intensive care unit admission and male. however, mortality rate among younger age group and patients with mildly disease is less. the us's data indicated that patients younger than 19 had milder covid-19 illness, with almost no hospitalizations or deaths reported [6] . based on a worldwide data, the elderly (aged over 60) were at a high risk of developing into death [5, 6, 9, 56] . the mortality in icu was extremely higher than non-icu patients, varied from 26 to 78% [58] [59] [60] [61] . about the gender ratio, there is a seemingly unquestionable pattern that covid-19 killed more men than women [62] . unlike the less report in the research from china, south korea or other asia areas, the reports from europe and american reflect the male gender is the risk factor for heavy illness. to figure out the general situation around the world, here we analyzed the data from 53 countries, compiled centrally and individually verified by authors against country-specific reports [63], shown that the case-fatality rate among male is about 35% higher than female (ir = 1. 35 based on the data collected from selected articles [12, 15, 16, 58, (details of selected articles were put in the additional file 3), we conducted the meta-analysis using a random-effects model to identify the clinical feature of covid-19. fever (76.70, 95% ci: 64.86-85.44%) and cough (67.76, 95% ci: 60.06-74.61%) were the most fig. 2 case fatality rate of countries reported over 20,000 cases, 2020*. *data was collected until 14 july 2020 (i.e. the 196th day of year 2020). the cfr of a country was not included on those dates when the country reported less than 100 cases, with the consideration that the cfr may not be reliable if the size of infected population was small common symptoms. other common symptoms included: olfactory (44.40%), gustatory (38.16%), dyspnea (37.49%), fatigue (29.93%), sputum production (17.85%), sore throat (16.17%) and headache (15.49%). all the other data showed in table 2 . besides, studies pointed out that most patients had more than one symptom [68, 70, 71] . additionally, there were 20.9% of patients without viral pneumonia symptoms [16] , which was opposite to previous studies [69, 70] . the asymptomatic cases varied from 21.9-49.5% [66, 68, 93, 94] . the top 3 common symptoms among mild and severe patients are summarized and displayed in a figure (fig. 3) [12, 16, 61, 70, [95] [96] [97] [98] . fever was found to be the most common symptom in all patients. in a study, 43.8% of patients had fever initially and the proportion increased to 87.9% following hospitalization [16] . the body temperatures of 44-47.1% of patients ranged between 38.1-39.0°c. the higher body temperatures (above 39.0°c), dyspnea and anorexia were more frequent among patients in severe conditions [16, 64, 98] . cough and fatigue were more widely reported among mild and severe patients. additionally, another study reported that dyspnea (76%) was the most common symptom among severe patients in the united states [99] . the proportion of patients who needed icu care varied based on the local pandemic circumstances. for example, the who speculated that around 13.8% of patients were in severe conditions in china [5] . however, 23-32% of patients needed icu care in wuhan [64, 69, 70] . currently documented covid-19 related complications include ards, arrhythmia, septic shock, acute cardiac injury, myocarditis, acute coronary syndrome, cardiomyopathy, acute respiratory injury, and acute renal injury, etc. [58, 64, 67, 69, 70, 100] . the ards was the most common complication, among both mild and severe patients [58, 64, 67, 69, 70] . most icu patients had a higher risk of developing ards and having complications [12, 70] . the progress of some patients with ards to septic shock was fast and quickly evolved into multiple organ failure finally [69] . among covid -19 patients, a decrease in leukocytes such as eosinophil and lymphocyte were commonly reported. this might be because the cytokine storm caused by the novel virus changes the peripheral of white blood cells and immune cells [12, 13, 15, 16, 69, 70] . severe lymphopenia was also common among the dead patients [12, 61] . myocardial zymogram abnormality was found in many patients. for instance, 76% of patients had an increase in lactate dehydrogenase, while 13% of patients had increases in creatine kinase [69] . the level of c-reactive protein was important to evaluate the infection [16] . most patients were found to have a higher level of c-reactive protein (86%) and serum ferritin (63%) compared to the normal range [69] . the biomarkers related to liver and renal damage were found to be abnormal among covid-19 patients. the abnormality of liver-related biomarkers was not widespread but yet still common in severe cases [12, 15, 16, 101] . besides, although only 7% of patients showed renal biomarker abnormalities, renal damage might contribute to the final multi-organ failure and death outcome [102, 103] . the icu patients showed higher levels of white blood cells, neutrophil counts, d-dimer, creatine kinase, and creatine with longer prothrombin times [12, 16, 70] . compared to patients who survived, the patients who died had higher levels of d-dimer, high-sensitivity cardiac troponin i, serum ferritin, lactate dehydrogenase, il-6, blood urea, creatinine, white blood cell counts and neutrophil counts. severe lymphopenia was also common among dead patients [12, 61] . the computed tomography scan (ct scan) was widely used for disease diagnosis, prognosis, and management during the covid-19 [104] . the ct was found more sensitive for identifying sars-cov-2 patients than the rt-pcr assay (98% vs. 71%) in a study [105] . the ct evidence for confirming the highly suspected patients' positive may precede the rt-pcr results [106, 107] . most patients had ggo and the bilateral lung involvement [12, 69, [108] [109] [110] . one study found that bilateral lung involvement was more frequently shown in the intermediate course and late course, compared to the earlier clinical course [107] . the clinical course could be divided into four stages based on ct scan findings [110] . in the first stage (pre-symptom), ggo, unilateral and multifocal were observed among most patients in this stage [107, 110] . in the second stage (symptoms ≤1 week), lesions soon developed into bilateral and diffused except for ggo. this stage was considered a period from transition to consolidation. a mixed pattern of transition and consolidation develops during this stage. in the third stage (symptoms 1-2 weeks), the ggo was still common and the consolidation pattern showed. findings indicated an interstitial change, which was considered as the development of fibrosis. in the fourth stage (symptom 2-3 weeks), consolidation and mixed patterns were more common, and the ggo started to shrink [110] , the consolidation was gradually absorbed among patients who recovered at last [111] . among icu patients, the bilateral multiple lobular and sub segmental areas of consolidation were considered typical findings [12] . patients in severe condition showed diffuse lesions, with density increasing in both lungs. ct scans showed 'white lung' appearances, indicating the serious influence the infection has on patients' lung functions [112] . being old (≥65 years old), male sex, having a higher bmi value (> 35 kg/m 2 ), having co-morbidities (e.g. hypertension, diabetes, cardiovascular and cerebrovascular diseases, etc.), and developing complications were vital risk factors for patients to develop severe conditions [59, 70, 78, 95, 96, 113, 114] . the cytokine storm, raised inflammatory markers, elevated cardiac troponins, the requirement of mechanical ventilation, and the requirement of intensive care unit stay predict the bad outcome of admission patients [61] . findings from multiple studies showed that patients who are more than 65 years of age, with co-morbidities such as diabetes and heart diseases had a high mortality rate [61, 95, [115] [116] [117] . late hospitalization and bacterial infections were also considered high risk factors for disease progression [69, 96, 116] . smoking history could be a potential risk factor for developing severe conditions [69, 96] . people with underlying disorders were considered to be at a high risk of getting infected [5] . our review identified several research gaps. firstly, large amounts of data from african were missing from this review. as the number of people in african suffering from malnutrition, anemia, malaria, hiv/aids and tuberculosis is high, a large "low immunity population" has been created which has made the control and prevention of covid-19 in the region a challenge. the situation could be worsened by the limited health resources region [118] and hence, more african focused research is required to support africa in fighting the epidemic. secondly, the proportion of asymptomatic patients is large but the current transmission ability by asymptomatic patients might be weak. however, further exploration of risks posed by the group is needed as limited studies exist on the subject matter [119] . meanwhile, data on the distribution of asymptomatic patients in large-scale community groups is also lacking, prompting the need for large scale of active screening and testing to help identify them [93, 120] . this approach is however difficult and expensive for most countries to undertake as accurate strategies to identify asymptomatic currently are non-existent. further research focus on asymptomatic patients is needed. third, a 'super-spreader' was defined as infected individuals who infected numerous others during the sars outbreak. for example, a nephrotic hospitalized patient who infected 22 people was classified as a 'superspreader' during the sars in china. 19 in those 22 patients were medical workers who came in contact with the 'super-spreader'. the incidence rate among the medical workers was 59.38% (19/32) in the nephrotic department [121] . in the covid-19 era, the emergence of 'super-spreaders' were found in multiple places worldwide. a saudi arabian study linked the concept of 'super-spreaders' to 'super spreading' events noting that 'super-spreaders' might cause unexpected transmissions during the pilgrimage [122] , as huge numbers of people gather. reasons causing the super-spreading events might include: immune suppression, increased disease severity and viral load, asymptomatic individuals, and extensive social interactions [123] . however, the characteristics and features of how an individual becomes a super-spreader are still not clear [124] . summarizing the features of the 'super spreader' concept, as well as their characteristics and role in transmissions, are needed in future disease control [125] . fourth, it has been reported that some cured patients covid-19 retested positive by pcr after being discharged and quarantined at home in multiple places [39, 126] . the reason for this phenomenon is still unclear and hence further investigations are required for future pandemic control [127] . there existed some limitations in this review. firstly, this review was based on english and chinese resources only. as the covid-19 transformed from a regional outbreak to a global pandemic, comprehensive collection of the related information worldwide is needed. secondly, the clinical spectrum presented in this review is based on general population only, and thus a further subgroup analyzes in future may help to figure out more on the entire picture of the covid-19. for instance, although kawasaki disease was found in children in the uk and europe countries, other places did not report the gathering kawasaki disease cases [128] . 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selected by yx, zw, and hl. the data were extracted and analysed by yw, zw and hl. yx, zw and hl drafted the manuscript. yx, zw, gm, dw, and wt edited the draft. all authors read and approved the final manuscript. key: cord-284393-s9qp9a4e authors: wei, yiping; zeng, weibiao; huang, xiangyun; li, junyu; qiu, xingting; li, huadong; liu, dinghua; he, zhaofeng; yao, wenzhong; huang, ping; li, chao; zhu, min; zhong, chunlan; zhu, xingen; liu, jiansheng title: clinical characteristics of 276 hospitalized patients with coronavirus disease 2019 in zengdu district, hubei province: a single-center descriptive study date: 2020-07-29 journal: bmc infect dis doi: 10.1186/s12879-020-05252-8 sha: doc_id: 284393 cord_uid: s9qp9a4e background: we aimed to report the epidemiological and clinical characteristics of hospitalized patients with coronavirus disease-19 (covid-19) in zengdu district, hubei province, china. methods: clinical data on covid-19 inpatients in zengdu hospital from january 27 to march 11, 2020 were collected; this is a community hospital in an area surrounding wuhan and supported by volunteer doctors. all hospitalized patients with covid-19 were included in this study. the epidemiological findings, clinical features, laboratory findings, radiologic manifestations, and clinical outcomes of these patients were analyzed. the patients were followed up for clinical outcomes until march 22, 2020. severe covid-19 cases include severe and critical cases diagnosed according to the seventh edition of china’s covid-19 diagnostic guidelines. severe and critical covid-19 cases were diagnosed according to the seventh edition of china’s covid-19 diagnostic guidelines. results: all hospitalized covid-19 patients, 276 (median age: 51.0 years), were enrolled, including 262 non-severe and 14 severe patients. the proportion of patients aged over 60 years was higher in the severe group (78.6%) than in the non-severe group (18.7%, p < 0.01). approximately a quarter of the patients (24.6%) had at least one comorbidity, such as hypertension, diabetes, or cancer, and the proportion of patients with comorbidities was higher in the severe group (85.7%) than in the non-severe group (21.4%, p < 0.01). common symptoms included fever (82.2% [227/276]) and cough (78.0% [218/276]). 38.4% (106/276) of the patients had a fever at the time of admission. most patients (94.9% [204/276]) were cured and discharged; 3.6% (10/276) deteriorated to a critical condition and were transferred to another hospital. the median covid-19 treatment duration and hospital stay were 14.0 and 18.0 days, respectively. conclusions: most of the covid-19 patients in zengdu had mild disease. older patients with underlying diseases were at a higher risk of progression to severe disease. the length of hospital-stay and antiviral treatment duration for covid-19 were slightly longer than those in wuhan. this work will contribute toward an understanding of covid-19 characteristics in the areas around the core covid-19 outbreak region and serve as a reference for decision-making for epidemic prevention and control in similar areas. in december 2019, a series of pneumonia cases with similar symptoms were reported in wuhan, hubei province, china [1] . that pneumonia was later named coronavirus disease 2019 (covid-19) by the world health organization (who) [2] . the causative pathogen was identified as a novel enveloped rna beta coronavirus named severe acute respiratory syndrome coronavirus 2 (sars-cov-2) [3] . covid-19 is highly contagious and spreads rapidly through human-to-human transmission [4] [5] [6] . as of march 29, 2020 , there were 81,470 confirmed covid-19 cases and 3304 deaths in china, including 67,801 confirmed cases and 3186 deaths in hubei province, and 721,584 confirmed cases and 33, 958 deaths worldwide. however, many infected people have not been counted owing to a lack of timely diagnosis. covid-19 is a global pandemic. therefore, a comprehensive and in-depth understanding of the epidemiological and clinical characteristics of covid-19 is imperative for controlling the pandemic as soon as possible. the number of covid-19 cases in wuhan was large, the spread was fast, and the fatality rate was high. most of the clinical characteristics of covid-19 have been summarized from the samples of patients in wuhan [7] . controlling the epidemic in the areas around the core covid-19 outbreak region is an important link in blocking the spread of the disease. the chinese government has enlisted many volunteer doctors to support hospitals in these key areas. however, there are few reports on the clinical characteristics of covid-19 inpatients in these areas [8, 9] . thus, this study collected clinical data for covid-19 inpatients in zengdu hospital, a community hospital supported by 95 volunteer doctors and nurses from jiangxi province (about 300 miles from zengdu district). we describe the epidemiology, clinical features, laboratory findings, imaging features, and outcomes of covid-19 inpatients in zengdu district, which is a 3-h drive from wuhan city. we hope that our work will contribute toward an understanding of covid-19 characteristics in the areas around the core covid-19 outbreak region and provide a decision-making reference for epidemic prevention and control in similar areas. the study was approved by the institutional ethics board of suizhou zengdu hospital, which was established by the chinese government to treat covid-19 patients in zengdu district. all the patients diagnosed with covid-19, according to the interim guidance from the who [10] , in zengdu hospital from january 27 to march 11 were admitted and included in this study. the patients were followed up for clinical outcomes until march 22, 2020. only laboratory-confirmed cases that were defined as positive based on the results of highthroughput sequencing or real-time reversetranscriptase-polymerase chain reaction (rt-pcr) assay of nasal and pharyngeal swab samples were included. these confirmatory assays for sars-cov-2 were performed at the suizhou cdc in accordance with the guidelines developed by the who [11] . medication and treatment measures were selected according to the scheme recommended in the guidelines and each patient's condition [12] . a team of doctors who had treated these patients extracted the recent exposure history, clinical symptoms, laboratory findings, radiologic manifestations, and clinical outcomes from patients' medical records. all patients underwent at least one chest computed tomography (ct) scan, and data were extracted after the scans were reviewed by a dedicated imaging physician. all laboratory tests were performed according to treatment needs. the researchers obtained the outcome data of transferred patients by contacting the hospitals that received these patients, and also contacted the patients by phone if anything was unclear or information necessary for the study was missing from the medical record. according to the national treatment guideline, covid-19 severity was defined as mild, moderate, severe, or critical [13] . the mild type was defined as mild clinical symptoms and no radiological manifestations of pneumonia. the moderate type was defined as respiratory symptoms and pneumonia on imaging. the disease was defined as severe if one of the following criteria was met: respiratory rate of ≥30 beats per minute; finger oxygen saturation of ≤93% at resting state; and arterial blood oxygen partial pressure (pao 2 )/oxygen concentration (fio 2 ) of ≤300 mmhg. the critical type was defined as respiratory failure or shock and requirement of mechanical ventilation or intensive care unit (icu) monitoring and treatment. accordingly, the patients were divided into a non-severe group (mild or moderate disease type) and severe group (severe or critical disease type). due to limited medical facilities at the zengdu hhospital, critical patients were transferred to hospitals with superior treatment facilities. the incubation period was defined as the interval between the patient's earliest date of exposure to the transmission source and the date of the initial symptom. for patients who had recently visited wuhan, the earliest date of exposure was estimated as the median date of their stay in wuhan; for patients who had been in contact with people returning from wuhan, the earliest date of exposure was considered to be the earliest contact date, the earliest date of exposure was considered to be the earliest contact date. fever was defined as an axillary temperature of ≥37.5°c. lymphopenia, eosinopenia, and thrombocytopenia were defined as lymphocyte, eosinophil, and platelet counts of less than 1500, 100, and 150,000 of the corresponding cells per cubic millimeter. the smoking index was equal to the product of the number of cigarettes per day and smoking years. the length of covid-19 treatment was defined as the time interval from patient admission to the meeting of the cure and discharge criteria of the chinese management guidelines for covid-19 (version 6.0) [12] . the cure and discharge criteria were as follows: normal body temperature for more than 3 days; significantly improved respiratory symptoms; significantly improved acute exudative lesions on pulmonary imaging; and two consecutive negative results of the nucleic acid tests of sputum, nasopharyngeal swabs, and other respiratory tract samples. the primary composite end points were discharge from the hospital owing to being cured and transfer to another hospital because of condition deterioration. the secondary end points were cure or discharge rate and the length of hospital stay. statistical analyses were performed with spss (v.18.0; spss inc., chicago, il, usa). continuous variables are described as median values and interquartile ranges (iqrs), and categorical variables are reported as numbers and percentages. we used the mann-whitney u test, χ 2 test, or fisher's exact test to compare differences between the two groups. a two-sided α of less than 0.05 was considered statistically significant. we obtained data on the demographic characteristics, symptoms, and outcomes for 276 patients hospitalized in suizhou zengdu hhospital as of march 11, 2020. the severe group included 14 (5.1%) patients while the nonsevere group included 262 (94.9%) patients. the demographic and clinical characteristics of the patients are shown in table 1 . forty-three (15.6%) of the 276 patients had visited wuhan within 14 days before the study enrollment; 60.1% (166/276) of the patients had come into contact with people who had travelled to wuhan or were diagnosed with covid-19. the remaining 67 patients reported they had not been to wuhan, and it was unclear how these patients had been exposed to the transmission source; none of the patients had a history of exposure to the huanan seafood wholesale market or a wild animal. the incubation period calculated based on the data from 71 patients with a known exposure time was 6 days (iqr, 4-7 days). the longest incubation period was 20 days. a nurse in the fever clinic of suizhou zengdu hhospital was the only medical staff included in the study. the median age of the patients was 51 years (iqr, 41-58 years). the patients in the severe group were significantly older than those in the non-severe patients ( had at least one comorbidity; this percentage was significantly higher than that among the non-severe patients (21.4%, 56/262). table 2 shows the results of radiology and laboratory tests at admission. all 276 patients underwent ct at admission, and abnormal results were obtained for 95.7% (264/276) of the patients. the most common chest ct findings were bilateral patchy shadows figure 1 shows typical ground-glass shadows and bilateral patchy shadows in two patients. according to the results of the first examination after admission, 30.1% (83/276), 75.0% (204/276), and 31.5% (87/276) of the patients had leukopenia, lymphocytopenia, and thrombocytopenia, respectively. lymphocytopenia and thrombocytopenia were more obvious in the severe group compared to that in the non-severe group. the c-reactive protein levels were elevated in 60.9% (162/266) of the patients; the erythrocyte sedimentation rate of 90.0% (180/201) of patients and d-dimer levels of 53.7% (123/229) of patients were also elevated. elevated procalcitonin, creatine kinase, alanine aminotransferase, aspartate aminotransferase, and myoglobin levels were observed in 2.5, 11.1, 14.2, 22.3, and 8.0% of patients, respectively. as shown in table 3 , most of the patients (94.9%, 262/ 276) were cured and discharged from the hospital. ten out of 276 (3.6%) patients, all of whom belonged to the severe group, showed condition deterioration to a critical status and were transferred to suizhou central hospital, a superior hospital. eventually, five of them died and five survived. all five people who died received endotracheal intubation; one of the five survivors received endotracheal intubation, which was removed 20 days later. the remaining four only received non understanding the clinical characteristics of covid-19 inpatients in the areas around the core covid-19 outbreak region is very important for controlling the spread of covid-19 and decision-making for epidemic control. our study on 276 inpatients in zengdu hhospital confirms that covid-19 patients in the areas surrounding the core covid-19 outbreak region showed mainly mild and moderate illness with fever and lymphocytopenia as the main clinical features. older patients (age > 60 years) or those with underlying comorbidities are at higher risk of deteriorating to critical status. the length of hospital-stay and antiviral treatment duration for covid-19 were slightly longer than those in wuhan. all patients who tested positive for covid-19 by rt-pcr in the study region were admitted to the hospital, regardless of the severity of the patients' condition. there were several reasons why our hospital established such an admission standard. first, at that time, the outbreak was still in the early stage. the understanding of the epidemic situation in zengdu district, a residential a lymphocytopenia was defined as a lymphocyte count less than 1500 per cubic millimeter. eosinopenia was defined as an eosinocyte count of less than 100 per cubic millimeter. thrombocytopenia was defined as a platelet count of less than 150,000 per cubic millimeter. these are results of the first examination after admission resources to treat all the diagnosed patients. our admission criteria were formulated under such special circumstances, although this admission standard was different from the current international standard. moreover, compared to studies in which only seriously ill covid-19 patients were admitted, our admission criteria better reflect the disease characteristics in the area around the outbreak point, so as to provide a decision-making reference for hospitals in the residential area to decide which patients should stay at home for observation and which high-risk patients should be hospitalized in a timely manner. the patients in zengdu area show mainly showed mild and moderate illness, with a few patients showing severe and critical illness. in wuhan, as the site with the most serious covid-19 infection in china, many patients did not get timely diagnosis and treatment initially, and medical resources were insufficient to accommodate the sudden burst of patients. as a result, the proportion of severe cases reached 15.0-30.0% [14, 15] , while the rate of severe disease in other regions was 3-10% [16, 17] , similar to 5.1% in this study. this may be because, with the deepening of the understanding of covid-19 and the formulation of relevant guidelines [18, 19] , many patients were diagnosed and treated in a timely manner without deteriorating into severe disease. besides, the difference in admission criteria was also a reason why the rate of severe disease in this study was significantly lower than that in wuhan or abroad. the early common symptoms of covid-19 patients include fever, cough, sputum, and other symptoms of lower respiratory tract infection. as the most common symptom, in general, more than 80% of patients have a fever, but only 38.4% of the patients had a fever at the time of admission, which shows that the fever in many patients was intermittent. it also means a large number of patients with intermittent fever will be set free if instant body temperature readings are the only measure used for screening [2, 20] . the proportion of fever in critically ill patients increases significantly after hospitalization, and most of these new fever cases may be caused by secondary infection, so it is necessary for severe patients to receive antibiotics to prevent secondary infection [13] . covid-19 patients over 60 years old were more likely to show deterioration into critical illness. previous studies on severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) have confirmed that age was an important predictor of poor prognosis [20, 21] , and similar conclusions were obtained for covid-19 [22] . data obtained by nanshan zhong et al. [23] and zhongliang wang et al. [14] showed that the age of severe patients was significantly older than that of non-severe patients. consistent with these findings, among the patients we collected, the median age of severe patients was 65 years, while that of non-severe patients was 50 years. in addition, about 78.6% of the severe patients were more than 60 years old. these studies have shown that older covid-19 patients have a poor prognosis. covid-19 patients with comorbidities were also likely to show deterioration [24] . the studies by nanshan zhong et al. and daweiwang et al. [22] both showed high proportions of comorbidities in severe patients. a who survey reported that people with comorbidities had a higher risk of severe disease [25] . in a recent retrospective study of 25 death cases with covid-19 [24] , all of the deceased patients have comorbidities, which were considered to be one of the most important risk factors for death. in this study, 85.7% of the severe patients had comorbidities. this may be due to abnormal immune function and increased susceptibility to sars-cov-2 in patients with comorbidities [26, 27] . in addition, covid-19 damage to the lungs can aggravate some comorbidities, such as chronic obstructive pulmonary disease. antiviral drugs and glucocorticoids also have limited benefits for patients with comorbidities. in terms of laboratory tests, 75% of patients had lymphopenia, and more obvious findings were noted in severe patients. the novel coronavirus can induce a cytokine storm and inhibit the generation of lymphocytes [28, 29] , so lymphopenia is very common in patients with covid-19. the low absolute value of lymphocytes can be used as a reference indicator for clinical diagnosis of novel coronavirus infections [6] . lymphocytes showed a pronounced decline in severe patients than in non-severe patients, indicating that the degree of lymphocyte decline can be used to assess the severity of the disease [30] , and that continuous decline of lymphocytes is also one of the indicators of disease deterioration [13] . in the absence of nucleic acid detection and ct, this can be an important tool for determining the severity of the disease. the length of hospital stay in this study was slightly longer than that in wuhan, which was 11-12 days [23, 31] . this contradicted the finding that the length of hospitalization is positively related to disease severity because covid-19 severity in this study was significantly lower than that in wuhan. however, the allocation of medical resources is also an important factor affecting the length of hospitalization. the number of infected patients in wuhan was large and medical resources were scarce, so the hospital had to discharge inpatients as soon as possible to treat newly admitted patients. the inpatient data collected in this study were from a community hospital that was supported by many jiangxi doctor volunteers and medical supplies, which ensured sufficient medical resources. the characteristics of inpatients under this special medical setup were different from those at other hospitals. in particular, after the local epidemic is mostly controlled, some wastage of medical resources may be inevitable. for example, patients were allowed to stay in the hospital for some time to recover even after meeting the discharge criteria for covid-19, which was not possible in the hospital in wuhan. this was also the reason why the length of treatment for covid-19 (14 days) is significantly shorter than the length of hospitalization (18 days). in addition, hospitals in wuhan only accept patients who have been diagnosed as showing covid-19, while hospitals outside wuhan admitted many patients who were not diagnosed at admission and were also hospitalized for the 1-3 days it took for nucleic acid test results to arrive. three studies from regions with sufficient medical resources [32] [33] [34] , namely taizhou, guangdong, and shenzhen, can support our hypotheses since their median hospital stays were 18 days, 20 days, and 20 days, respectively, which were close to the results of this study. this study has several limitations. first, since it is a retrospective study with a limited number of patients, some conclusions need to be verified by studies with more rigorous design and larger samples. second, zengdu hhospital was a community hospital, and most of the critically ill patients had to be transferred to superior hospitals for treatment. we are temporarily unable to get information on the followup treatment and complications of these patients. third, when calculating the incubation period, we excluded the unclear contact date, resulting in fewer patients included, and the potential memory bias will also affect our results. fourth, our admission criteria were different from the current internationally recognized criteria, which limits comparability with other studies. however, our admission criteria were set in high-risk areas at the early stage of the epidemic to avoid the spread of the epidemic, which was essential and important. in addition, only pcr-confirmed covid-19 patients were included in this study and asymptomatic infections without pcr confirmation were omitted, so the characteristics we described are only suitable for pcr-confirmed covid-19 patients. most of the covid-19 patients in zengdu area had mild disease. older patients with underlying comorbidities had a high risk of progressing to severe disease. a large number of patients with intermittent fever will be omitted by the temperature checks that are currently widely being deployed. the length of hospitalization and antiviral treatment for covid-19 were slightly longer than those in the wuhan area. this work will contribute to our understanding of the disease characteristics in the areas around the covid-19 core outbreak point and provide reference data for decision-making for epidemic prevention and control in such special areas. 10 department of respiratory medicine, jiangxi province hospital of integrated chinese and western medicine, nanchang, china. 11 department of general practice, the first people's hospital of fuzhou, fuzhou, china. 12 department of pediatric neurology, ganzhou women's and children's hospital of jiangxi province coronavirus infections-more than just the common cold clinical management of severe acute respiratory infection when novel coronavirus (2019-ncov) infection is suspected: interim guidance. in: world health organization who. coronavirus disease 2019 (covid-19) outbreak. 2020 journey of a thai 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severity and fatality of sars-cov-2 infection: a metaanalysis covid-19 and the cardiovascular system characteristics of lymphocyte subsets and cytokines in peripheral blood of 123 hospitalized patients with 2019 novel coronavirus pneumonia (ncp). medrxiv 2020 clinical and immunologic features in severe and moderate coronavirus disease 2019 t-cell immunity of sars-cov: implications for vaccine development against mers-cov clinical course and outcome of 107 patients infected with the novel coronavirus, sars-cov-2, discharged from two hospitals in wuhan clinical characteristics of 60 discharged cases of 2019 novel coronavirus-infected pneumonia in taizhou, china clinical outcomes of covid-19 cases and influencing factors in guangdong province covid-19 in a designated infectious diseases hospital outside hubei province publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations we thank all the medical staff who participated in treating patients and all the patients enrolled in this study. the data of these patients have been published for the first time. all the authors who are not from zengdu hospital are volunteers from different hospitals in jiangxi province, and these volunteers work with doctors and nurses from zengdu hospital to fight against covid-19. special thanks to the 82 other volunteers from jiangxi province for their contributions. not applicable. authors' contributions ljs, zxg, wyp and hxy designed the study. hp, lc, zm, lhd, and ldh were responsible for collecting the epidemiological and clinical data; qxt examined the ct images and extracted the data; hzf, ljy, and zcl were responsible for processing the statistical data; and zwb, ywz, and lhd wrote the paper. zxg participated in the design and revision of the manuscript. all authors read and approved the final manuscript. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. the datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. this study was approved by the ethics committee of suizhou zengdu hospital. written informed consent has been obtained from all participants. the data used in this study was anonymized before its use. not applicable. the authors declare that they have no competing interests to disclose. key: cord-314591-ylokznn5 authors: quilty, billy j.; diamond, charlie; liu, yang; gibbs, hamish; russell, timothy w.; jarvis, christopher i.; prem, kiesha; pearson, carl a. b.; clifford, samuel; flasche, stefan; klepac, petra; eggo, rosalind m.; jit, mark title: the effect of travel restrictions on the geographical spread of covid-19 between large cities in china: a modelling study date: 2020-08-19 journal: bmc med doi: 10.1186/s12916-020-01712-9 sha: doc_id: 314591 cord_uid: ylokznn5 background: to contain the spread of covid-19, a cordon sanitaire was put in place in wuhan prior to the lunar new year, on 23 january 2020. we assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of covid-19 in other major cities in mainland china. methods: we estimated the number of infected travellers from wuhan to other major cities in mainland china from november 2019 to february 2020 using previously estimated covid-19 prevalence in wuhan and publicly available mobility data. we focused on beijing, chongqing, hangzhou, and shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. to do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. we also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios to simulate the effect of local non-pharmaceutical interventions. results: we find that in the four cities, given the potentially high prevalence of covid-19 in wuhan between december 2019 and early january 2020, local transmission may have been seeded as early as 1–8 january 2020. by the time the cordon sanitaire was imposed, infections were likely in the thousands. the cordon sanitaire alone did not substantially affect the epidemic progression in these cities, although it may have had some effect in smaller cities. reduced transmissibility resulted in a notable decrease in the incidence of infection in the four studied cities. conclusions: our results indicate that sustained transmission was likely occurring several weeks prior to the implementation of the cordon sanitaire in four major cities of mainland china and that the observed decrease in incidence was likely attributable to other non-pharmaceutical, transmission-reducing interventions. since late 2019, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), the causative agent of coronavirus disease 2019 (covid19) , has spread to over 114 countries and was declared a pandemic on 11 march 2020 [1] . some countries have enacted cordon sanitairetype travel restrictions, either to prevent the export of infections from an initial disease epicentre (such as wuhan in january 2020 [2] or northern italy in march 2020 [3] ) to other countries and regions or to prevent the import of infections from high-risk countries or regions (such as the usa's ban on travel from europe [4] ). cordon sanitaires aim to curb the number of infected travellers entering a region with a high proportion of susceptible individuals, where they may seed additional chains of transmission. however, historically, they at best delay, rather than prevent outbreaks elsewhere [5] . hence, the efficacy of cordon sanitaires in averting or delaying outbreaks in other locations is an open question. chinese authorities imposed a cordon sanitaire on the city of wuhan on 23 january 2020 [2] and extended the travel restrictions to the whole of hubei province by 26 january 2020 [6] . the restrictions were imposed 1 day prior to the lunar new year (lny) holidays and during chunyun, the 40-day holiday travel period that marks the largest annual human migration event in the world [7] . at the same time, other public health interventions, such as physical distancing, were also enacted across china [8] . this study aims to assess the impacts of the cordon sanitaire around wuhan, the epicentre of the covid-19 pandemic, on reducing incidence and delaying outbreaks in other well-connected large population centres in mainland china. we used publicly available mobility data based on location-based service (lbs) provided by baidu huiyan, to construct four mobility scenarios. combined with daily estimated prevalence of covid-19 in wuhan before 11 february 2020 by kucharski et al. [9] , we simulated the daily importations of infected travellers to beijing, chongqing, hangzhou, and shenzhen to assess the risk that they would cause sustained local transmission. we obtained daily prefecture-level human mobility data, expressed by a relative index scale, for mainland china from baidu huiyan for both the 2019 and 2020 travel periods surrounding the lny, known as chunyun. the platform aggregates mobile phone travel data from an estimated 189 million daily active users, processing > 120 billion daily positioning requests mainly through wifi and gps [10] . we examined the proportions of the total outflow leaving wuhan and entering all other prefectures in china (excluding wuhan). we then selected beijing, chongqing, hangzhou, and shenzhen for further analysis as major population centres with substantial travel with wuhan and a wide geographic spread. we assume that the early transmission dynamics of sars-cov-2 in cities of this size were similar to that in wuhan. to estimate the absolute number of daily travellers leaving wuhan, we assumed that each unit of baidu's migration index corresponds linearly to 50,000 travellers. this was chosen as the most credible value after synthesising evidence from several sources [8, [11] [12] [13] [14] (see additional file 1: supplementary appendix 1). we calculated the total number of daily travellers leaving wuhan and entering each city by taking the product of the scaling factor, the total daily outflow index from wuhan, and the daily proportion of travellers from wuhan entering the four cities. daily estimated covid-19 prevalence in wuhan was retrieved from the exposed (incubating) and infectious compartments of a published seir model on the early dynamics of covid-19 transmission in wuhan [9] . we estimated the number of daily infected arrivals in a destination city as a poisson process governed by the daily number of travellers and prevalence in wuhan (additional file 1: supplementary appendix 2). each day, we simulated this arrival process 100 times to capture the uncertainty in the process; this represents 7100 samples for the 71 days for each city in each scenario. we assumed that individuals would travel regardless of their infection status, and wuhan was the sole source of infected individuals and populations within destination cities mixed homogeneously. we examined four travel scenarios (table 1) : scenario 1 is based on the observed travel pattern in 2020 and represents the chunyun period with cordon sanitaire introduced on 23 january. scenario 2 represents a counterfactual travel pattern used to evaluate how the covid-19 outbreak would spread if no cordon sanitaire was implemented. this was based upon the actual travel from wuhan for the equivalent chunyun period in 2019. in scenario 3, we synthesised a hypothetical travel pattern to represent a typical non-chunyun period with cordon sanitaire introduced on 23 january, using outward travel flow on representative non-chunyun days in 2019. scenario 4 is a variation on scenario 3 in which no cordon sanitaire was implemented. we extended the corresponding outflow time series to the early stages of the outbreak (22 november 2019), by assuming the outflow from wuhan to equal to the average daily outflow on representative non-chunyun days, whilst accounting for weekday effects. the pairwise travel flow proportions between wuhan and each other prefecture-level city was only available between 1 january and 1 march, 2020, so an approximation of the general flow magnitude was used for dates outside of the observed range (22 november-31 december) and in simulated aspects of our scenarios, i.e. chunyun affected travel days in non-chunyun scenarios. a more detailed description of how each scenario was formulated is in additional file 1: supplementary appendix 3. as cases in china during the early epidemic were likely underreported [15] , we used a stochastic branching process model to simulate outbreaks in each of the four cities. consistent with the prevalence estimates from wuhan [9] , we began simulating travel from wuhan on 22 november 2019 and calculated incidence up to 1 february 2020. for each simulated infected arrival in each city on a given day, an independent branching process is generated, with: a negative binomial offspring distribution with a time-varying mean effective reproduction number (r e ) with baseline 2.2 [16] and overdispersion (k, variability in the number of secondary cases resulting from an infected case) of 0.1 [17] a log-normal serial interval (si) with mean of 4.7 days and standard deviation of 2.9 [18] we assume that in the initial phases of the epidemic (prior to the cordon sanitaire), the effective daily reproduction number (r e ) was 2.2 [16, 19] . the date at which the probability of sustained transmission exceeded a threshold of 95% (i.e. an outbreak occurring) given r e of 2.2 and k = 0.1 was used to evaluate the effect of travel restrictions (details in additional file 1: supplementary appendix 4) [20] . a sensitivity analysis for k using the lower and upper bounds from endo et al. [17] (0.04, 0.2) and h1n1-like (2.0) [21] overdispersion in r e is shown in fig. 4 . we also perform a sensitivity analysis on the serial interval, using a gamma-distributed si of mean 7.5 days and standard deviation of 3.4 days [19] (additional file 1: figure s3 and s5) [18, 22] . to simulate the effect of local non-pharmaceutical intervention measures (npis) such as physical distancing and workplace and school closures in addition to travel restrictions [23] , we compare r e = 2.2 in the absence of interventions (no change, unmitigated local outbreak), to 1.1 (50% reduction, slowing epidemic, r e > 1), or 0.55 (75% reduction, suppressing epidemic, r e < 1). we assume additional interventions took effect on the same date as the introduction of the cordon sanitaire, 23 january 2020. all analyses were carried out using r version 3.6.2. the branching process model was implemented using the package projections version 0.4.1 [24] . a gradual increase in the outflow from wuhan in the weeks prior to the lny was observed in both 2020 and 2019, exemplifying the chunyun period ( fig. 1 ). comparing the 23 days prior to the introduction of the cordon sanitaire in scenarios 1 and 2, we estimate daily outflow was 21.7% (95% ci 9.78-33.6%) higher in 2020 than the equivalent period in 2019. a surge in volume in the 3 days preceding the cordon sanitaire can be seen in scenario 1 (2020), where an estimated 1.69 million left wuhan, in line with other estimates [8] . a similar outflow immediately before the lny observed in scenario 2 (2019) suggests the surge cannot necessarily be attributed to upcoming travel restrictions. this is further reflected by the 22.5% between-year increase during this 3-day window not being substantially greater than the average daily outflow increase. the cordon sanitaire had a stark effect on reducing the total outflow from wuhan. comparing the mean daily outflow in the 23 days preceding restrictions with the 23 days after, volume fell by 92.7%, from 345,000 (95% ci 299,000-390,000) average daily travellers to 25, 300 (95% ci 8590-42,000). in comparison, volume fell by 30.2% during the equivalent period in 2019 from 290, 000 (95% ci 252,000-328,000) to 203,000 (95% ci 177, 000-228,000). after restrictions were imposed, travel volume declined to a low plateau over 5 days, during which approximately 330,000 people left. on the lowest day (3 february), we estimate 10,500 people left wuhan, which likely represents only essential journeys. in our hypothetical scenarios, we simulated the outbound flow with the additional travel volume due to chunyun removed. by comparing scenarios 2 and 4 during chunyun (10 january-18 february, 2020) we we found that in all but one prefecture with over 7 million inhabitants, the cordon sanitaire on 23 january did not substantially change the time at which sustained transmission was likely to occur (additional file 1: figure s1 a-f), but the picture was more mixed in smaller cities. of the four representative major cities selected for further analysis, during their pre-restriction travel phase in scenario 1 (1 january-23 january, 2020): beijing experienced a high volume of travel with approximately 1510 (95% ci 1200-1820) mean daily travellers from wuhan; chongqing had the highest at 1650 (95% ci 1320-1970); hangzhou received relatively fewer with 451 (95% ci 362-541); and shenzhen had a medium travel volume from wuhan with 820 (95% ci 664-976) mean daily travellers. effect of the cordon sanitaire on importations of infected persons to other major chinese cities we estimate infected individuals began arriving on a daily basis in other major population centres in mid-december in scenario 1 (observed chunyun travel profile and cordon sanitaire imposed) (fig. 2) . the estimated median number of infected arrivals on a given day peaked prior to the travel restrictions at 37 (95% uncertainty interval (ui) in beijing, 95 (95% ui 77-115) in chongqing, 13 (95% ui [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] in hangzhou, and 33 (95% ui 23-44) in shenzhen. travel restrictions reduced the number of infected arrivals to below 1 in all four cities within 2 days (fig. 2a) . in scenario 2 (chunyun travel profile without cordon sanitaire), the number of daily infected arrivals decreases slightly after the chunyun travel period (fig. 2a) . in cities with populations below 7 million, infected individuals began arriving later, so the cordon sanitaire may have acted to delay or prevent the arrival of infected individuals (additional file 1: figure s1 a-f). in scenario 3 (non-chunyun with travel restrictions), the estimated number of daily infected arrivals is marginally lower than scenario 1, peaking at 35 (95% ui in beijing, 39 (95% ui 28-50) in chongqing, 11 (95% ui 5-17) in hangzhou, and 25 (95% ui [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] in shenzhen. due to the volume of outbound travel from wuhan in scenario 1, we estimate that sustained local transmission was likely to have already occurred in the four cities in early january, several weeks prior to the introduction of the cordon sanitaire (table 2) . on the date travel restrictions from wuhan were imposed, local infections were likely to be in the thousands in the four cities (table 2) . outbreaks started later and were smaller on the date of the shutdown in hangzhou and shenzhen compared to beijing and chongqing, which reflects the relative volume of travel from wuhan. no substantial difference was observed in the daily incidence in the scenarios with and without travel restrictions in the four cities after the cordon sanitaire was imposed on 23 january; there were enough infected people to sustain local transmission in the absence of imported infections ( fig. 3 and additional file 1: figure s4 ). after the implementation of the cordon sanitaire on 23 january, the trajectory of the epidemic is determined primarily by reductions in r e to simulate local transmission-reducing interventions. in an unmitigated outbreak where r e remains at 2.2, incidence continues to increase exponentially in both scenarios; with r e reduced to 1.1, incidence steadies; and with r e reduced to 0.55, incidence decreased towards zero. the incidence after 23 january did not differ in scenarios with or without the implementation of the cordon sanitaire, and no additional effect was observed due to the cordon sanitaire after reducing r e . no substantial differences were observed in the estimated cumulative number of infections by 1 february with and without cordon sanitaire in any of the four cities, after accounting for uncertainty resulting from the importation process and variability in the number of secondary cases resulting from an infected case (overdispersion) (fig. 3) . decreasing the overdispersion parameter k from the baseline 0.1 to 0.04 [17] results in a delay to the likely date of an outbreak (fig. 4) ; despite this, an outbreak was highly probable in all four cities prior to the date of the cordon sanitaire. increasing k to 0.2 [17] , 0.54 [16] , and 2.0 (influenza-like) [21] further advanced the likely date of an outbreak. by utilising publicly available mobility data to model the spread of the outbreak from wuhan to other large population centres in china, we find that infected travellers from wuhan likely led to local transmission in other major chinese cities weeks before the cordon sanitaire. cities with more travellers from wuhan likely experienced higher incidence sooner. modelling the trajectory of the outbreaks up to 1 february, in scenarios with and without the effect of the cordon sanitaire, we find no substantial differences in the cumulative number of infections generated. by comparing chunyun and non-chunyun travel scenarios, no substantial difference was observed in terms of the cumulative number of infections generated by 1 february. this is likely due to the consistently high volume of travel these cities receive from wuhan year round, resulting in enough infected travellers arriving to seed chains of transmission even during a period of regular travel volume. this however may differ in smaller cities which receive highly seasonal influxes of travellers from wuhan relating to chunyun. the increase in mobility in 2020 compared to 2019 prior to lny could be explained by a variety of factors, including year-to-year variations and potential factors related to covid-19, such as the rumours of a rapidly growing outbreak and impending travel restrictions. in northern italy, a leaked covid-19 plan might have driven thousands to flee south [25] . our simulated number of arrivals of covid-19 infections for shenzhen by late january is broadly consistent with results shown in an observational study in guangdong province [26] (see additional file 1: supplementary fig. 3 median daily incidence of covid-19 (shaded areas indicate 50% and 95% confidence intervals) in beijing, for chunyun vs. non-chunyun and cordon sanitaire imposed (red, solid) vs. no cordon sanitaire (blue, dashed) and for varying values of the effective reproduction number r e , where r e = 2.2 (no change, unmitigated local outbreak), reduced from 2.2 by 50% to 1.1 (mitigation of outbreak, r e > 1), and 75% to 0.55 (suppression of outbreak, r e < 1) appendix 5, figure s6 and figure s7 ) [27] [28] [29] . however, the simulated number of locally transmitted cases around the same time is considerably higher than that observed. this disparity could be explained by testing programmes oversampling individuals with a recent travel history from highly affected areas, inflating the proportion of cases that were imported from outside guangdong and missing cases which obtained the virus locally [30] . furthermore, in scenarios when r e was set to 0.55 after 23 january (fig. 3 and additional file 1: figure s4) , we also see case numbers decline at a similar rate and timeframe to the epidemic observed in guangdong [23] , suggesting stringent local npis played a key role in suppressing the outbreak. in the formulation of the travel scenarios, we assumed that the baidu huiyan mobility index values were relative and linear and corresponded to 50,000 travellers per unit. this was based on widely quoted estimates of people leaving wuhan and the inter-city capacity of the travel network [8, 11-14, 31, 32] (additional file 1: supplementary appendix 1). however, the index may represent a different number of travellers, or the scale may even be nonlinear and the result of a more complex function, but without other evidence we assume linearity, as have other studies [8, 13] . if we chose a higher scaling factor, similar to ones used in other studies [12, 13] , it is likely that infected travellers would have arrived even earlier and in greater numbers to the four destination cities. additionally, by reconstructing travel outflows for both dates outside of the observed range (22) (23) (24) (25) (26) (27) (28) (29) (30) (31) and simulated aspects of our scenarios, i.e. chunyun affected travel days in non-chunyun scenarios, the actual travel pattern may not have been accurately represented. further assumptions were also made surrounding the pairwise travel flows, as observed data was only available for 2020, and the travel flows between wuhan and each other prefecture-level city may have differed in 2019. we only considered wuhan to be the sole source of infected individuals, and we only accounted for travellers making single-leg journeys to their destination. as such, we may underestimate the number of infected persons arriving by not considering the number of travellers which may have stopped in an intermediate location, become infected, and then arrived at the destination to seed local transmission, or indeed infected travellers arriving from outside of wuhan. hence, most of our assumptions likely underestimated the number of travellers from wuhan, and our conclusions would likely be the same even if the true number was higher. however, we also assumed that individuals would travel regardless of their infection status, which may overestimate the number of infections in destination cities. in our model, we assume all chains of transmission are independent and populations in each city mix homogeneously. these assumptions are likely only valid in the early stages of an epidemic; however, as we only model the initial introduction of cases and their contact networks, the effect of changing these assumptions is unlikely to alter our conclusions. moreover, the overdispersion parameter k likely captures the spread of r e and acts to counter the assumed homogeneous population mixing. reducing the overdispersion parameter k from 0.1 (~10% of individuals responsible for 80% of transmission [17] ) to 0.04 (~5% of individuals responsible for 80% of transmission) resulted in a delay to the date of an outbreak, yet not past the date of the cordon sanitaire. as recent studies have shown [8, 9, 33] , strict physical distancing measures soon decreased the effective reproduction number to 1 or less in wuhan and other cities in china. by incorporating this decrease into our model, we find that cordon sanitaire alone, implemented after outbreaks were likely to be established in other cities, was likely ineffective in stopping or slowing outbreaks of covid-19 in other major population centres. to have a greater impact, the cordon sanitaire would need to be implemented earlier, as investigated in [34, 16] , and be accompanied by other npis, such as general physical distancing and school and work closures [8, 23] . similarly, it is unlikely that cordon sanitaires in other countries with well-established, geographically dispersed outbreaks will substantially delay covid19 spread. an open question is whether travel restrictions may be more efficacious to prevent or delay reintroductions after the lifting of other npis. whilst earlier restrictions on travel from wuhan may have had a larger impact, in countries with a highdegree of inter-city travel, it may be difficult to implement such highly disruptive travel restrictions at an early stage of the epidemic, before local transmission has occurred in other cities. we find that local transmission in the four cities we studied (here defined as the probability of sustained transmission exceeding a 95% threshold) was most likely established between 1 january and 8 january; it was only on 8 january that the aetiology of the "mystery pneumonia" (which was not yet confirmed to spread from person-to-person [35] ) was determined as a novel coronavirus, and the first death occurred [36] . it is difficult to see how the cordon sanitaire could have been justified any earlier, as almost every aspect of covid-19 virology and epidemiology was unknown. hence, it is likely that the sustained decline in covid-19 incidence in other cities of china several months into the outbreak is primarily due to other public health measures to reduce the disease transmissibility, i.e. to reduce the reproduction number to 1 or below [9, 23, 33] . the cordon sanitaire may have been more efficacious in delaying outbreaks internationally, as the relative number of travellers is orders of magnitude lower [8, 37] ; the same may also apply to lower-traffic destinations from wuhan within china, such as small cities geographically distant from wuhan, as observed in tian et al. [8] . we found a mixed picture in these cities, where the cordon sanitaire may have been more efficacious at delaying or preventing outbreaks (additional file 1: figure s1 a-f). however, covid-19 transmission dynamics may differ in comparison to large cities, and as such, we chose to focus on the effect of travel restrictions in large cities with large volumes of travel from wuhan, where data on r and k from the early outbreak in wuhan are likely generalisable. furthermore, these destinations with low traffic from wuhan are more likely to be seeded by outbreaks in other, comparatively closer, large cities first. hence, our assumption of a single outbreak source would have been much less realistic. our estimated dates of introduction in other cities are earlier than those observed [1] and reported in other studies [38] . this is due in part to correction for underreporting, both by using the estimated daily prevalence in wuhan from kucharski et al. [9] , which is significantly higher than the confirmed number of cases [20] , and by not relying on reported cases in other provinces. the effect of underreporting is likely more pronounced early in the outbreak prior to a well-defined case definition or widespread testing [15] . hence, reconstructing the early outbreak through a simulation approach was more appropriate in this setting. we concur with tian et al. 2020 [8] that prohibiting travel alone did not act to reduce the number of covid-19 infections in four major cities outside of wuhan or hubei and that other local control measures were likely instrumental in reducing incidence. likewise, kraemer et al. [38] conclude that whilst a decrease in the growth rate was observed in large cities after the cordon sanitaire was imposed, this is difficult to disentangle from local control measures. in conclusion, the introduction of cordon sanitaire-type travel restrictions around a covid-19 epidemic centre after community transmission is already occurring in other well-connected population centres on its own likely has little effect on altering their epidemic trajectories. stringent npis in cities are more likely to have a bigger impact in reducing incidence and pressure on healthcare systems. further research should examine the role of travel restrictions during the partial lifting of npis across china and elsewhere. supplementary information accompanies this paper at https://doi.org/10. 1186/s12916-020-01712-9. additional file 1 : supplementary appendix 1-5. table s1 -various scaling factors calculated from different sources. table s2 -parameters used to estimate the total number of travellers leaving wuhan and entering other prefecture-level cities for each scenario. table s3 . bivariate regression results where y = number of imported cases into guangdong (by date of symptom onset) and x = imported cases into guangdong (by date of arrival), for an increasing amount of day lags. figure s1. date at which the mean probability of sustained transmission breaches 95% in each prefecture, by region (a-f). figure s2 . location of wuhan and the four cities of interest in mainland china. figure s3 . delay distributions for the serial interval of covid-19 infection from literature. figure s4 . median daily incidence of covid-19 in the four cities of interest. figure s5 . median daily incidence of covid-19 in the four cities of interest with alternative serial interval of mean 7.5 days (sd: 3.4). figure s6 . estimated daily infected arrivals in guangdong province. figure s7 . observed imported cases by date of symptom onset vs. predicted imported cases by date of arrival with a lag of 4 days. authors' contributions bjq, cd, yl, kp, pk, rme, and mj conceived the study. bjq and cd designed and programmed the model and made the figures. yl, hg, twr, and cij provided the data. yl, hg, twr, cij, kp, cabp, sc, sf, pk, rem, and mj consulted on the analyses. bjq, cd, yl, and mj wrote the manuscript. the cmmid covid-19 working group members contributed to processing, cleaning, and interpretation of data; interpreted the study findings; contributed to the manuscript; and approved the work for publication. all authors interpreted the findings, contributed to writing the manuscript, and approved the final version for publication. novel coronavirus (2019-ncov) situation reports virus-hit chinese city shuts public transport. bbc news. 2020 il governo firma il decreto coronavirus: l'italia divisa in 3 zone (translated: the government signs the coronavirus decree: italy divided into 3 areas). la repubblica trump's virus travel ban on europe comes into force effectiveness of travel restrictions in the rapid containment of human influenza: a systematic review tracing the largest seasonal migration on earth an investigation of transmission control measures during the first 50 days of the covid-19 epidemic in china early dynamics of transmission and control of covid-19: a mathematical modelling study the novel coronavirus, 2019-ncov, is highly contagious and more infectious than initially estimated incorporating human movement data to improve epidemiological estimates for 2019-ncov. medrxiv evaluating new evidence in the early dynamics of the novel coronavirus covid-19 outbreak in wuhan, china with real time domestic traffic and potential asymptomatic transmissions. medrxiv translated: ten days before the spring festival, wuhan railway express sent more than 4 million passengers, and public transportation delivered more than 80 million passengers using a delay-adjusted case fatality ratio to estimate under-reporting. cmmi d repository pattern of early human-to-human transmission of wuhan estimating the overdispersion in covid-19 transmission using outbreak sizes outside china serial interval of novel coronavirus (covid-19) infections early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia introducing the outbreak threshold in epidemiology superspreading and the effect of individual variation on disease emergence epitrix: small helpers and tricks for epidemics analysis the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study leaked coronavirus plan to quarantine 16m sparks chaos in italy. the guardian genomic epidemiology of sars-cov-2 in guangdong province incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china virological assessment of hospitalized patients with covid-2019 the natural history and transmission potential of asymptomatic sars-cov-2 infection translated: guidelines for the epidemiological investigation of new coronavirus pneumonia) translated: beijing's three major railway stations have the highest peak passenger flow before the festival, and 620,000 people are expected to leave beijing by train translated: during the spring festival transport, capital airport is expected to have 11. 51 million passengers in and out of hong kong) age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in china effect of non-pharmaceutical interventions for containing the covid-19 outbreak in china a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster china reports first death from new virus. the new york times the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak the effect of human mobility and control measures on the covid-19 epidemic in china publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the mobility data was sourced from baidu haiyan migration dashboard at https://qianxi.baidu.com/. the code for this analysis is available on github at https://github.com/ bquilty25/wuhan_travel_restrictions. neither patients nor the public were involved with the design, conduct, reporting, or dissemination plans of our research. as this work is a simulation study, there are no participants to which we can disseminate the results of this research. competing interests mj is a board member for the journal. ae received a research grant from taisho pharmaceutical co., ltd. we declare no other competing interests.received: 24 april 2020 accepted: 16 july 2020 key: cord-339743-jxj10857 authors: liu, h.; bai, x.; shen, h.; pang, x.; liang, z.; liu, y. title: synchronized travel restrictions across cities can be effective in covid-19 control date: 2020-04-06 journal: nan doi: 10.1101/2020.04.02.20050781 sha: doc_id: 339743 cord_uid: jxj10857 mobility control measures are of crucial importance for public health planning in combating the covid-19 pandemic. previous studies established the impact of population outflow from wuhan on the spatial spread of coronavirus in china and hinted the impact of the other three mobility patterns, i.e., population outflow from hubei province excluding wuhan, population inflow from cities outside hubei, and intra-city population movement. however, the overall impact of all mobility patterns, or the impact of the different timing of mobility restriction intervention, are not systematically analyzed. here we apply the cumulative confirmed cases and mobility data of 350 chinese cities outside hubei to explore the relationships between all mobility patterns and epidemic spread, and estimate the impact of local travel restrictions, both in terms of level and timing, on the epidemic control based on mobility change. the relationships were identified by using pearson correlation analysis and stepwise multivariable linear regression, while scenario simulation was used to estimate the mobility change caused by local travel restrictions. our analysis shows that: (1) all mobility patterns correlated with the spread of the coronavirus in chinese cities outside hubei, while the corrleations droppd with the implemetation of travel restrictions; (2) the cumulative confirmed cases in two weeks after the wuhan lockdown was mainly brought by three patterns of inter-city population movement, while those in the third and fourth weeks after was significantly influenced by the number of intra-city population movement; (3) the local travel restrictions imposed by cities outside hubei have averted 1,960 (95%pi: 1,474-2,447) more infections, taking 22.4% (95%pi: 16.8%-27.9%) of confirmed ones, in two weeks after the wuhan lockdown, while more synchronized implementation would further decrease the number of confirmed cases in the same period by 15.7% (95%pi:15.4%-16.0%) or 1,378 (95%pi: 1,353-1,402) cases; and (4) local travel restrictions on different mobility patterns have different degrees of protection on cities with or without initial confirmed cases until the wuhan lockdown. our results prove the effectiveness of local travel restrictions and highlight the importance of synchronized implementation of mobility control across cities in mitigating the covid-19 transmission. previous studies prove it is the population mobility that accelerates the spatial spread of the epidemic, while travel restrictions could contribute to the epidemic control. [5] [6] [7] [8] [9] [10] [11] [12] [13] the spring migration ("chunyun" in chinese) of 2020 started on jan 10, which is the earth's most massive annual human migration. 13 although wuhan, the capital city of hubei province, suspended all in and out public transport since 10:00 am jan 23, 2020, about five million people already left wuhan before the quarantine. 14 studies show that while the wuhan lockdown greatly slowed the spread of covid-19, 6-10 the number of population emigration from wuhan highly correlated to the imported cases in other cities in china. 8, [11] [12] [13] [15] [16] [17] [18] while the impact of the population outflow from wuhan is well established, the impact of other mobility patterns on the epidemic trajectory has not been well understood. local population mobility for a city includes both intra-city and inter-city patterns. the inter-city mobility can be categorized into three sources, i.e., from wuhan, from hubei province (excluding wuhan), and from cities outside hubei. as nearly two-thirds of population outflow from wuhan flooded into other cities within the hubei province, 13, 17 it is important to consider the population outflow from hubei (excluding wuhan) as a potentially most significant source of epidemic transmission risk after jan 23. the intra-city population movement is also an essential factor-research shows that cities introduced pre-emptive intra-city movement restrictions have 33.3% less confirmed cases in the first week of the epidemic outbreak compared to those started restrictions after the emerging of confirmed cases, 6 pointing to the importance of timing of introducing these measures. for inter-city population movement among cities outside hubei, which are restricted after the wuhan lockdown, different studies hold inconsistent reviews. on the one hand, the implementation of inter-city travel restrictions cannot significantly reduce the number of confirmed cases during the first week of city outbreaks; 6 on the other hand, the transmission model of the covid-19 cannot be accurately established without the inter-city connections. 19 most of these existing studies are based on one or two mobility patterns, and the overall impact of these four mobility patterns on the spread of the covid-19 is not well understood. the uncertainty of the number of confirmed cases in the early stage of the epidemic spread, 5, 19 ranging from 427 (officially confirmed) to potentially over 10,000 underscores the importance of considering all four mobility patterns in the covid-19 spread, perhaps more so than the number of confirmed cases. in this study, we aim to investigate the relationship between population mobility, both inter-city and intra-city, and the spread of covid-19. based on the mobility change, the impact of local travel restrictions in other cities, besides the wuhan lockdown, on the epidemic control was estimated. given that the three mobility patterns, except the population outflow from wuhan, are heavily influenced by policy measures introduced by the central and local governments, such investigate is important in evaluating the effectiveness and understanding the influence of timing of different measures, which can in turn inform policy interventions in the future. we collected the number of laboratory-confirmed cases from daily official reports from the health commissions of the 34 provincial-level administrative units from jan 23, 2020. the provincial reports include the total instances as well as the breakdown for cities. the city-level data we used includes 367 cities, i.e., four cities directly under the central government, 333 prefecture-level cities, and 29 countylevel cities directly under the provincial government, covering all the areas of mainland china. a total of 350 cities are from outside hubei. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . to capture population movement among and within cities, we derived the mobility data from the baidu qianxi (http://qianxi.baidu.com/). 20 the data is calculated and analyzed from the location based service (lbs) of both baidu map and one flight path monitoring app --baidu tianyan. the data of both 2019 and 2020 were acquired, aligned by the chinese lunar calendar, from the start of spring migration (jan 10, 2020). the data of population inflow from wuhan, population inflow from hubei excluding wuhan, and intercity population movement were all calculated based on the baidu mobility index. the baidu mobility index records daily outflow and inflow to and from each of the 367 cities, which is comparable among cities. we assume there were five million people outflowed from wuhan between the start of the spring emigration and the wuhan lockdown, and scaled the index to approximate values of population size. for each day, the top 100 destination cities for population outflow from wuhan and other cities in hubei were recorded. we believe the data are representative of population outflow from wuhan and from hubei excluding wuhan. 19 for the inter-city connections, we used the daily inflow values of each city. the number of population migration from hubei was excluded since it was considered separately. the data of the intra-city population movement was counted based on the baidu intra-city mobility index. the intra-city mobility index, ranging from 0.3 to 8.0, reflects the proportion of people traveling within cities in the resident population. we used the 0.1 times of the daily intra-city mobility index, ranging from 3.0% to 80.0%, multiplied with the value of permanent population as the proxy daily population intra-city travel data. the data of the permanent population at the end of 2018 was retrieved from the statistical yearbook of provinces and cities. the imported cases and local infected ones might bring by different mobility patterns. thus, we used the cumulative confirmed cases of two time periods in cities outside hubei to study their relationship with different mobility data. the cumulative confirmed cases in two periods were computed to simulate the epidemic spread at different stages. the first period, referred hereafter as stage one, was the first two weeks after the wuhan lockdown, from jan 24 to feb 06. since the incubation period for the covid-19 usually ranged from one to 14 days, the majority of imported cases would be identified in this period. the second period was the two weeks after stage one, referred hereafter as stage two, from feb 07 to feb 20. most of the confirmed cases in this period should be infected in cities outside hubei. the ratio of new confirmed cases in the population outflow was typically used to estimate the virus transmission risk of population outflow. however, the epidemic outbreak might be underestimated at the early stage due to the lack of attention or detection ability. until the wuhan shutdown, only 427 cases were confirmed as positive for covid-19, while the 86% of all infections might be undocumented. 19 facing such a big gap, we investigate the relationship between mobility and epidemic spread without considering the proportion of the number of confirmed cases in population migration. to identify the impact of different mobility patterns on the epidemic spread, we used linear regression models to assess the relationship between population mobility data and the confirmed cases. 6 in stage one, the confirmed cases could be imported from hubei (both wuhan and cities outside wuhan), from cities outside hubei, or from the locality. therefore, the analysis was performed using the model: . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint ߝ is the constant coefficient that reflects information residue. since the mean incubation period of covid-19 was 5.2 days (95% confidence interval [ci], 4.1 to 7.0), 21 changing across studies, 7,22,23 we used the mobility data in one week before the stage one in the model. 7 the data of ‫ܧ‬ ሺ ‫ݓ‬ ሻ was from jan 17 to jan 23, while the data of ܱ and ‫ܫ‬ were all from jan 17 to jan 30. , we used the data after the wuhan lockdown because it was not the main risk of transmission before that. 17 thus, the data of ‫ܧ‬ ሺ ݄ ሻ were from jan 23 to the suspension of all interprovincial transport to and from hubei, jan 29 (table s1 ). as for stage two, the imported cases from hubei were not considered: ‫ܥ‬ is the number of initial confirmed cases until feb 06. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint the statistical analysis included two steps. first, pearson correlation analysis was applied to check whether different mobility patterns were correlated with the spread of covid-19 in cities outside hubei in two time periods. correlated data would be introduced to the following linear regression. second, stepwise multivariate linear regressions were built to explore the explanatory capacity of mobility data to the confirmed cases. a model with the highest adjusted r 2 was taken as the best-fit one. cities without confirmed cases until the end of each stage were excluded from the study. besides for all the cities with confirmed cases after the wuhan lockdown ‫ܥ(‬ we assume, after the wuhan lockdown, the local travel restrictions in cities outside hubei contributed to the epidemic control by influencing population mobility. 10, 16 data for three mobility patterns, except the population outflow from wuhan, in two scenarios were obtained under assumptions (table s2) . we assume the transmission conditions and virus characteristics in china would remain unchanged, and the best-fit models generated from the regression analysis were used to estimate the number of confirmed cases in cities outside hubei based on the mobility data. the differences between the estimated ones and the actually reported ones are caused by the implementation of local travel restrictions, implying their impact on the epidemic control. to simulate the scenario of no travel restrictions in cites outside hubei (scenario 1), we used the 2019 baidu data and assumed the mobility scale captured in 2019 would be similar to those of the equivalent time period during 2020. 19 therefore, we adopted the mobility direction of 2020 and the mobility scale of . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint 2019 to simulate the population mobility after jan 23, 2020, when there were no local travel restrictions. all data before the wuhan lockdown remained unchanged. the daily population outflow from hubei (excluding wuhan), inter-city population movement, and intra-city population movement after feb 03, 2019, aligned by the chinese lunar calendar with jan 23, 2020, were used as proxy mobility data for the no local travel restrictions status in cities outside hubei. to understand the role of the relative timing imposition of local travel restrictions in other cities from the wuhan lockdown, our scenario 2 assumes more timely travel restrictions being imposed in cities outside hubei. the same models and methods were used as above, and the only change was the mobility data. before jan 30, cities successively suspended their inter-provincial transport to and from hubei, and restricted their inter-city and their intra-city population movement to varying degrees. that is to say, the inter-city and intra-city population movements were all limited after jan 30. we assume all travel restrictions in cities outside hubei were imposed at the same time as the wuhan lockdown. the daily population outflow from hubei excluding wuhan, and inter-city and intra-city population movement from jan 31 to feb 06 replaced those from jan 23 to jan 30, as proxy mobility data for the timely restricting travels status. the pearson coefficients indicate positive statistical correlations between all mobility patterns and the number of confirmed cases in both stage one and stage two (p<0.01) (table 1-1 and 1-2, figure s1 ). it suggests that cities with more population inflow from wuhan and other cities in hubei, more population migration from cities outside hubei, and more intra-city population movement would have more . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . the best-fitting linear regression models for epidemic development in both stage one and stage two are listed in table 2 . in stage one, three mobility patterns, i.e., population inflow from wuhan and other cities in hubei, and inter-city population movement, together with the number of initial confirmed cases, could explain 73.3% of the inter-city differences in newly reported infections in cities outside hubei. the intra-city population movement is highly correlated with the inter-city one (r=0.812, p<0.01), but its impact on the number of cumulative confirmed cases is less than the inter-city one. this result implies the existence of imported cases from cities outside hubei. in stage two, intra-city population movement and the number of initial confirmed cases could explain 50.9 % of the inter-city differences in newly reported infections in cities outside hubei. the impact of inter-city population movement is not significant. in stage one, the epidemic spread in cities outside hubei, with or without initial confirmed cases, is significantly influenced by population inflow from hubei, including from wuhan and other cities in . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint hubei. meanwhile, the inter-city population movement from cities outside hubei and intra-city population movement have varied impact. for cities without initial confirmed cases, both inter-city and intra-city population movements significantly influenced the epidemic development. in other words, four kinds of mobility patterns jointly affected the epidemic spread in these cities. for cities with initial confirmed ones, both inter-city (from cities outside hubei) and intra-city population movement have no significant impact on their epidemic development. two reasons might cause it. one is that the directly imported cases from hubei took the majority of reported ones in this stage, namely the significance of population inflow from hubei subjugating others. the cities with initial confirmed cases are the leading destinations for population outflow from hubei. these cities, taking 32.6% of cities outside hubei, accommodated 57.9% of population outflow from wuhan before its closure and 68.1% of population outflow from hubei excluding wuhan after the wuhan lockdown. the second reason is, in these cities, both inter-city (from cities outside hubei) and intra-city population movement are highly correlated with the number of population inflow from wuhan (r=0.700 and 0.748 respectively, p<0.01). the inter-city and intra-city mobility data were excluded from the best-fit model due to multicollinearity. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint most of the estimated increase in stage one is due to the population inflow from hubei after the wuhan lockdown. if only the population outflow from hubei was prohibited after the wuhan lockdown, i.e., the inter-city and intra-city population movement were not restricted in cities outside hubei, the estimated increase in the number of confirmed cases is 576 (95%pi: 437-716). thus, more than two-thirds of the expected increase in confirmed cases is due to the population outflow from hubei (excluding wuhan) if there were no travel bans except the wuhan lockdown. intra-city travel ban plays a significant role in preventing local infections. our results show there are 248 cities that have confirmed cases in stage two. if there is no intra-city travel restriction in these cities, the confirmed cases are estimated to increase by 33.1% (95%pi: 19.3%-46.9%) of observed ones. the intracity travel bans make the inter-city population movement from jan 31 to feb 13, after the public holiday of the spring festival, decreased to 50.1% of that in the last year, ranging from 23.7% to 87.8%. for these cities, the inter-city population movement was averagely decreased to 15.8% of that in the last year, ranging from 2.8% to 55.7%. it probably because of the strict inter-city travel ban that makes the influence of inter-city population movement insignificant on local infections. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint although the travel restrictions in chinese cities outside hubei have played essential roles in the epidemic control, our results suggest that more timely travel restrictions after the wuhan lockdown could better control the spread of the virus. if all cities outside hubei imposed their inter-city, including to and from hubei, and intra-city travel bans at the same time as the wuhan lockdown, these cities would report 1,378 mobility control measures are of crucial importance for public health planning in the outbreak of the in this study, we explore the relationships between mobility and epidemic spread and if the whole hubei province was not quarantined after the wuhan lockdown, further national seeding and subsequent infections might become inevitable. by mar 12, 2020, hubei excluding wuhan has more confirmed cases (17, 795) than china excluding hubei (13, 032) . 24 our results suggest that, in cities outside hubei, the travel restriction of hubei (excluding wuhan) is more effective than other inter-city . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint and intra-city travel bans in controlling the development of the epidemic in two weeks after the wuhan lockdown. on jan 26, all airports and railway stations in hubei were closed. 25 before jan 30, all other provinces in mainland china suspended their inter-provincial road transport to and from hubei (table s1) for cities without reported infections before the wuhan lockdown, the preventive prohibition of both inter-city and intra-city population movement is essential to their epidemic control. the prohibition of inter-city population movement from cities outside the hubei and intra-city population movement prevented 405 more confirmed cases (95%pi: 342-468) in stage one (table s3) , occupying 69.9% of the number of preventions by all local travel bans. the travel controls in cities without initial confirmed cases tend to be relatively late or loose than those in cities having initial infections. from jan 24 to jan 30, 2020, the inter-city population movement from cities outside hubei and intra-city population movement in cities without initial confirmed cases decreased on average to 64.4% and 72.6% of those in the same period of 2019, while the percentage are averagely 59.2% and 65.2% for cities with initial confirmed cases ( table . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint s2). the local travel restrictions were necessary and practical to cities without initial confirmed cases, even if they were not that strict. different mobility patterns influenced the covid-19 spread in different periods. our results show, in the early stage of epidemic development, it is the inter-city mobility, including from wuhan, from hubei excluding wuhan, and from other cities outside hubei, that promotes the spatial spread of the virus. after the quarantine of the whole hubei and the prohibition of inter-city transport, the importance of restricting the intra-city population movement is highlighted. if there were no restrictions on intra-city population movement, the confirmed cases in cities outside hubei might increase 33.1% (95%pi: 19.3%-46.9%) in the third and fourth weeks after the wuhan lockdown. the intra-city travel restrictions played vital roles in the epidemic control in china. it is worth noting that china has implemented many non-pharmacological interventions, not limited to these travel restrictions. source control measures, like isolating people with the virus, monitoring or quarantining symptoms of healthy contacts, requiring masks for individuals in all public places, etc., have been introduced to reduce potential secondary infections. 26, 27 it is the intensive source control that reduces new local infections. the contribution of population movement from wuhan or hubei to subsequent epidemic development might also be dampened due to the implementation of source control measures. 7 without the implementation of combined source control measures, our study, at least in the model of stage two, might have different results. our study quantified the relationships between mobility patterns and epidemic trajectory in china and highlighted the importance of synchronized travel restrictions across cities. several policy implications . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint can be drawn. first, the geographical extension of the quarantine should be carefully considered by the government before the official announcement. in the early stage of epidemic development, there might be a nonnegligible number of infected but undetected people in the areas that have geographical connections and frequent traffic with the epidemic-stricken ones, like other cities in hubei. in particular, there are many asymptomatic virus careers that are highly contagious. 23, 28 on the other hand, the expansion of the quarantined area would also bring substantial economic losses. whether to include farther hinterlands, and if so to what extent, will need to be carefully considered carefully in making the quarantine decision. second, our results show the importance of timely and active local countermeasures by cities outside of the epicenter. while actual travel control measures may differ across cities, simply by compressing the time gap between wuhan and other cities could further reduce the covid-19 outbreak. it is important for countries and governments to impose timely interventions to combat the pandemic. lh and bx designed the experiments. lh and lz collected data. lh analysed data and wrote the first draft, and ly made the figures. lh, bx, sh, and px interpreted the results and contributed the final manuscript. all authors approved the final version for submission. we declare no competing interests. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.04.02.20050781 doi: medrxiv preprint who announces covid-19 outbreak a pandemic ) 2. who. coronavirus disease 2019 (covid-19) situation report -52 there were no newly confirmed cases in four consecutive days in all provinces except for hubei cities and prefectures in hubei excluding wuhan have no new confirmed cases for 9 consecutive days covid-19: challenges to gis with big data the impact of transmission control measures during the first 50 days of the covid-19 epidemic in china the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak the effects of human mobility and control measures on the covid-19 epidemic in china impact of international travel and border control measures on the global spread of the novel 2019 coronavirus outbreak transmissibility of coronavirus disease 2019 (covid-19) in chinese cities with different transmission dynamics of imported cases temporal relationship between outbound traffic from wuhan and the 2019 coronavirus disease (covid-19) incidence in china estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china covid-19 control in china during mass population movements at new year. the the press conference on covid-19 in hubei distribution of the 2019-ncov epidemic and correlation with population emigration from wuhan estimation of local novel coronavirus (covid-19) cases in wuhan, china from off-site reported cases and population flow data from different sources risk assessment of exported risk of novel coronavirus pneumonia from hubei province nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the lockdown of hubei is in process: 17 cities stopped public transportation covid-19: what is next for public health? taking the right measures to control covid-19. the lancet infectious diseases can we contain the covid-19 outbreak with the same measures as for sars? the lancet infectious diseases we collated epidemiological data and mobility data from publicly available data sources. all the data sources we used are documented in the main text and supplementary tables. key: cord-298881-u6uqroi0 authors: huang, ian; lim, michael anthonius; pranata, raymond title: diabetes mellitus is associated with increased mortality and severity of disease in covid-19 pneumonia – a systematic review, meta-analysis, and meta-regression() date: 2020-04-17 journal: diabetes metab syndr doi: 10.1016/j.dsx.2020.04.018 sha: doc_id: 298881 cord_uid: u6uqroi0 background and aims: diabetes mellitus (dm) is chronic conditions with devastating multi-systemic complication and may be associated with severe form of coronavirus disease 2019 (covid-19). we conducted a systematic review and meta-analysis in order to investigate the association between dm and poor outcome in patients with covid-19 pneumonia. methods: systematic literature search was performed from several electronic databases on subjects that assess dm and outcome in covid-19 pneumonia. the outcome of interest was composite poor outcome, including mortality, severe covid-19, acute respiratory distress syndrome (ards), need for intensive care unit (icu) care, and disease progression. results: there were a total of 6452 patients from 30 studies. meta-analysis showed that dm was associated with composite poor outcome (rr 2.38 [1.88, 3.03], p < 0.001; i(2): 62%) and its subgroup which comprised of mortality (rr 2.12 [1.44, 3.11], p < 0.001; i(2): 72%), severe covid-19 (rr 2.45 [1.79, 3.35], p < 0.001; i(2): 45%), ards (rr 4.64 [1.86, 11.58], p = 0.001; i(2): 9%), and disease progression (rr 3.31 [1.08, 10.14], p = 0.04; i(2): 0%). meta-regression showed that the association with composite poor outcome was influenced by age (p = 0.003) and hypertension (p < 0.001). subgroup analysis showed that the association was weaker in studies with median age ≥55 years-old (rr 1.92) compared to <55 years-old (rr 3.48), and in prevalence of hypertension ≥25% (rr 1.93) compared to <25% (rr 3.06). subgroup analysis on median age <55 years-old and prevalence of hypertension <25% showed strong association (rr 3.33) conclusion: dm was associated with mortality, severe covid-19, ards, and disease progression in patients with covid-19. coronavirus disease 2019 (covid -19) has been declared as a public health emergency by the world health organization (who) on 30 january 2020. at the time this paper is written, covid-19 has inflicted more than 1.2 million people globally with overall mortality rate of 5.7%. [1] although the majority of covid-19 patients present with mild or no symptoms, some patients will develop severe pneumonia, acute respiratory distress syndrome (ards), multi-organ failure, and death. clinical predictors may provide vital clues regarding efficient resource planning and allocation during a pandemic. diabetes mellitus (dm) is one of the most prevalent chronic conditions with devastating multi-systemic complication and was estimated to have inflicted 463 million people in 2019. [2] it is not yet known whether people with dm are more susceptible to covid-19, but several studies have reported the association between severe covid-19 infection with dm. [3, 4] it was postulated that the angiotensin converting enzyme 2 (ace2) may be the plausible explanation of this association. [5] in this study, we aimed to perform a systematic review and meta-analysis in order to investigate the association between dm and poor outcome in patients with pneumonia. our hypothesis is that dm is associated with poor outcome in patients with covid-19 pneumonia. to the best of the authors knowledge, this is the first systematic review, meta-analysis, and meta-regression that comprehensively describe the association between dm and outcome in covid-19. research articles that evaluate the association between covid-19 and clinically validated definition of mortality, severe covid-19, ards, icu care, and disease progression. we included all research articles in adult patients diagnosed with covid-19 with information on dm and clinical grouping or outcome of the clinically validated definition of mortality, severe covid-19, ards, icu care, and disease progression. the following types of article were excluded: articles other than original research (e.g., review articles, letters, or commentaries); original research with samples below 20 or case reports and series; articles not in the english language; articles on research in pediatric populations (17 years of age or younger). we performed systematic literature search from pubmed and europepmc with the search terms 1) "covid-19" or "sars-cov-2" and "characteristics", 2) "covid-19" or "sars-cov-2" and "diabetes", english, medline. duplicate results were removed. the remaining articles were independently screened for relevance by its abstracts with two authors (mal and ih). the full text of residual articles was assessed according to the inclusion and exclusion criteria. the search was finalized on april 8 th , 2020 the study was carried out per the preferred reporting items for systematic reviews and meta-analyses (prisma) guideline. data extraction was performed independently by two authors (ih and rp), we used standardized forms that include author, year, study design, age, gender, cardiovascular diseases, hypertension, dm, need for icu care, and severe covid-19. the outcome of interest was composite poor outcome that comprised of mortality, severe covid-19, ards, need for icu care, and disease progression. ards was defined as per world health organization (who) interim guidance of severe acute respiratory infection (sari) of covid-19, including the acute onset, chest imaging, and origin of pulmonary infiltrates, and oxygenation impairment. [6] severe covid-19 was defined as patients who had any of the following features at the time of, or after, admission: (1) respiratory distress (≥30 breaths per min); (2) oxygen saturation at rest ≤93%; (3) ratio of partial pressure of arterial oxygen (pao2) to fractional concentration of oxygen inspired air (fio2) ≤300 mmhg; or (4) critical complication (respiratory failure, septic shock, and or multiple organ dysfunction/failure). [7] statistical analysis review manager 5.3 (cochrane collaboration) and stata version 16 were used for metaanalysis. dichotomous variables were calculated using mantel-haenszel formula with random effects models regardless of heterogeneity. the effect estimate was reported as risk ratios (rrs) along with its 95% confidence intervals (cis) for dichotomous variables, respectively. p-value was two-tailed, and the statistical significance set at ≤0.05. random effects meta-regression was performed using restricted-maximum likelihood for prespecified variables including age, gender, hypertension, cardiovascular disease, and copd. subgroup analysis was performed for each component of composite poor outcome. to assess the small-study effect, we performed regression-based harbord's test for dichotomous outcome. begg's funnel-plot analysis was performed to qualitatively assess the risk of publication bias. initial search yields 298 records, and 281 records remained after the removal of duplicates. 238 records were excluded after screening the title/abstracts. after evaluating 43 full-text for eligibility, 13 full-text articles were excluded because: no outcome of interest: severe, mortality, ards, disease progression. 30 studies were included in the qualitative synthesis and meta-analysis [ figure 1 ]. [3, 8, [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] 9, [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [10] [11] [12] [13] [14] [15] [16] there were a total of 6452 patients from 30 studies. this meta-analysis showed that dm was associated with composite poor outcome (rr 2.38 [1.88, 3 .03], p<0.001; i 2 : 62%, p<0.001) [ figure 2 ]. subgroup analysis showed that dm was associated with mortality (rr 2. 12 meta-regression showed that the association between dm and composite poor outcome was affected by age (p=0.003) [ figure 3a ] and hypertension (p<0.001) [ figure 3b ], but not gender (p=0.895), cardiovascular diseases (p=0.5) [ figure 3c ], and copd (p=0.47). multivariable meta-regression by including two covariates in single analysis showed age (p=0.334) and hypertension (p=0.107) effect is probably dependent on each other. subgroup analysis for studies with median age ≥55 years-old ( the funnel-plot analysis showed a qualitatively symmetrical inverted funnel-plot for the association between dm and composite poor outcome [ figure 4a ]. regression-based harbord's test showed indication of small-study effects for dm and composite poor outcome (p=0.004) [ figure 4b ]. this comprehensive meta-analysis of 30 studies showed that dm was associated with poor outcome that comprises of mortality, severe covid-19, ards, and disease progression in patients with covid-19. this association was influenced by age and hypertension. further analysis based on meta-regression showed that magnitude of risk linked to dm as a single factor was greater in studies with younger and non-hypertensive patients, which is yet to be addressed by the existing literature. meta-regression showed that the association between dm and poor outcome was influenced by age and hypertension. age and prevalence of hypertension was inversely proportional with the effect of dm on poor outcome. in other words, the effect estimate of dm was less in older and hypertensive patients. subgroup analysis further demonstrates the vast difference in rr. meta-regression also showed that age and prevalence of hypertension seemed to be dependent on one another, this is further demonstrated by subgroup analysis showing that the rr for age <55 years-old, prevalence of hypertension <25%, and both of them combined varies only slightly. the association between dm (as a single risk factor) with composite poor outcome in covid-19 was greater in younger people and without hypertension). the presence of older age and hypertension may attenuate the association of dm with composite poor outcome. hence, the total risk is expected to be higher in older patients with ht, but the magnitude of dm as a single risk factor is greater in younger people without hypertension. it is not yet known whether people with dm are more susceptible to covid-19, but several studies have reported a greater risk of severe covid-19 in diabetic patients. [3, 4] diabetic individuals have a greater risk of respiratory infections due to compromised immune system, especially the innate immunity. [5, 37] even transient hyperglycaemia may temporarily affect innate immune responses to infection. [38] it was hypothesized that ace2 may be the key pathfinder of covid-19 severity in diabetic individuals. [5] ace2 is a type 1 integral membrane glycoprotein expressed in the epithelial cells of cardiovascular, pulmonary, renal, brain and intestinal tissue, it acts by breaking down angiotensin ii into angiotensin 1-7. [37, 39, 40] this enzyme acts by counteracting the inflammatory actions of angiotensin ii, lowering the concentration of pro-inflammatory cytokine interleukin (il)-6, increasing the anti-inflammatory, and increasing the antioxidant action of angiotensin 1-7, escalating the levels of surfactant protein d and promoting vasodilation. [41] the novel coronavirus responsible for covid-19 is expected to act similary to severe acute respiratory syndrome (sars-cov). both utilize ace2 to bind and gain entry to the host pneumocytes. [39] viral surface spike (s) protein of covid-19 binds to ace2 after spike protein activation by transmembrane protease serine 2 (tmprss2). [40] routine use of acei and arb as a medication for chronic conditions upregulates ace2 expression, [5, 37] thereby facilitating entry of sars-cov-2 into the pneumocytes and consequently cause severe and fatal infection. [42] among other diabetic medications, the use of liraglutide and pioglitazone have also been found to be related with increased ace2 regulation in animal studies. [42, 43] the interconnection between ace2, renin-angiotensin system (ras) signalling, aging, dm, hypertension, and severity of covid-19 may not be as simple as it may seem. as we described before, our meta-regression analysis showed that the association between dm and poor outcome was interdependent on age and hypertension. one of the possible rationale behind this finding is the use of medications, particularly acei or arb in hypertensive individuals. the risks and benefits associated with acei/arb use in covid-19 patients remains controversial [44] , a specific type of arb has been shown to ameliorate lung injury in sars-cov infection in animal model. [45] it is unfortunate that all of the included studies did not provide report on diabetic or hypertensive medications. furthermore, the link between those specific variables could be in line with the hypothesis of alghatrif et al. [46] older hypertensive individuals have lower ace2 levels but a higher ras signalling, this difference is further expressed in covid-19 patients in which ace2 developed into a critically low levels and ras signalling is exaggerated even more. such disturbance result in a potentially decreased susceptibility to the disease, but a greater severity. in contrast, younger people without hypertension have higher ace2 levels and lower ras signalling, which transforms into a modestly low ace2 levels and modestly increased ras signalling due to covid-19 infection. this results in a possibly increased susceptibility to the disease, but a lesser severity. our meta-regression result may support the aforementioned hypothesis. the use of acei/arb is expected in patients with both dm and htn; and we observe that the age and htn were in parallel, studies with older subjects having higher prevalence of hypertension. hence, the clinical significance of dm in the older patients may be attenuated by the risk of hypertension and acei/arb use (which was hypothesized to increase severity in older patients). dysfunctional pro-inflammatory cytokine responses in diabetic patients might also be the underlying cause of severe covid-19. [37, 47, 48] diabetic patients have been shown to have an elevated pro-inflammatory cytokine level, in particular il-1, il-6 and tumor necrosis factor (tnf)-α. [48] different markers, including c-reactive protein, fibrinogen and d-dimer were also found to be elevated in diabetic patients who contracted covid-19. [47] thus, this condition may further exaggerate the cytokine storms in covid-19 leading to a more severe disease. [37, 48, 49] dm was shown to be associated with poor outcome in patients with covid-19 and was influenced by age and hypertension. the association was stronger in younger patients and should alert physician even though the patient only presented with one comorbidity. this indicates that dm is a potential prognostic marker that should be explored in triage. we encourage including dm in studies investigating prognostic model for patients with covid-19. moreover, this finding adds the needs of further studies concerning the use of acei/arb in covid-19. data on diabetic/hypertension medications were lacking in the included studies, hence, cannot be analysed. since acei/arb is often used in dm, it may have influence on prognosis. most of the articles included in this meta-analysis were preprints; nevertheless the authors have made exhaustive efforts to ensure that only sound studies were included. most of the reports were from china, hence, the samples might overlap across the reports. the included studies were retrospective in design. dm was associated with mortality, severe covid-19, ards, and disease progression in patients with covid-19. the association was weaker in the older and hypertensive patients. the data used to support the findings of this study are included within the article the authors declared no conflict of interest global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045 clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study diabetes is a risk factor for the progression and prognosis of covid-19 covid-19 and diabetes clinical management of severe acute respiratory infection (sari) when covid-19 disease is suspected report of the who-china joint mission on coronavirus disease 2019 ( covid-19 ) clinical features of patients infected with 2019 novel coronavirus in wuhan, china clinical course and outcomes of critically ill patients with sars-cov-2 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entry depends on ace2 and tmprss2 and is blocked by a clinically proven protease inhibitor potential harmful effects of discontinuing ace-inhibitors and arbs in covid-19 patients are patients with hypertension and diabetes mellitus at increased risk for covid-19 infection? activation of the glp-1 receptor by liraglutide increases ace2 expression, reversing right ventricle hypertrophy, and improving the production of sp-a and sp-b in the lungs of type 1 diabetes rats contentious issues and evolving concepts in the clinical presentation and management of patients with covid-19 infectionwith reference to use of therapeutic and other drugs used in co-morbid diseases (hypertension, diabetes etc) angiotensin-converting enzyme 2 protects from severe acute lung failure the dilemma of coronavirus disease 2019, aging, and cardiovascular disease covid-19 and diabetes mellitus: unveiling the interaction of two pandemics immune dysfunction in patients with diabetes mellitus (dm) covid-19: consider cytokine storm syndromes and immunosuppression ≤40 (53%) cad: coronary artery disease; covid-19: coronavirus disease 2019; cld: chronic lung/pulmonary disease; cvd: cardiovascular disease; icu: intensive care unit ih and rp conceived and designed the study. ih, rp, and mal acquired the data. ih and mal drafted the manuscript. ih and rp performed data extraction and interpreted the data. ih and mal performed extensive research on the topic. rp reviewed and performed extensive editing of the manuscript. all authors contributed to the writing of the manuscript. ih and rp performed the statistical analysis. none key: cord-286683-mettlmhz authors: ortiz-prado, esteban; simbaña-rivera, katherine; gómez-barreno, lenin; rubio-neira, mario; guaman, linda p.; kyriakidis, nikolaos c; muslin, claire; jaramillo, ana maría gómez; barba-ostria, carlos; cevallos-robalino, doménica; sanches-sanmiguel, hugo; unigarro, luis; zalakeviciute, rasa; gadian, naomi; lópez-cortés, andrés title: clinical, molecular and epidemiological characterization of the sars-cov2 virus and the coronavirus disease 2019 (covid-19), a comprehensive literature review date: 2020-05-30 journal: diagn microbiol infect dis doi: 10.1016/j.diagmicrobio.2020.115094 sha: doc_id: 286683 cord_uid: mettlmhz abstract coronaviruses are an extensive family of viruses that can cause disease in both animals and humans. the current classification of coronaviruses recognizes 39 species in 27 subgenera that belong to the family coronaviridae. from those, at least seven coronaviruses are known to cause respiratory infections in humans. four of these viruses can cause common cold-like symptoms. those that infect animals can evolve and become infectious to humans. three recent examples of these viral jumps include sars cov, mers-cov and sars cov-2 virus. they are responsible for causing severe acute respiratory syndrome (sars), middle east respiratory syndrome (mers) and the most recently discovered coronavirus disease during 2019 (covid-19). covid-19, a respiratory disease caused by the sars-cov-2 virus, was declared a pandemic by the world health organization (who) on 11 march 2020. the rapid spread of the disease has taken the scientific and medical community by surprise. latest figures from 20th may 2020 show more than 5 million people had been infected with the virus, causing more than 330,000 deaths in over 210 countries worldwide. the large amount of information received daily relating to covid-19 is so abundant and dynamic that medical staff, health authorities, academics and the media are not able to keep up with this new pandemic. in order to offer a clear insight of the extensive literature available, we have conducted a comprehensive literature review of the sars cov-2 virus and the coronavirus diseases 2019 (covid-19). the viral membrane contains the spike (s) glycoprotein that forms the peplomers on the virion surface, giving the virus its 'corona'or crown-like morphology in the electron microscope. the membrane (m) glycoprotein and the envelope (e) protein provide the ring structure. within the virion interior lies a helical nucleocapsid comprised of the nucleocapsid (n) protein complexed with a single positive-strand rna genome of about 30 kb in length [16] . the first genome of sars-cov-2 named wuhan-hu-1 (ncbi reference sequence nc_045512) was isolated and sequenced in china in january 2020 [12, 16] . the sars-cov-2 genome has similarities to other viruses: approximately 96% similarity to the bat coronavirus batcov rath13; an estimated 80% similarity with sars-cov [16] , and an estimated 50% identity with mers-cov [17, 18] . sars-cov-2 has a positive-sense single-stranded rna genome. it is approximately 30,000 bases in length and comprises of a 5′ terminal cap structure and a 3′ poly a tail. according to wu et al. [19] , this novel coronavirus (ivdc-hb-01/2019 strain) has 14 open reading frames (orfs) encoding 29 proteins. the 5' terminus of the genome contains the orf1ab and orf1a genes. orf1ab is the largest gene and encodes the pp1ab protein that contains 15 non-structural proteins named nsps (nsp1-nsp10 and nsp12-nsp16). orf1a encodes the pp1a protein and also has 10 nsps (nsp1-nsp10) [19] . the 3' terminus of the genome contains four structural proteins: spike (s) glycoprotein; envelope (e) protein; membrane (m) glycoprotein and nucleocapsid (n) phosphoprotein. it also contains 8 accessory proteins (3a, 3b, p6, 7a, 7b, 8b, 9b and orf14) [20] (figure 3b ). the global scientific community from 58 countries have united to study this novel coronavirus by sequencing and submitting 12,059 sars-cov-2 genomes to the global initiative on sharing all influenza data (gisaid) (https://www.gisaid.org/) between december 2019 and april 2020 [21, 22] . sars-cov-2 has accumulated mutations in its rna genome as the outbreak progresses. as an intracellular obligate microorganism, the coronavirus exploits the host cell machinery for its own replication and spread. since virus-host interactions form the basis of diseases, knowledge about their interplay is of great importance, particularly when identifying key targets for antivirals. j o u r n a l p r e -p r o o f ace2 is a type i membrane protein that participates in the maturation of angiotensin, a peptide hormone that controls vasoconstriction and blood pressure [30] . in the respiratory tract, ace2 is widely expressed on the epithelial cells of alveoli, trachea, bronchi, bronchial serous glands [31] , and alveolar monocytes and macrophages [32] . xu et al. reported the [33] rna-seq profiling data of 13 organs with para-carcinoma normal tissues from the cancer genome atlas (tcga; https://www.cancer.gov/tcga) and 14 organs with normal tissue from fantom5 cage (https://fantom.gsc.riken.jp/). these were used to validate the expression of the human cell receptor ace2 in the virus and may indicate the potential infection routes of sars-cov-2 [34] . interestingly, the ace2 receptor is expressed more in oral cavity than lung. this potentially could indicate that susceptibility and infectivity of sars-cov-2 is greater from oral mucosa surfaces [33] . following the binding of the rbd in the s1 subunit to the receptor ace2, sars-cov-2 s protein is cleaved by the cell surface-associated transmembrane protease serine 2 tmprss2, which activates s2 domain for membrane fusion between the viral and cell membrane [35] . a functional polybasic (furin) cleavage site was found at the s1-s2 boundary through the insertion of 12 nucleotides [13, 29, 36] . the s673, t678 and s686 residues of o-linked glycans flank the cleavage site and are unique in sars-cov-2 [29] . in addition to the s glycoprotein -ace2 receptor complex, wang following the release and uncoating of viral rna to the cytoplasm, coronavirus replication starts with the translation of orf1a and orf1b into polyproteins pp1a and pp1ab via a frameshifting mechanism (figure 4 ) [38] . subsequently, polyproteins pp1a and pp1ab are processed by internal viral proteases, including the main protease m pro , a potential drug target whose crystal structure was recently determined for sars-cov-2 [15] . polyprotein cleavage yields 15 mature replicase proteins, which assemble into a replicationtranscription complex that engages in negative-strand rna synthesis. both full-length and multiple subgenomic negative-strand rnas are produced. the former serves as template for new full-length genomic rnas and the latter template the synthesis of the subgenomic mrnas required to express the structural and accessory protein genes residing in the 3′proximal quarter of the genome [37] . coronavirus rna replication occurs on a virusinduced reticulovesicular network of modified endoplasmic reticulum (er) membranes [39] . the assembly of virions is quickly ensued with the accumulation of new genomic rna and structural components. the n protein complexes with genome rna, forming helical structures. then, the transmembrane m protein, localized to the intracellular membranes of the er -golgi intermediate compartment (ergic) , interacts with the other viral structural proteins (s, e and n proteins) to allow the budding of virions [40, 41] . following assembly and budding, virions are transported in vesicles and eventually released by exocytosis. normal immune responses against the majority of viruses involve a rapid containment phase mediated by innate immunity components and -if necessary-a delayed, yet more sophisticated adaptive immunity phase that should be able to eradicate the pathogen andhopefully-generate long-lasting immunological memory. the former includes antiviral type i interferons (ifns), macrophage and neutrophil activation that leads to proinflammatory cytokine production and nk cells on the other hand, anti-viral adaptive immune responses involve a virus-tailored coordinated attack by antigen specific cd8+ cytotoxic t cells (ctls), the th1 subset of cd4+ t helper cells that orchestrates the j o u r n a l p r e -p r o o f immune response against viruses and other intracellular pathogens, specific antibody producing plasma cells, and finally the production of memory t and b cell subsets. immune responses following sars-cov-2 infection can be a double-edged sword. a rapid and robust type i ifn orchestrated response can lead to virus clearance and -given that antiviral lymphocytes are activated and expanded-immune memory. conversely, a late activation of innate immunity, possibly owing to is usually associated with severe pathology that can lead to pneumonia, ards, septic shock, multi-organ failure and, eventually, death. in this line, a delayed type i ifn response and inefficient sars-cov-2 clearance by alveolar macrophages can promote excessive viral replication that can lead to severe pathology accompanied by increased viral shedding and, thus, viral transmissibility. accordingly, in patients whose immune system is weakened or otherwise dysregulated, such as older men with comorbidities, severe covid-19 is clearly more likely to occur [42] [43] [44] . a recent study has demonstrated that the average duration of sars-cov-2 viral shedding was 20 days after covid-19 onset, raising a debate as to the optimal time of patient isolation [45] . however, in terms of transmission viral shedding seems to be more relevant in the early phases of the infection as it can precede covid-19 symptoms by 2-3 days whilst up to 50% of infections are associated with viral shedding by asymptomatic cases [46] [47] [48] therefore, individuals that mount efficient containment-phase immune responses accompanied by decreased inflammatory responses will not experience infection-or immune response-mediated overt manifestations, but may be important silent spreaders of sars-cov-2. type i ifns are mainly produced by plasmacytoid dendritic cells (pdcs) and have a plethora of antiviral effects such as blocking cell entry and trafficking of viral particles, inducing rnase and dnase expression to degrade virus genetic material, enhancing presentation of viral antigens by mhc-i, inhibiting protein synthesis, inducing apoptosis of j o u r n a l p r e -p r o o f infected cells and activating anti-viral subsets such as macrophages and cytotoxic nk cells and t lymphocytes [49] . pathogen recognition receptors like cytosolic rig-i and mda-5 [50, 51] or endosomal toll like receptors (tlrs) 7 and 8 that recognize viral rna [52] are responsible for the activation of signaling cascades that activate the transcription factors nf-kb, interferon regulatory factor (irf) 3 and irf7 that translocate to the nucleus and induce proinflammatory cytokines and type i interferon (ifn) production. in turn, type i ifns activate the downstream jak-stat signal pathway resulting in expression of ifnstimulated genes (isgs) [53, 54] . our experience from sars-cov and mers-cov infection has shown that delayed type i ifn production and excessive recruitment and activation of infiltrating proinflammatory cells (neutrophils and monocytes-macrophages) are possible mediators of lung dysfunction and bad prognostic factors for the outcome of the infection. delayed type i ifn production allows for highly efficient viral replication that, in turn, results in recruitment of hyperinflammatory neutrophils and monocytes. therefore, the pathogen recognition receptors (prrs) of these proinflammatory cells recognize high numbers of their ligands and subsequently secrete excessive amounts of proinflammatory cytokines that lead to septic shock, lung pathology, pneumonia or acute respiratory distress syndrome. it has been shown that in severe cases both sars-cov and mers-cov fruitfully employ an immune evasion mechanism whereby early type i ifn responses to viral infection are dampened [54] . this can be achieved by blocking signaling both upstream, as well as downstream of type i ifn expression. sars-cov can inhibit irf3 nuclear translocation, whereas mers-cov can impede histone modification [56] . additionally, both viruses can inhibit ifn signaling by decreasing stat1 phosphorylation [57] . due to the many sequence similarities of sars-cov-2 with sars-cov and mers-cov it would be enticing to speculate that similar mechanisms are also present, however further studies are needed to shed light to this hypothesis. hyperactivated neutrophils and monocytes-macrophages are the usual source of the cytokine storm. in this aspect, absolute neutrophil counts and neutrophil to lymphocyte j o u r n a l p r e -p r o o f ratio (nlr) were strongly associated with disease severity in a large cohort of covid-19 patients and were proposed as markers of adverse disease prognosis [58] . interestingly, the increased amounts of proinflammatory cytokines in serum associated with pulmonary inflammation and extensive lung damage described both in sars [59] and mers diseases [60] were also reported in the early study of 41 patients with covid-19 in wuhan [41] . evidence shows that the leading cause of covid-19 mortality is respiratory failure caused by acute respiratory distress syndrome (ards). there is an association with a cytokine storm mediated by high-levels of proinflammatory cytokines including il-2, il-7, il-10, g-csf, ip-10, mcp-1, mip-1a and tnf-α. ards was associated with increased fatality and subsequent studies confirmed il-6 and c-reactive protein are significantly upregulated in patients that died compared to convalescent patients [56] moreover, a recent study of 452 patients in wuhan identified that severe cases showed significantly higher cytokines and chemokines such as tumor necrosis factor-α (tnf-α), il-2, il-6, il-8 and il-10 expressed [58] . in accordance with these findings, therapeutic strategies are being tested. a phase 3 randomized controlled trial of il-1 blockade (anakinra) in sepsis has shown significant survival benefit in patients with hyperinflammation, without apparent increased adverse events [61] . currently, a multicenter, randomized controlled trial of tocilizumab (il-6 receptor blockade, licensed for cytokine release syndrome), is being trialed in patients with covid-19 pneumonia presenting with high levels of il-6 in china (chictr2000029765) [62] . moreover, several clinical trials are exploring if the well-established antiviral [63] and anti-inflammatory effects of hydroxychloroquine will be effective in treating patients with covid-19 as has previously been suggested for sars-cov infection [64] . this has also been demonstrated in vitro for sars-cov-2 [65] . in contrast, janus kinase (jak) inhibition has been proposed as a potential treatment in order to reduce both inflammation and cellular viral entry in covid-19 [66] . thus, it comes as no surprise that in a recent correspondence, lancet authors have identified the following potential therapeutic options for cytokine storm syndrome including ards the use of corticosteroids, selective cytokine blockade (eg, anakinra or tocilizumab) and jak inhibition [67] . j o u r n a l p r e -p r o o f virus presentation to the different t cell subsets stands on the crossroads between innate and adaptive immune responses. studies on sars-cov and mers-cov [72] presentation have identified several susceptibility and protection conferring hla alleles. the dearth of similar data regarding sars-cov-2 antigen presentation to t cells and possible virus evasion mechanisms of this process suggests it is a virgin investigation field to be explored. apart from the sustained inflammation and cytokine storm, lymphopenia has been implicated as a major risk factor for ards and mortality in the context of covid-19 [73] . similar findings were described for sars-cov infected patients who had considerable decreases of cd4+ t and cd8+ t cells [69] . however, in convalescent patients specific tcell memory responses to sars-cov were still found six years post infection [74] . showed no reactivity with viral antigens. however, the small number of sera used (n=4) implies that further investigation is needed to corroborate these results [78] . nonetheless, since we are currently in early stages of sars-cov-2 pandemic more studies need to be carried out to shed light on antibody persistence (both igm and igg) and protective effects. recently, macaques re-challenged with sars-cov-2 after a primary infection did not show signs of re-infection, suggesting that protective immunity and memory responses were fruitfully mounted. this finding can also impact vaccine production strategies [79] . importantly, covid-19 convalescent sera was shown to hold promise as a passive immune therapy alternative to facilitate disease containment [80] . to the best of our knowledge, at j o u r n a l p r e -p r o o f least one pharmaceutical company, takeda, is preparing to purify antibody preparations from covid-19 convalescent sera against sars-cov-2 [81] . a recently published case report of a patient with mild-to-moderate covid-19 revealed the presence of an increased activated cd4+ t cells and cd8+ t cells, antibody-secreting cells (ascs), follicular helper t cells (tfh cells), and anti-sars-cov-2 igm and igg antibodies, suggesting that both cellular and humoral responses are important in containing the virus and inhibiting severe pathology [82] . antibody dependent enhancement (ade) is a mechanism whereby non-protective antibodies produced during an infection with an agent either mediate increased uptake of this agent into target cells or cross-recognize a different pathogen and facilitate its entrance to target cells [83] . evidence emerging over the past two decades suggests that antibodies against different coronavirus can cross-react to some extent and mediate ade [84] . ade in the context of sars-cov was thought to be mediated by antibodies produced against 229e-cov [85] and was contemplated as contributing to high mortality rates in china [86] . the described mechanism suggests that low affinity or low title anti-spike protein antibodies rather than neutralizing the virus result in fc receptor mediated infection of immune cells, further aggravating the dysregulation of anti-sars-cov immune responses [87] . indeed, in vitro as well as in vivo experimental models have shown that ade hinders the ability to manage inflammation in the lung and elsewhere. this may lead to ards and other hyperinflammation-induced clinical manifestations also observed in several of the documented cases of severe covid-19 [88, 89] . while the molecular and immunological host response to sars-cov-2 infection has not yet been fully elucidated to confirm ade is occurring, anti-sars-cov-2 antibodies have been shown to partially cross-react with sars-cov, suggesting enhancement is a possibility. with this in mind, ade in populations previously exposed to other coronavirus can partially explain the geographic discrepancies observed in covid-19 pathogenesis and severity. finally, ade can have several implications in vaccine development as low-affinity or low-titer antibody producing vaccines can increment susceptibility rather than confer protection against the pathogen as has previously been described for a dengue vaccine [90] [91] [92] . j o u r n a l p r e -p r o o f detection methods based on nucleic amplification are often used in the case of sars-cov, mers-cov and other viruses, because have high sensitivity and specificity, particularly in the acute phase of infection [93] . case identification and surveillance of covid-19 spread although rt-qpcr assay is considered the gold-standard method to detect viruses such as sars-cov and mers-cov [94, 95] , currently available rt-qpcr assays targeting sars-cov-2 have important considerations. firstly, due to the genome similarity of j o u r n a l p r e -p r o o f sars-cov-2 to sars-cov (82% of nucleotide identity [96] ), some of the primer-probe sets described by different groups and listed in the who coronavirus disease (covid19) technical guidance [97] , have cross-reaction with sars-cov and other bat-associated sars-related viruses, therefore, it is important to run confirmatory tests. loop-mediated isothermal amplification (lamp) is a one-step isothermal amplification reaction that couples amplification of a target sequence with four to six primers, to ensure high sensitivity and specificity, under isothermal conditions (63-65°c), using a polymerase with high strand displacement activity [129] . in the case of an rna sample, lamp, is preceded by the reverse transcription of the sample rna. rt-lamp has been used before for the detection of various pathogens [130] . including sars-cov-2 and other respiratory viruses [131, 132] . recently, it received emergency use authorization (eua) from the u.s. j o u r n a l p r e -p r o o f serological tests also, called immunoassays, are rapid and simple alternatives for screening of individuals that have been exposed to sars-cov-2 based on the qualitative or quantitative detection of sars-cov-2 antigens and/or anti-sars-cov-2 antibodies. there are several types of serological tests available, including elisa (enzyme-linked immunosorbent assay), iift (indirect immunofluorescence test), lateral flow immunoassays and neutralization tests. immunoassays assays are very useful because they allow to study the immune response(s) to sars-cov-2 in a qualitative and quantitative manner. in addition, help to determine the precise rate of the infection [78, 133] , and to determine more precisely the fatality rate of the infection [78] . several sars-cov-2 targeted serological tests are commercially available or in development [134] . a recently developed kit, reported a sensitivity of 88.66% and specificity of 90.63% [135] using sars-cov-2 igg-igm combined antibody rapid (within 15 minutes) test [135] . despite their simple and fast readout and their potential for being used outside laboratory environments (bedside, small clinics, airports, train stations, etc.), serological tests have a critical disadvantage; given the fact that antibodies specifically targeting the virus would normally appear after 6 days or longer [136] after the illness onset [137] , tests based on this principle have a lag period of approximately 4 to 7 days post-infection. during this lag period, infected and non-infected individuals will both result in a negative output. in addition, it is important to highlight that because serological tests depend on the ability to produce antibodies, intrinsic immunological differences and/or responses between individuals, can significantly affect the outcome of these tests. recently, some commercially available immunoassays received ce mark for professional use [138, 139] , and therefore are registered as in vitro diagnostic devices. currently, there are a plethora of antibody tests for covid-19 with variable performance (sensitivity varying from 45 to 100%, specificity from 96 to 100%, reviewed in (foundation for innovative new diagnostics) [134] . different manufacturers of serological assays declare that their assays have no cross reactivity to other human coronaviruses and other respiratory viruses. however, despite the data provided by manufacturers, recent studies highlighted that several of the commercially available tests have sensitivity and/or specificity issues that should be considered for using and analyzing results of many of these tests [140] [141] [142] [143] [144] . j o u r n a l p r e -p r o o f as mentioned before, immunoassays -particularly tests detecting anti-sars-cov-2 igm and/or igg-indicate that the person has been exposed to the virus. in the case of other viral infections, having antibodies targeting a pathogen has often been considered an indication of having immunity against that pathogen [145] . based on this idea, some governments have suggested using serological tests, to determine who has developed immunity against sars-cov-2 and provide positive individuals a "risk-free certificate" or "immunity passports", which would enable them to travel or to return to work, assuming that they are protected against re-infection [146]. however, based on the limited knowledge of how immunity to this virus works [147] , there is not enough evidence to declare a person immune, or to confirm that people who have anti-sars-cov-2 antibodies are protected from a re-infection. even though covid-19 can be diagnosed using qpcr as the gold standard, inadequate access to reagents and equipment has slowed disease detection even in developed countries such as the us. several low cost and rapid tests using different approaches have been described. unlocking) technique for the detection of covid-19 and the detectr (developed by mammoth biosciences) prototype rapid detection diagnosis kit using crispr to detect the sars-cov-2 in human samples have been described [148] . the use of rna aptamers, have recently emerged as a powerful background-free technology for live-cell rna imaging due to their fluorogenic properties upon ligand binding, a technology that could be of use to diagnose sars-cov-2 infection [149] . finally the use of next generation sequence (explify®) might be used to detect and identify bacterial, viral, fungal, and parasitic pathogens by their unique genome sequences [107] . in covid-19 symptomatic infection, the clinical presentation can range from mild to ventilation assistance [151] . the spectrum of symptoms of covid19 infection are characteristic of a mild disease in most of the cases, however, it is important to point that the progression could lead to a severe respiratory distress. asymptomatic infection (while incubation occurs) was described both in the first cases in wuhan and in other cohorts. a group of isolated patients were screened for sars-cov-2, where 17% (629 cases) were positive for the test, and half of these cases had no symptoms. on the other hand, there are reports of cases without overt symptoms in which there were ground glass images in the chest tomography in up to 50% of patients [152] . of the asymptomatic cases studied in wuhan city, the 2.5% of people exposed developed specific symptoms in 2.2 days, and the remaining 97.5% were symptomatic in the following 11.5 days (ci, 8.2 to 15.6 days). the median estimated incubation period was 5.1 days (95% ci, 4.5 to 5.8 days) [153] . some patients with initially mild symptoms had symptom progression over the course of one week [154] . the descriptive studies available so far have concluded that the majority of cases are mild infections (more than 80% of cases); with up to 15% of patients being sever j o u r n a l p r e -p r o o f in most cohorts, and less than 5% have been considered as critical cases with high vital risk [155] . in a study describing 138 patients with covid-19 pneumonia in wuhan, the most common clinical characteristics at the onset of the disease were described. this is consistent with other international cohorts (table 3 ) [150] . it is important to note that fever is not always present and up to 20% of patients could had a low grade temperature between 37.5 to 38 degrees celsius or normal temperature [156] . if these patients required hospitalization, 89% developed a fever during the course of the illness. rarer accompanying symptoms included headache without warning signs, odynophagia and rhinorrhea. gastrointestinal symptoms such as nausea and watery diarrhea were relatively rare [151] . dyspnea develops after a median of 5 to 8 days from the onset of symptoms. it is important to notice that, if dyspnea is an important clinical finding, not all the patients with this j o u r n a l p r e -p r o o f symptom will develop severe respiratory distress or require oxygen supplementation [150] . according to world health organization (who) guidelines, covid-19 infection can present as pneumonia without signs of severity, and could be managed in the outpatient setting. this is applicable to those patients who do not need supplemental oxygen [157] . as previously mentioned, the most serious manifestation of covid 19 infection is pneumonia, characterized by cough, dyspnea, and infiltrates on chest images; the latter is indistinguishable from other viral lung infections. acute respiratory distress syndrome (ards) is a major complication of covid pneumonia in patients with severe disease. this develops in 20% after a median of eight days. mechanical ventilation is implemented in 12.3% of cases [158] . in different case reports, the need for supplemental oxygen via the nasal cannula was required in approximately 50% of hospitalized patients. 30% required non-invasive mechanical ventilation, and less than 3% required invasive mechanical ventilation with or without extracorporeal membrane oxygenation (ecmo) [159] . it is important to mention that the proportion of severe cases is highly dependent on the study population and may be related to the epidemiological behavior of the infection in each country. additionally, the number of people tested will influence the denominator. in italy, the average age of people infected with covid-19 is between 60 and 65 years, and 16% of those hospitalized require admission to the intensive care unit (icu) [160]. the who recommendations had established that severe covid-19 disease could be defined by the following parameters in table 4 [157] . [162] . among the established risk factors for the development of ards is age greater than 65 years, diabetes mellitus and hypertension, in at least 40% of patients [151] . it should be clarified that, although advanced age is identified as a risk factor for a severe infection, those of any age may suffer from severe illness from covid-19. the descriptions made so far of the patients from china have determined that almost 90% of the patients were between the ages of 30 and 79 years (cohort of 44,500 cases) [155] . in other population settings, such as in the united states, more than 60% of confirmed the clinical characteristics of symptomatic cases and their severity has been described. in addition to the symptoms reported by the patients, the findings on physical examination may be absent during mild coivd-19 infection. those with moderate to severe covid-19 infection have various signs during pulmonary auscultation, however the most common findings include: wet rales; global decrease in respiratory sounds and increased thrill [164] . early recognition is essential to classify cases as potential cases and initiate one of the most important measures to contain the pandemic, isolation. 2. anyone who has resided or been traveling in areas where widespread community transmission has been reported. 3. any patient who has had potential exposure through attending events or has spent time in specific settings where cases of covid-19 have been reported. the scenarios described respond to the context of a high suspicion of covid-19 infection. the world health authorities (cdc, who) continually update these contexts. there have been multiple case definitions and clarifications regarding when to perform a covid-19 test: • they have pointed out the importance of fever, cough and dyspnea as sentinel symptoms, since these should form part of the clinical judgment that guides doctors. this allows to expand the group of suspicious patients. • in cases of severe respiratory distress of undetermined etiology and that do not meet the previously indicated criteria, a screening for covid-19 would be indicated. • in areas of limited resources, the suggestion is to prioritize cases that require hospital care, and in this way guide the epidemiological fence to order isolation and protect the most vulnerable people (chronically ill and over 65 years of age), as well as test those with the greatest possibility of exposure (travelers and health personnel). currently, there is no laboratory data profile that is framed in covid 19 infection. from a cohort of 43 patients confirmed with covid 19, these findings were classified as mild, moderate and severe disease [165] . high levels of d-dimer and more severe lymphopenia have been associated with mortality due to a prothrombotic state that determines multi-organ failure. in general, leukopenia and / or leukocytosis can be found in the interpretation of blood biometry, however, the most widely described finding is lymphopenia [166] . it should be considered that in the context of viral pneumonia biomarkers such as procalcitonin and pcr are not useful, as often these biomarkers are in the normal range for patients with covid-19. among other findings, descriptive studies have reported considerable elevations of lactate dehydrogenase and ferritin as well as alteration in aminotransferases; although elevation ranges for these parameters have not been established [167] . about the imaging findings, covid 19 viral pneumonia has similar features on imaging to other viral infections. although computed tomography (ct) is the test of choice, it is not useful for a definitive diagnosis due to the wide variety of images that can be found in patients with covid 19 infection. this statement is derived from a large cohort of more than 1000 wuhan patients, where rt-pcr confirmation of covid 19 and chest ct images of these patients were correspondingly analyzed. ct images were determined to have a sensitivity of 98%; however, the specificity was only 25% [168] . in general, the majority of descriptive studies concur that the finding of ground glass opacifications is most common. it is typically basal and bilateral, and rarely associated with underlying consolidation. a multicenter chinese study that retrospectively reviewed the ct scans of 101 patients found that 87% had typical ground-glass images and up to 53% had this finding along with consolidations. these findings were more frequent in the most j o u r n a l p r e -p r o o f severe and older age groups of patients [169] . pleural effusion (4%), and lymphadenopathy (2.7%) [170] . the emergence and outbreak of sars-cov-2, the causative agent of covid-19, has rapidly become a global concern that highlights the need for fast, sensitive, and specific tools to monitor the spread of this infectious agent. diagnostic protocols to detect sars-cov-2 using real-time quantitative polymerase chain reaction (rt-qpcr) were listed on the world health organization (who) website as guidance, however, various institutions and governments have chosen to establish their own protocols that might not be publicly available or listed by who. there are important challenges associated with close surveillance of the current sars-cov-2 outbreak. firstly, the rapid increase of cases has overwhelmed diagnostic testing capacity in many countries, highlighting the need for a high-throughput, scalable pipelines for sample processing [171, 172] . secondly, given that sars-cov-2 is closely related to other coronaviruses [96] , some of the currently available nucleic acid detection assays can result in false positives [173] . thirdly, critical concern for molecular detection is the low sensitivity reported for rt-qpcr assays [168] and serological tests [135] , particularly in the early stages of infection. additionally, most of the available rt-qpcr assays require sample processing and equipment only available in diagnostic and/or research laboratories. it is important to mention that coinfection is a possibility, as some reports from italy and in spain, less than 1% of cases in a cohort correspond to plwh, which have had a satisfactory evolution and less than half required an intensive care unit [177] . in the us, of the 5,700 hospitalized patients in the new york area, only 47 patients had hiv, while in san francisco, data was published on 1,233 people who had diagnosed with sars-cov-2 infection, of which less than 3% had hiv and none of them developed severe covid-19 [178] . despite the existence of in vitro studies on the efficacy of the use of lopinavir / ritonavir, it is currently known that its effect in cases of moderate and severe covid-19 is null, and therefore at the moment no recommendation can be given nor how treatment, much less as prophylaxis [179] . this clarification is important given that there is a belief that plwhs could be protected if they take antiretroviral therapy. therefore, current recommendations for plwhs are to maintain antiretroviral therapy with the goal of controlling hiv as well as following the same standards of care as the general population to avoid acquiring a sars-cov-2 infection [180] . regarding sars-ncov infection in pregnant women, there is currently limited evidence about the effect of the virus on the mother or fetus. however, due to the physiological changes typical of pregnancy, especially on the immune system (immunosuppression) and the cardiopulmonary system, pregnant women are thought to be more susceptible to developing severe symptoms when they acquire the viral respiratory disease. in 2009, when influenza a h1n1 infection occurred, only 1% of the infected population were pregnant, yet they accounted for 5% of infection-related deaths [181] . pregnancy (25%) [182] . in another study of 11 pregnant patients infected with mers-cov, 9 presented adverse results (91%), 6 neonates were admitted to the neonatal intensive care unit (55%) and three of them died (27%) [183] . however, it is important to note the small sample size which could increase the risk of bias and low power of the study. with information obtained so far from the wuhan sars-cov-2 outbreak, the infection appears to be less severe for pregnant women, compared to previous sars-cov and mers-cov outbreaks [181] . however, it is important to take into account that the data from covid-19 infection should be monitored with a doppler ultrasound every two weeks, due to the risk of developing intrauterine growth restriction [187, 188] . the time of termination of the pregnancy, as well as the method, also depend on several factors, including gestational age, maternal condition in relation to sars-cov-2 infection, presence of maternal comorbidities, and fetal condition. decisions must be made collaboratively during multidisciplinary team discussions, with individualized management plans established for each patient [189] . a diagnosis of covid-19 alone is not an indication for the termination of pregnancy, rather it should be made in combination with consideration of morbidity and mortality of both the fetus and mother. after delivery, the use of corticosteroids is recommended for antenatal fetal lung maturation, with betamethasone or dexamethasone [190] ; taking special care in critically nursing patients, as this may worsen their condition, and may delay delivery, which is necessary for the management of these patients [187, 191] . the symptoms children present with are similar to adults, as is the incubation period ranging from 1 to 14 days (mean of 5.2). a cough is the most frequent presenting symptom (65%) followed by fever (60%). there is a higher occurrence of gastrointestinal symptoms including diarrhea (15%), nausea, vomiting (10 %) and abdominal pain. these gastrointestinal symptoms are usually more variable in children than adults and are sometimes the only clinical manifestation in associations with fevers. [192, 193] . the clinical progression and disease severity in pediatric patients is markedly different from that of adults. over 90% of affected children are asymptomatic or have mild to moderate disease [192] . the majority of serious cases in children are related to those with significant comorbidities such as heart disease, immunosuppression, etc. to date of this review, only a few cases of children without underlying comorbidities have died as a result of covid 19 have been reported. this difference of severity of illness between adults and j o u r n a l p r e -p r o o f children has not been clarified, however, several theories have been postulated. these include that children express more ace2 receptors in their lungs which confer some protection to severe injuries such as those caused by rsv and which would decrease dramatically with age [194, 195] . immunological factors may also influence outcomes, as in childhood we are most exposed to frequent challenges including recent seasonal viruses such as rsv in the winter months. most likely, it is multifactorial and depends on factors from both the host and the virus itself [195] . abnormal radiological (ct) findings are found in asymptomatic children and consist of bilateral lung lesions (50%). elevated crp (creactive protein), procalcitonin pct (80%), and liver enzymes are present in most affected children, unlike adults in whom pct is not a reliable marker. virus elimination via the stool even after the negativity in the nasopharyngeal mucosa and the disappearance of symptoms makes them a potential source of contagion through the fecal-oral route [196] . patients with cancer are generally more susceptible to infections than healthy people, because they have a state of systemic immunosuppression that is exacerbated during chemotherapy or radiotherapy [197] . in china, according to national surveillance data, coronavirus infection occurs in 1.3% of patients with malignant tumors. this is a much higher proportion than the general incidence of 0.3% [198] . p<0.0001) even after adjusting for age [197] . further research, completed in a tertiary hospital in wuhuan -china similarly found that 25% of patients with cancer and sars-cov-2 infection died, most of them over 60 years of age [199] . due to these findings, it has been proposed by many international entities that during the pandemic, for prevention, an individualized plan based on the patient's specific conditions is required, with the aim to minimize the number of visits to health institutions.  for early-stage patients with need of post-surgical adjuvant chemotherapy, especially those whose clinical, pathologic, and molecular biologic staging suggest a better prognosis, the start time of adjuvant chemotherapy may be delayed up to 90 days after surgery without affecting the overall effect of treatment [200] .  for patients with advanced cancer, the main approach should be to minimize hospitalization in covid-19 positive installations. replacing the existing intravenous treatment regimen with oral chemotherapy during this special period may be considered, to ensure that treatment is not interrupted for a long time during the pandemic [201] . however, if there is a suspicion of covid-19 infection in this population group, the same updated diagnostic guidelines and the corresponding management should be followed depending on their severity of illness. moreover, an individualized follow-up plan should be outlined due to higher likelihood of complications in this group of population [202] . it should be noted that patients attending out-patient appointments for cancer have higher levels of anxiety, depression and other mental health problems than the general population. studies have shown that approximately 50% of malignant tumor survivors have a moderate to severe fear of tumor recurrence [203] . for this reason, psychologist surveillance of outpatients in quarantine or during hospitalization should be considered. reported complications derived from covid-19 describe a severe disease that requires management in an intensive care unit (icu) in approximately 5% of proven infections. j o u r n a l p r e -p r o o f appear to be most susceptible to the life-threatening complications. the risk of patient-topatient transmission in the icu is currently unknown, therefore adherence to infection control precautions is paramount [204, 205] . progressive deterioration of respiratory function is undoubtedly the most common and lifethreatening complication of the infection. the prevalence of hypoxic respiratory failure in covid-19 patients is 19%, and it can progress to acute respiratory distress syndrome (ards), with the need of mechanical ventilation support at 10.5 days on average. one study found that between 10 and 32% of hospitalized patients require admission to the icu due to respiratory deterioration [205] . as respiratory complications are the most common cause of severe deterioration, early identification of them will undoubtedly help in timely support. support provided should be adapted to take into account risk factors such as advanced age, neutrophilia and organic dysfunction for the development of ards. the diagnostic support of pulmonary tomography is undoubtedly a valid tool; images in patients with different clinical types of covid-19 have characteristic manifestations, but it can become an operational problem due to the difficulty in performing imaging on critically ill patients. on the contrary, lung ultrasound at the bed-side could provide an alternative to radiographs and tomography during the diagnosis of covid-19 [206, 207] . since more than 70% of hospitalized patients will require supplemental oxygen, it is recommended that oxygen should be started when pulse oximetry values fall below 90%. an upper-limit of 96% saturation should be established, since higher values have been shown to be harmful [208, 209] . hemodynamic deterioration has a variability of presentation, this depends on the study population and the definition [223] , the presence of shock in the intensive care unit may be present between 25 to 35% [204, 224] . cardiomyopathy related to viral infection is one of j o u r n a l p r e -p r o o f the main causes of hemodynamic detriment, occurring in up to 23% of patients with covid-19 [43] . hemodynamic failure is one of the main causes of death in these patients, with percentages of up to 40%, inconclusive risk factors are associated to date such as diabetes, hypertension, lymphopenia, and elevation of d-dimer [225] . acute kidney injury (aki) is present in up to 12% of critically ill patients, podocytes and proximal tubule cells are potential host cells for sars-cov-2, caused by the virus induced cytopathic effect. the diagnosis is based on markers of early kidney injury and urinary output [210] . initial management of shock is based on fluid resuscitation, based on the application of dynamic parameters to predict response to fluids, such as variation in stroke volume (svv), variation in pulse pressure volume (ppv) and change in stroke volume with passive leg elevation or fluid challenge above static parameters [225] . variables such as skin temperature, capillary refill time and/or serum lactate measurement are currently valid tools to assess shock. the volume of liquids used in resuscitation should be restricted and administered in relation to dynamic assessment. a liberal water resuscitation strategy is not recommended, rather a balance of crystalloids over colloids as resuscitation liquids should be encouraged and avoiding the use of hydroxyethyl starches, albumin, dextrans or gelatins [226, 227] . indirect evidence suggests that the target mean arterial pressure (tam) for patients with septic shock is 65 mmhg using vasoactive support [228] . the recommendation of norepinephrine use as the first agent is maintained. if norepinephrine is unavailable, vasopressin or epinephrine could be used, avoiding the use of dopamine as the initial vasopressor due to the potential development of arrhythmias [229, 230] . in patients with covid-19 and shock with evidence of cardiac dysfunction and persistent hypoperfusion despite fluid resuscitation and norepinephrine use, dobutamine as inotropic is recommended. given the development of refractory septic shock, the suggestion of the use of hydrocortisone in continuous infusion is maintained, as indirect evidence, this in favor of reducing the length of stay in the icu and the resolution time of the shock [229] . according to the investigative mission of the who in china, the case-fatality rate ranged other reports from china have coincided with this clinical risk profile, for example, a study that included 41 confirmed cases, 12 patients who had ards had as main underlying diseases: diabetes and high blood pressure. of these cases, 6 patients died [156] . according to who, the recovery time is estimated to be two weeks for patients with mild infections and three to six weeks for those with serious illnesses. on the other hand, cdc established that people who had symptoms in the mild to moderate spectrum and maintained home isolation have a resolution of 3 days after the fever decrease, and there was a substantial improvement in respiratory symptoms, even without use of medications. isolation may be limited to 7 days from resolution of symptoms, however, it must be adapted to the population circumstances of the epidemic [158] . the evolution of the epidemiological curve in covid-19 outbreak makes consider containment strategies in china primarily, and other countries based on nonpharmaceutical interventions (npis). according to the who, the most effective measure is hands washing [231] . combination as public health measures reduced contact rates in the population and therefore reduce virus transmission (table 6 ) [232] . table 6 non -pharmacological measures. increasing the level of hand cleanliness to 60% in places with a high concentration of people, like all airports in the world would have a reduction of 69% in the impact of a potential disease spreading [233] . the epidemiological evolution of the covid-19 pandemic through phases has required the application of specific measures according to the time or phase in which the virus is found in each country. the evolution in the non-pharmacological measures has been as variable as the pharmacological ones, in such a way, since january to march, it was ensured that the use of face masks was limited only to people who had contact with epidemiological foci, not to healthy people [234] . this concept was also reinforced by cdc, in order to optimize the use of masks for health workforce. definitely the course of the pandemic was changing rapidly, which also demanded the change from containment measures to mitigation. the recommendations in the current context remain regarding the use of a facial mask in the community, but its optimization is important for health professionals. the use of the mask is not a substitute for handwashing and social distancing measures, as these ones together allow avoiding viral particles in aerosols or drops, as a low cost and accessible measure for general population [235, 236] . there is still non-specific information for the recommendation of masks, in general, having in several studies claims that surgical or cotton cloth masks do not prevent the spread of the sars-cov-2 virus [237] . the evidence about the transmission of the virus in the asymptomatic period also changed the containment measures, suggesting the community use of masks. it is from this that the recommendations for the rational use of masks arise since in some j o u r n a l p r e -p r o o f countries the massive use of n95 masks was reported, masks indicated for the use of medical personnel [238] . regarding to this non pharmaceutical recommendations, the studies suggest to priories the resources on vulnerable population, in endemic areas, older people, adult with comorbidities and health workforce. studies are still needed on the duration of the protective effect of the masks and above all the possibility of their reuse for resource optimization. meanwhile the most important recommendation continues to be its use in addition to hand hygiene and social distancing [238] . therapeutic j o u r n a l p r e -p r o o f this effect is reinforced by azithromycin. there were the best results in terms of viral load reduction, even though is mentioned some limitations in the study like small sample size, a short long-term outcome follow-up, and dropout of six patients from the study [246] . concerning to mortality rates, a study was conducted in new york with 1376 patients (0.63-1.85). thus, it concludes that the use of hcq is not associated with either a decreased or increased clinical impairment, intubation or death [247] results reinforced by other study in 1438 hospitalized patients with covid-19 diagnosis in new york city, whom received treatment with hydroxychloroquine, azithromycin, or both drugs was not associated with significantly reduction in mortality [248] . relating to safety of this drug, in a study carried out in 200 patients in which the theoretical complications of the use of hcq and its combination with macrolides (azithromycin) were assessed by serial electrocardiograms, the following results were obtained. in 5% of patients (10) received chloroquine, 95% (191) received hcq, and 59% (119) [252] . supportive therapies in immune regulation, together with the use of antivirals, are important to take into account, especially in those patients in a serious and critical state, in which they could improve the clinical response and perhaps avoid residual lung injuries. the convalescent plasma is extracted from recovered individuals from an infection, being an antibody transfer medium to provide passive immunity (neutralizing antibodies and globulin). the goal is to provide a rapid immune response until the patient can develop their own active immune response in the hope that there will be clinical improvement [253] . improvement in most individuals, as well as viral suppression 7 days after treatment [255] . in the same country, at the shenzhen hospital, 5 cases of patients with severe covid-19 were reported who met criteria for acute respiratory distress syndrome (ards), who were administered convalescent plasma (titration greater than 1: 1000 and neutralizing antibodies greater than 40). it was found that clinical recovery occurred approximately 12 days after the transfusion (4 patients) and 3 of the 5 patients were discharged 55 days after admission. it is important to mention that this group of patients also received antivirals, methylprednisolone and all the necessary support measures in intensive care [256] . other drugs like ivermectin, nitazoxanide, and others have been studied in the context of covid-19 treatment, but the results are inconsistent. all of the clinical trials evidence, supporting or against the use of mentioned drugs are detailed in (supplementary table 2 ). this review summarized some drug repurposing agents previously known to has efficacy against other virus like sars-cov, mers-cov, influenza. actually, exist some new drugs with high potential action on targets for covid-19 therapeutics. it is important to notice that there is no specific treatment for the coronavirus approach. in context of the scientific evidence exposed and the particular clinical features of each patient, the reader will be able to make the best clinical and therapeutic decisions. when it comes to vaccine design and manufacturing, the main objectives are to ensure its safety, its efficacy in activating specific adaptive immune responses and the production ofideally-long term memory. thus, eliciting protective immune responses including neutralization antibodies and/or ctl generation is of paramount importance. huge challenges need to be tackled in order to minimize the long and cumbersome process of vaccine generation. among them, candidate antigen targets need to be identified, immunization routes and delivery systems investigated, animal models set, adjuvants optimized, scalability and production facility considered, target population selected, and vaccine safety and long-term efficiency evaluated. currently there are no approved vaccines against any human coronavirus, suggesting that their generation is quite novel. several candidate vaccines against sars-cov had shown promise reaching phase i or phase ii clinical trials [258, 259] , but the rapid containment of sars-cov expansion rendered them redundant, did not allow for a test population for phase iii trials and, therefore, put their further assessment to a halt. ctl memory could last up to 11 years after infection [260] . these data suggest that vaccine strategies employing viral structural proteins that can elicit effective, long-term memory t cell responses could yield fruitful results. on the other hand, the s1 spike protein region containing the ace receptor binding domain (rdb) is the obvious option when neutralizing antibody responses are considered [261] [262] [263] . indeed, a candidate sars vaccine antigen consisting of the rbd of sars-cov spike protein was created and found it could elicit robust neutralizing antibody responses and long-term protection in vaccinated animals [264] . the fact that covid-19 convalescent sera shows potential as a therapeutic approach [80] aligns with the theory that efficient b cell responses are mounted and lead to production of protective antibodies. two different groups, using an immunoinformatic approach mapped several ctl and b cell epitopes on different proteins of the virus [265, 266] . moreover, various ctl epitopes were found to be binding mhc class i peptide-binding grooves via multiple contacts, illustrating their probable capacity to elicit immune responses [265, 266] . consequently, these identified b and t cell epitopes could be potential targets for therapeutic vaccines. however, important safety considerations should be taken into account before releasing a new vaccine in the market. previous studies on macaque models have shown that a vaccineinduced anti-spike protein antibody at the acute stage of sars-cov infection can provoke severe acute lung injury [267] . similar observations of sars-cov vaccine-induced pulmonary injury have also been described in multiple several murine and monkey animal models [268] . an additional factor that needs to be checked in phase ii and iii trials is that the vaccine does not cause ade of the pathogen, as has previously been described. such concerns have risen in the context of a dengue vaccine [269] . the pharmaceutical companies that are currently on a race to produce a vaccine for covid-19 along with the vaccine developing strategies they are using are summarized in table 8 and figure 7 . as can be easily deduced from table 8 hospitalization and admission to already heavily charged icus due to these pathologies that could prove critical for weaker health systems that would struggle to carry the burden of combined outbreaks. moreover, vaccinating health care workers is crucial for reducing the risk of absence due to disease, thereby strengthening the healthcare workforce and minimizing the risk to infect covid-19 hospitalized patients with additional pneumoniacausing pathogens. lastly, covid-19 patients vaccinated for influenza and streptococcus pneumoniae allow their immune system to focus on one pathogen and, therefore, give it a better fighting chance against sars-cov-2 infection [276] . high risk groups prioritized for vaccination for these two pathogens include pregnant women, persons with immunocompromised immune systems (either due to congenital or acquired immunodeficiencies), children, adults ≥ 65 years and health care professionals. j o u r n a l p r e -p r o o f heat or chemical treatment inactivation. f) attenuated live pathogen vaccine strategies consist in administering a live pathogen that due to cell culture passaging has lost its virulence. they usually elicit robust and long-term memory immune responses without the need to administer an adjuvant. g) in dna vaccines the dna codifying a highly immunogenic antigen is administered and captured by professional antigen presenting cells (apcs) leading to antigen production and presentation by these cells. h) moderna's vaccine candidate already in phase i clinical trials uses an mrna vaccine approach whereby the genetic information codifying for the s protein of sars-cov-2 is delivered in lnps to enhance absorption by apcs. once uptaken by apcs the mrna induces the expression of s antigen that is subsequently mounted on and presented by mhc molecules to elicit adaptive immune response. numerous studies confirm that climate has an impact on virus (i.e., influenza, coronavirus, etc.) spread through manipulating the 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sha: doc_id: 316757 cord_uid: p370gjjn what emerged in december 2019 as a cluster of respiratory ailments with inexplicable etiological findings in wuhan has now claimed roughly 259 lives, sickened nearly 12 thousand more, and spread to at least 26 more nations including hong kong, taiwan and macao. this article is protected by copyright. all rights reserved. in virus taxonomy, coronaviruses belong to the subfamily orthocoronavirinae. these are known to be a family of enveloped non-segmented positive-sense ribonucleic acid (rna) viruses belonging to the family coronaviridae and the order nidovirales. there are four known genera for coronaviruses, namely: alpha-, beta-, gamma-, and delta-coronavirus. all of the four genera are believed to have a zoonotic origin and infect both animals and humans. whereas the alpha and beta genera originate from bats, the gamma and delta genera are derived from avian and pig gene pools. [6] [7] [8] [9] given the high occurrence of coronaviruses, the large genetic variety and recurrent recombination of their genomes, and increasing human-animal interface undertakings, new coronaviruses are likely to emerge sporadically in humans owing to periodic spillover events and common cross-species infections. this explains the human infections of novel coronaviruses, such as severe acute respiratory syndrome coronavirus (sars-cov) in 2002, and the middle east respiratory syndrome coronavirus (mers-cov) in 2012. once in humans, the virus has the likelihood to spread from human-to-human, mainly causing respiratory diseases. [10] [11] [12] in late december 2019, some local health facilities reported cases of patients with pneumonia of unknown causes that were epidemiologically related to seafood and wet animal wholesale according to a recent publication by chan et al, 14 the disease has shown person-to-person or nosocomial transmission features, implying that it can easily pass on from one person-to-another. one of the authors, dr. yuen kwok-yung, describes the disease as "asymptomatic walking pneumonia" due to its ability to be transboth hospitals, named huoshenshan and leishenshan: meaning "fire god mountain" and "thunder god mountain respectively," are said to be able to accommodate 2500 beds collectively, after their completion on 5th february. 24 an image of the current state of the huoshenshan hospital is shown in figure 2 . 25 a novel coronavirus outbreak of global health concern. the lancet offline: 2019-ncov outbreak-early lessons global health concern stirred by emerging viral infections outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus coronaviridae: the viruses and their replication fields international committee on taxonomy of viruses (ictv) coronavirus infections and immune responses clinical features of patients infected with 2019 novel coronavirus in wuhan, china. the lancet recent advances in the detection of respiratory virus infection in humans emerging coronaviruses: genome structure, replication, and pathogenesis chinese researchers reveal draft genome of virus implicated in wuhan pneumonia outbreak a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-toperson transmission: a study of a family cluster. the lancet centre for health protection of the hong kong special administrative region government. chp provides further information on cluster of pneumonia cases in wuhan updated understanding of the outbreak of 2019 novel coronavirus (2019-ncov) in wuhan nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study. the lancet the reuters news beijing wikipedia. novel coronavirus with wuhan virus genetic code in hand, scientists begin work on a vaccine updates on wuhan 2019 novel coronavirus epidemic key: cord-306189-ugxou9z1 authors: bherwani, hemant; nair, moorthy; musugu, kavya; gautam, sneha; gupta, ankit; kapley, atya; kumar, rakesh title: valuation of air pollution externalities: comparative assessment of economic damage and emission reduction under covid-19 lockdown date: 2020-06-10 journal: air qual atmos health doi: 10.1007/s11869-020-00845-3 sha: doc_id: 306189 cord_uid: ugxou9z1 air pollution (ap) is one of the major causes of health risks as it leads to widespread morbidity and mortality each year. its environmental impacts include acid rains, reduced visibility, but more importantly and significantly, it affects human health. the price tag of not managing ap is seen in the rise of chronic obstructive pulmonary disease (copd), cardiovascular disease, and respiratory ailments like asthma and chronic bronchitis. but as the world battles the corona pandemic, covid-19 lockdown has abruptly halted human activity, leading to a significant reduction in ap levels. the effect of this reduction is captured by reduced cases of morbidity and mortality associated with air pollution. the current study aims to monetarily quantify the decline in health impacts due to reduced ap levels under lockdown scenario, as against business as usual, for four cities—delhi, london, paris, and wuhan. the exposure assessment with respect to pollutants like particulate matter (pm(2.5) and pm(10)), no(2), and so(2) are evaluated. value of statistical life (vsl), cost of illness (coi), and per capita income (pci) for disability-adjusted life years (daly) are used to monetize the health impacts for the year 2019 and 2020, considering the respective period of covid-19 lockdown of four cities. the preventive benefits related to reduced ap due to lockdown is evaluated in comparison to economic damage sustained by these four cities. this helps in understanding the magnitude of actual damage and brings out a more holistic picture of the damages related to lockdown. the cost of development has had a major impact on the ecosystem balance. one major fallout is the jeopardized air environment (mage et al. 1996) . this is mainly due to a plethora of emission of pollutants such as pm 10 , pm 2.5 , no 2 , so 2 , etc. from various anthropogenic activities such as transportation, industrial processes, mining activities, waste burning, biomass burning, residential cooking, etc. gupta et al. 2020; humbal et al. 2019; bherwani et al. 2019; gautam et al. 2016) . deteriorated air causes long-and short-term health effects such as chronic obstructive pulmonary disease (copd), asthma, respiratory mortality, cancer, cardiovascular mortality, etc. (kim et al. 2015; ghorani-azam et al. 2016; maji et al. 2017; cohen et al. 2017; landrigan et al. 2018) among humans. this global threat is considered as one the leading cause for mortality and accounts for 7 million lives every year, estimating a total cost of more than 4% of the gdp (who 2020). extensive studies have been carried out by various researchers (gulia et al. 2015; maji et al. 2017 & maji et al. 2018 in heavily polluted cities to quantify the healthrelated monetary burden upon the exposure of human in the deteriorated air environment. severe acute respiratory syndrome coronavirus 2 (sars-cov-2) outbreak firstly identified in wuhan city, china (who 2020; gautam and hens 2020; gautam and trivedi 2020; gautam 2020a ) has now become a pandemic across the globe, resulting in about 3.5 million cases in just about 4 months who 2020) . the pandemic has declared global health emergency enforcing lockdown measures in activities (i.e., social contact, non-essential business, mobility, etc.) to flatten the epidemic curve. lockdown measures have shut down industries, halted vehicular traffic, and have had a huge impact on the daily routine of the people. due to this, considerable improvement in air quality levels of countries such as spain (tobias et al. 2020) , india (gautam 2020b) , brazil (nakada and urban 2020) , and china (sharma et al. 2020) ,and in cities such as bangkok, tokyo, paris, and new york (he et al. 2020) has been reported. the plummet in pollutant concentration is obvious due to the restriction in anthropogenic activities. the air quality during the lockdown period for majorly polluted cities (i.e., delhi, wuhan, paris, and london) is of high significance in determining the baseline pollution level and attributable health risk, to evaluate the potential fluctuation in monetary damages. assessment in terms of the number of lives affected is important, but a common baseline matrix such as "money" carries a much better message for the sake of understanding and decision making (gautam 2020a ). an unprecedented attempt has been made to quantify the economic benefit due to reduction in an excess number of health risk subject to mortality/morbidity attributable to lower air pollutant (pm 2.5 , pm 10 , no 2 , and so 2 ) concentration in wuhan, paris, london, and delhi. figure 1 indicates the geographical location of the cities. the monitored ground-based pollutant concentration are compared with who ambient air quality guidelines (who 2006) to evaluate the relative risk associated with each disease and thereby, the subsequent damage cost. the economic benefit/loss is calculated for each city based on the difference in excess number of health cases attributable to pollutant concentration during the lockdown period for 2020 and 2019. the study has also considered the overall benefit due to mass reduction in air pollutant level over the potential economic loss to the local and national government as an outcome of lockdown. population for the years of valuation is estimated to evaluate the extent of health damages due to ap in a particular city. population data is collected for 2019 and 2020 for calculating the number of people affected due to ap. the population of delhi, london, paris, and wuhan has increased from 185, 91.8, 109.6, and 82. 6 lakhs in 2019 to 195, 83.60, 93.00, and 110.2 lakhs in 2020, respectively (economic survey of delhi 2019). lockdown is imposed in many countries due to the outbreak of covid-19 (wang et al. 2020a; dutheil et al. 2020; gautam 2020b) . in delhi, the lockdown was imposed from march 22 (economic times 2020), in paris from march 18, 2020 (jon et al. 2020) , in london form march 23 (the hindu 2020), and in wuhan, it started from january 23. to analyze the ap levels, 31 days of lockdown is taken for the four cities and the respective data for ap as shown in table 1 along with dates of lockdown. average of 24-h mean data of pm 2.5 , pm 10 , so 2 , and no 2 values are taken in the period of lockdown that is 31 days for the four cities in 2020, and the same duration is taken in 2019 and values are shown in table 1 . number of people are affected by mortality and morbidity due to the exposure of harmful pollutant concentrations by taking the 24-h mean values for 31 days for these cities is evaluated. the values of people getting affected are calculated on the basis of daily data of pollutants in comparison to daily values of who guidelines. the daily values are averaged for month and shown here. so 2 has been found within limits throughout the study period for both the years. short-term health effects such as chronic obstructive pulmonary disease (copd), asthma, respiratory mortality, cardiovascular mortality, and respiratory diseases due to excess pollution level during lockdown period (number of days (n) = 31) for the current and previous years were estimated using linear exposure-response curve (lerc) method. the assessment was carried considering various factors such as relative risk r r (m) due to mean pollutant concentration, population attributable to risk (par) due to exposure of pollutant, baseline incidence cases (i e ) per 10 5 population corresponding to mortality/morbidity health impacts, and the total population of the city (n). equations (1)-(3) are used for estimating earlier mentioned variables. where c m is monitored daily ambient air concentration of pollutant "k" (daily values of average pollutant loads given in table 1 ). c p is permissible standard for the pollutant "k" (who guideline values). the standards preferred are as put forth by who in 2006. rr is relative risk for the pollutant "k," and the values for r r and i e are discussed in table 2 . ρ(c) is the proportion of population being exposed to the pollutant "k" (100% exposure is considered in our study). i ne is the estimated number of cases. the monetary burden due to health risk is calculated using the methods of vsl, coi, and daly for mortality and morbidity endpoints. for valuation, morbidity and mortality are evaluated via separate methods. the valuation of mortality is done using vsl which is usually available for each country based on assessments done for either labor wages or insurance settlements. the data on vsl is inflated to the year 2019 (which is the base year of valuation for this research) in the native currency of the reference and is compiled in table 3 . the exchange rate/conversion factor is used for converting the native currency to usd while the inflation is carried out to bring the value to the base year of 2019. the formula for evaluation of monetary damages of mortality is given as follows: where er is the exchange rate (imf 2020) and ir is the inflation rate (the world bank 2019). on similar lines to mortality, morbidity is valued using cost of illness (coi) and daly and is added to get total morbidity-related damage assessment. the data related to daly is taken from the who database and is given for the select cities in table 4 . daly indicates the years of life lost and thus can be valued using the annual income of an individual. the per capita income (pci) of the selected cities with their referenced and converted values to usd ( 2019) is shown in table 5 . the formula related to daly-related morbidity damage valuation is given in eq. (5). another important related to morbidity is evaluated cost of treatment of the disease, which is done using coi. coi includes total cost incurred such as medicinal cost, travel cost, hospital admission, and lost day. cost of illness of morbidity of each city is shown in table 6 as compiled from the literature and converted to usd (2019). for the respiratory disease of paris, the literature was not available, and hence, the corresponding values in london are used. similarly, literature indicated very high costs for copd for wuhan, and hence, indian costs for copd are normalized with reference to asthma costs and used for valuation. the formula for evaluation of morbidity based on coi is given as follows: based on the above inputs, the valuations of morbidity-and mortality-related damages of ap are carried out and explained in the "results and discussion" section. in order to understand the true magnitude of the damages, it is compared to economic damages sustained during the lockdown. the prevention of ap provided a benefit at the cost of economic damage. for this, economic damage sustained by each city during the lockdown is calculated and compiled, as shown in table 7 . the gross domestic product (gdp) of the city is compared with the gdp of the country to understand the citywide damages as literature only reported country-level damages. ambient air quality for delhi, london, paris, and wuhan cities for the lockdown month with the number of days for the years 2019 and 2020 as shown in table 1 is considered for calculating the health damage cost due to air pollutants. during the lockdown days due to limited transportation and industrial output, air pollution is significantly reduced (wang et al. 2020b ). some of the air pollutants came within the world health organization (who) guidelines (jordan 2020) just a few days into the lockdown. no 2 concentration for all the cities during the lockdown is less than the who limit every day, whereas breach is observed for the year 2019. pollutant such as pm 2.5 , pm 10 , no x , and so 2 results in various health damages such as respiratory diseases, copd, cardiovascular diseases, and mortality. these pollutants are considered to calculate corresponding health damage cost. it can be observed that so 2 concentration was below the acceptable permissible limit set by international guidelines (who 2006) . hence, no health damage due to pollutant was considered. the daily mean of pm 2.5 , pm 10 and daily averages for no 2 during the month of lockdown days in 2020 and the same month for the previous year 2019 was found beyond the acceptable limit, thereby health damage assessment is carried out by certain set of formulas (eqs. (1)(3)) (maji et al. 2017) . in order to quantify the impacts in monetary terms, it is essential to understand the mechanism by which the impact happens. the impact pathway approach (bherwani et al. 2019; ghorani-azam et al. 2016 ) reveals how emitted pollutants lead to different adverse outcomes on human wellbeing and other natural environments. in the current research, we are primarily focusing on human health impacts of ap, and the same is quantified in monetary terms. basic parameter of the number of people affected under morbidity and mortality are calculated using eqs. (1)-(3) using the available data. the factors for each of the pollutant parameter are taken from table 2 . the reference concentration for the pollutants is taken from the who guidelines. the cases of morbidity and mortality under each heading of disease for each city are summarized in table 8 . while standard deviations have been reported in pollutant concentration, relative risks, and baseline incidences, the resolution of calculation for multiplicative parameters using standard deviation may yield complex variations in the results. hence, the morbidity and mortality assessments have been done on average values. from table 8 , it can be seen that pm 2.5 is the most damaging parameter affecting many people in all cities. the highest cases are reported in delhi due to pm; however, no cases due to no 2 in 2019. since it has the highest number of cases to start with, the lockdown indicates the highest reduction as well. while this will hold true for monetary benefit as well or not is discussed later. wuhan indicates the second-highest number of people affected; however, reduction in 2020 appears to be low. london and paris show a similar size of cases. figure 2 indicates the morbidity and mortality between the two years 2019 and 2020. the valuation of morbidity is carried out for cardiovascular and respiratory diseases, including general respiratory ailments, asthma and copd. coi is used to include the expenditure of treatment, including the outpatient and in-patient costs related to the ailment. the coi for each city, based on national averages, have been used for diseases, as indicated in table 6 . the valuation of the cost of treatment of morbidity is evaluated using eq. (6). apart from the treatment expenditure, the reduction in functionality of an individual also leads to massive losses to the economy. this is often evaluated as daly and is valued as well. for valuation, per capita income is used as a surrogate measure for the individuals getting effected along with dalys associated with their diseases. the data related to daly and per capita income based on city gdp averages is given in table 4 and table 5 , respectively. the daly-related valuation is carried out using eq. (5). the morbidity valuation is shown in table 9 while fig. 3 represents a comparative loss of all cities due to ap morbidity in the years 2019 and 2020. it can be seen from fig. 3 that the highest benefit in terms of absolute numbers and in terms of percentage reduction of about 38% is seen by delhi, which also happens to be one of the most polluted cities in the world. the lockdown scenario must have brought down the pollution levels drastically bringing a huge benefit to the city. in terms of change, paris also sees a considerable reduction with morbidity damages reduced by almost 35%. the city of wuhan and london see a similar kind of drop in terms of percentage reduction of about 19 to 20%. while the morbidity damages are in millions of dollars, it is evident that they have reduced considerably as compared to the previous year, indicating that the lockdown has improved air quality thereby saving of millions of dollars and more importantly an improved health and associated intangibles. mortality valuation is done using vsl, which is usually evaluated for low-to moderate-income groups in order to avoid overshooting the valuations. the value of statistical life for individuals staying in different countries is given in table 3 and is used for the mortality air qual atmos health cases as evaluated by the relative risk and baseline incidences reported by who. table 10 gives the mortality valuation under each category of disease for the respective pollutants. the equation used for valuation for mortality damages is given in the "methodology" section as eq. (4). figure 4 gives a year-wise comparison of the benefits produced by lockdown in 2020 in terms of mortality reduction. it is to be noted that mortality damages are reported as total mortality, and within that, there is respiratory and cardiovascular mortality. the total mortalities of particulate matter and nitrogen dioxide have been added to get the total value of damage related to mortality, which then further includes mortalities related to other factors of ap. a similar result is obtained as in case of morbidity. delhi has the greatest benefit with almost 49% reduction in damages related to mortality due to lockdown followed by paris with 39% reduction, london with 29%, and wuhan having 26% reduction. further, in terms of absolute numbers, the reduction of damages is highest in delhi, followed by london, wuhan, and paris, respectively. overall, mortality and morbidity represent the total loss due to ap in the select cities. the damages have been added and compared to the economic damages caused during the considered lockdown of these cities. the economic damages have been reported at the country level; the ratio of the gdps of the corresponding cities is taken to normalize the damages for cities. the raw data with respect to economic damages and gdp ratios are given in table 7 . the overall damages and economic damages are shown in table 11 . valuation of ap damages for 2019 and 2020 gives an understanding of the magnitude of damages which occurs due to ap. due to lockdown, there is a drastic reduction in ap as indicated by 2020 scenario in table 8 and table 11 , leading to the prevention of ap-related damages. it can be seen from table 11 that the highest prevention happens in terms of absolute magnitude and percentage in delhi. london has the second-highest amount of prevention in terms of absolute numbers but falls behind paris in terms of percentage benefit. wuhan has the lowest prevention in terms of magnitude and percentage. when compared with the economic damages, as indicated in fig. 5 above, actually wuhan has the highest normalized benefit due to ap reduction, followed by delhi, london, and paris, respectively. this is evidently shown in terms of damage prevented per unit economic damage, which is highest for wuhan 1.85, followed by delhi 1.19, london 0.11, and paris 0.03. this study highlights that although the world is fighting with covid-19 and suffering from huge economic losses, due to reduced cohesive situation for work, the environment is benefitted. this further is demonstrated in monetary terms for reduced health damages related to air pollution. the exposure and impact assessment is carried out for delhi, london, paris, and wuhan, using relative risk and baseline indices of various air pollutants including pm 2.5 , pm 10 , and no 2 . the study further incorporates monetization of the impacts for 2019 and 2020, to gauge the magnitude of impact reduction of air pollution under covid-19 lockdown scenario. the monetary assessment of damages is done using econometric approaches like vsl, coi, and pci for daly. the key conclusions are summarized as follows: 1. pm 2.5 is one of the major contributors to the burden of disease related to ap. delhi, being one of the most polluted cities globally, is the worst affected. pm 10 and no 2 impacts are also considerable, while so 2 is found within who guidelines limits for both 2019 and 2020. monetarily, the impact is curtailed by average 36% in mortality and about 28% in morbidity in the year 2020 due to substantial reduction in ap amid reduced anthropogenic activities owing to covid-19 lockdown. in terms of an absolute number of people affected, an average 31% reduction is for combined mortality and morbidity for all cities. impacts of no 2 are zeroed for the year 2020. for pm 2.5 mortality cases, delhi sees the highest fall in the number of cases for 2020 from 2019, followed by paris, wuhan, and london, in that order. it can be seen the trend in mortality damages between the cities is not similar to morbidity, indicating that there could be other compounding factors like age, life expectancy, and standard of living in these cities. 4. the total of morbidity and mortality damages reduction in 2020 is compared with the economic damages being reported for the cities. it is reported that london (18.6b$) suffered maximum economic damage during its respective lockdown days, while wuhan suffered the lowest (0.56b$). paris (15.81b$) and delhi (5.36b$) suffered the second-highest and lowest damages, respectively. delhi, london, wuhan, and paris prevented ap damages worth 6.4b$, 2.09b$, 0.97b$, and 0.47 b$, respectively, in 2020. this indicates that wuhan and delhi could extract better worth from prevention of damages from lockdown as compared to their lockdown losses. this might be due to the fact that both these cities are highly polluted as compared to paris and london and are economically developing as well. wuhan is actually higher as the economic damages incurred by that city are the lowest. the lowest recovery is made by paris, while london stands at second-lowest. it is apparent that while quantifying ap damages in terms of exposure and affected population is fruitful, there are more insights which can be explored to understand the true magnitude of the damage caused by it. the monetary evaluation gives a common denomination for comparison and for making a rational decision for policy formulation. the above research of four major global cities demonstrates that while the world is suffering from enormous economic damage, the lockdown has created some positive for the air environment and hence the human health as well. while the above analysis might hold true for the majority of the cities suffering from a probable of ap, a detailed analysis should be carried out for the respective city before making decisions. accounting of the cost and benefits due to halting of anthropogenic activities gives us a clear indication of 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decisions that can be trusted changes in air quality during the lockdown in barcelona (spain) one month into the sars-cov-2 epidemic focus on wuhan london's economic income per capita is double that of rest of the uk prevalence and economic burden of cardiovascular diseases in france in 2013 according to the national health insurance scheme database direct medical costs of hospitalizations for cardiovascular diseases in a novel coronavirus outbreak of global healthconcern severe air pollution events not avoided by reduced anthropogenic activities during covid-19 outbreak air quality guidelines: global update 2005: particulate matter, ozone, nitrogen dioxide, and sulfur dioxide metrics: disability-adjusted life year (daly): quantifying the burden of disease from mortality and morbidity coronavirus disease (covid-2019) situation reports. geneva: world health organization publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations acknowledgments authors acknowledge council of scientific and industrial research (csir), india, and its constituent laboratory national environmental engineering research institute (neeri) for providing the support for the research. the manuscript is checked for plagiarism using licensed ithenticate software wide krc no.: csir-neeri/ krc/2020/may/csum-drc-dir/1. key: cord-304925-9gvx3swf authors: xie, zhixiang; qin, yaochen; li, yang; shen, wei; zheng, zhicheng; liu, shirui title: spatial and temporal differentiation of covid-19 epidemic spread in mainland china and its influencing factors date: 2020-07-14 journal: sci total environ doi: 10.1016/j.scitotenv.2020.140929 sha: doc_id: 304925 cord_uid: 9gvx3swf abstract this paper uses the exploratory spatial data analysis and the geodetector method to analyze the spatial and temporal differentiation characteristics and the influencing factors of the covid-19 (corona virus disease 2019) epidemic spread in mainland china based on the cumulative confirmed cases, average temperature, and socio-economic data. the results show that: (1) the epidemic spread rapidly from january 24 to february 20, 2020, and the distribution of the epidemic areas tended to be stable over time. the epidemic spread rate in hubei province, in its surrounding, and in some economically developed cities was higher, while that in western part of china and in remote areas of central and eastern china was lower. (2) the global and local spatial correlation characteristics of the epidemic distribution present a positive correlation. specifically, the global spatial correlation characteristics experienced a change process from agglomeration to decentralization. the local spatial correlation characteristics were mainly composed of the‘high-high’ and ‘low-low’ clustering types, and the situation of the contiguous layout was very significant. (3) the population inflow from wuhan and the strength of economic connection were the main factors affecting the epidemic spread, together with the population distribution, transport accessibility, average temperature, and medical facilities, which affected the epidemic spread to varying degrees. (4) the detection factors interacted mainly through the mutual enhancement and nonlinear enhancement, and their influence on the epidemic spread rate exceeded that of single factors. besides, each detection factor has an interval range that is conducive to the epidemic spread. j o u r n a l p r e -p r o o f total of 116 countries or regions in the world appeared to be hit by the covid-19 epidemic, and more than 130,000 people have been diagnosed. with the continuous spread of the covid-19 epidemic, several countries or regions of the world have been forced to take emergency measures such as closing cities, stopping production, suspending school classes, and restricting population movement, causing great harm to economic development and residents' health (an and jia, 2020) . therefore, it has become an urgent scientific problem to grasp the spatial and temporal changes of the covid-19 epidemic spread, and clarify the driving mechanism. since the outbreak of covid-19 epidemic, scholars have carried out abundant studies on the epidemic spread and achieved fruitful research results, which are of great guiding significance for the prevention and control of the epidemic. joseph et al. (2020) estimated the size of the epidemic by using a mathematical model based on the data of confirmed cases of covid-19 and residents' travel (including via trains, planes, and roads), and concluded that about 75,815 people were infected in the wuhan city during the early outbreak stage of the epidemic. david et al. (2020) compared covid-19 with other viruses, claiming that a sustained epidemic would pose a serious threat to global health, and proposing that the goal of sustainable development could be achieved by building a human-environment-animal health alliance. liu et al. (2020a) used the exponential growth and maximum likelihood estimation method to determine the transmission dynamics of covid-19 in wuhan, and found that the average incubation period of the virus was 4.8 days, and the basic regeneration index reached 2.90 (95% confidence interval (ci): 2.32-3.63) and 2.92 (95% ci: 2.28-3.67). ai et al. (2020) used the statistical analysis method to investigate the impact of lockdown measures in wuhan (january 23, 2020) on the covid-19 epidemic spread in other parts of china. they claim that if the closure j o u r n a l p r e -p r o o f measures were implemented 2 days in advance, it could have been possible to effectively prevent from being infected of 1,420 people, if the city was closed 2 days later, there would have been 1,462 more infections. bai et al. (2020) used the transmission dynamics model to describe the evolution rule of the epidemic based on the data of confirmed covid-19 cases in the shaanxi province, revealed that the high incidence areas were mainly located in xi 'an, ankang, and hanzhong, and that the outbreak peak period was in early february 2020, with the basic regeneration index of the epidemic spread reaching 2.95. wang et al. (2020a) used the spearman correlation analysis method to find the relationship between the incidence of covid-19 and the baidu migration index in guangdong province, and found that there was a positive correlation between the daily incidence and the 3-day migration index. wang et al. (2020b) used the complex network model to explore the impact of resuming work in surrounding cities on the epidemic situation in hubei province on february 17, february 24, and march 2, and came to a conclusion that resuming work on march 2 would not cause a second outbreak of the epidemic. yan et al. (2020) predicted the trend of the covid-19 epidemic by building a time-delay dynamics model, and claimed that the epidemic could be controlled in the short period if the prevention and control efforts were kept unchanged. chen and cao (2020) made an epidemiological analysis of the daily confirmed cases in china, affirming that the situation of epidemic prevention and control in china was severe, and that targeted control measures should be formulated for the returning of enterprises and personnel in the future. liu et al. (2020b) analyzed the spatial and temporal characteristics of the epidemic spread in guangdong province, and found that the prevention and control measures adopted were effective, and high-risk areas were located in economically developed areas. liu et al. (2020c) used the statistical analysis method to analyze the temporal and spatial j o u r n a l p r e -p r o o f characteristics and the transmission path of the covid-19 epidemic in zhuhai, revealing that the input from the epidemic area and family gatherings were the causes of epidemic spread. the research report published by the yellow river civilization (ai et al., 2020; wang et al., 2020b) . although some scholars try to reveal the epidemic spread rules from a geographical perspective, they mainly focus on the spatial and temporal evolution characteristics of the epidemic, and seldom discuss the driving causes of the epidemic spread (liu et al., 2020c) . (2) in terms of research methods, current studies employ mainly the correlation analyses and regression analyses method, while the application of modern information technology and spatial analysis method are relatively limited (wang et al., 2020a) . (3) in terms of research scale, scholars generally investigate the epidemic spread characteristics at the city or regional scale, and there are few studies at the national level (liu et al., 2020b; liu et al., 2020b) . (4) in relation to data sources, the data of covid-19 cases can be obtained very easily; however, there are great difficulties in obtaining environmental and socio-economic data related to the epidemic spread, which is why current researches lag behind in the driving j o u r n a l p r e -p r o o f mechanism of epidemic spread. in this paper, the number of confirmed covid-19 cases in mainland china was taken as the measurement index, and the spatial and temporal differentiation of the epidemic spread were described by the exploratory spatial data analysis method. then, the key factors affecting the covid-19 epidemic spread were identified by using the geodetector method, so as to provide references for clarifying the epidemic spread rule, formulating some protection policies, and promoting the resumption of work and production. the basic research objects of this paper are the administrative units at prefecturebaidu migration data in the paper is from january 11 to 23, 2020, specifically referring to the top 100 cities toward which people move out of wuhan every day. the winter average temperature data for each unit are from the weather network (https://www.tianqi.com). in addition, since it is impossible to obtain data on the population, gross domestic product, and number of beds in medical institutions for each region during the covid-19 epidemic period, this paper employs the corresponding data in 2018, which is derived from the 2019 provincial statistical yearbooks or the 2018 statistical bulletins. using the cumulative number of covid-19 cases as an indicator to measure the epidemic spread rate is biased due to the large differences in base population for different regions of mainland china. therefore, the cumulative number of covid-19 cases was divided by the number of days to calculate the epidemic spread rate, using the following formula: where v i represents the epidemic spread rate in region i; s i represents the cumulative number of covid-19 cases in region i by february 20; m represents february 20; and n i represents the date of the first confirmed case in region i. j o u r n a l p r e -p r o o f the exploratory spatial data analysis method was used to verify whether the observed value of a unit has spatial correlation with the observed values of its neighboring units (li et al., 2018) . the global moran's i index is used to measure the global spatial correlation, while the local moran's i index in lisa (local indicators of spatial association) was used to measure the local spatial correlation (rong et al., 2016) . their formulas (anselin, 1995; gallo and ertur, 2003) are as follows: where i is the global moran's i index; x i and x j are the observed values of unit i and j; w ij is the spatial weight matrix (with 1 as adjacent, and 0 as non-adjacent), s 2 represents the variance; k represents the number of observation units; i* is the local moran's i index; w pq is the normalized form of the spatial weight matrix; and z p , z q are the normalized forms of the observed values in unit p and q. spatial differentiation is a basic characteristic of geographical phenomena, the geodetector method can measure the degree of spatial stratified heterogeneity and test its significance, through the within-strata variance less than the between strata variance . the geodetector method comprises four modules: factor detection, interaction detection, risk detection and ecological detection. the factor detection is expressed by q value (wang and xu, 2017) , its formulas are as follows: where q represents the explanatory power of detect factor x on the spatial distribution of detected factor y, the value of q ranges from 0 to 1; h=1,…, l, which represents the stratification of the detect factor x and detected factor y; n h and n are the number of samples for the layer h and the whole study area; ℎ 2 and 2 are the variance of y value for the layer h and the whole study area; ssw and sst are the sum of intra-layer variances and the total variance of the whole study area. the interaction detection can identify the explanatory power of the detect factors x1 and x2 to the detected factor y, whose operation steps are as follows: first, we calculate the q values of x1 and x2, respectively. second, a new layer x1∩x2 can be obtained by stacking the layer x1 and x2, on this basis, the q (x1∩x2) value can be calculated. third, the interaction type between x1 and x2 can be determined by comparing q (x1), q (x2), and q (x1∩x2) values. the risk detection is used to determine whether there exists a significant difference in the mean value of an attribute between the two sub-regions, which is tested by the t-statistic. its formula is as follows : where y h represents the average value of epidemic spread rate in the layer h, n h is the number of samples in the layer h, var represents the variance. we can compare whether there are significant differences in the influence of any detect factors x1 and x2 on the spatial distribution of the detected factor y by using the ecological detection, which is measured by the f-statistic. where 1 and 2 represent the sample sizes of the detect factors x1 and x2; 1 and 2 are the sum of the variances in the layers formed by x 1 and x 2 ; and l 1 and l 2 are the number of layers of x 1 and x 2 . the null hypothesis h 0 is: if h 0 is rejected at the significance level of , which indicates that x1 and x2 have significantly different effects on the spatial distribution of y. the arcgis software was used to classify the cumulative number of covid-19 cases in the following categories: 0; 1-50; 51-100; 101-300; and >300 persons. the epidemic spread rate was classified into the following categories: <1; 1-3; 3-5; 5-7; and >7 persons/day ( figure 1 ). j o u r n a l p r e -p r o o f (1) global spatial correlation characteristics in this paper, the cumulative number of confirmed covid-19 cases and the epidemic spread rate were taken as variables, the spatial weight matrix based on geographical adjacency was selected, and the global moran's i index, the p test value and the z statistic score of the cumulative number of confirmed covid-19 cases and the epidemic spread rate were calculated by using the geoda software, so as to clarify the global spatial correlation characteristics (table 1) . respectively, passing the significance test at the 1% level, implying that the spatial pattern of the epidemic spread rate was also characterized by a clustering distribution. (2) local spatial correlation characteristics the global moran's i index has the defect of ignoring the instability of local spatial processes. therefore, it is necessary to draw a lisa cluster map to analyze the local spatial correlation characteristics of covid-19 epidemic (figure 2 ). cluster areas were located in anqing, lu'an, jiujiang, nanyang, qianjiang, shennongjia forest region, and changde; and the range of 'low-low' cluster was basically consistent with that of february 6. in terms of quantity change, the number of units classified in the 'high-high' cluster first increased and then decreased; the number of units included in the 'high-low' cluster continued to decrease until they disappeared; that in the 'low-high' cluster experienced a process of initial decline and then rose again; and the number of units belonged to the 'low-low' cluster showed an increasing trend. therefore, it is not difficult to see that the layout trend of the j o u r n a l p r e -p r o o f cumulative number of confirmed covid-19 cases at the time nodes has not changed fundamentally, and was dominated by the 'high-high' and 'low-low' type. this indicates that the local spatial correlation characteristics of the confirmed covid-19 cases were also dominated by a positive correlation, although the clustering trend was weakened. overall, the 'high-high' cluster areas showed a layout trend from centralization to decentralization, which tended to be stable over time, especially for wuhan and its surrounding areas. there was a contiguous layout trend of the 'lowlow' cluster areas, which were mainly located in inner mongolia, gansu, ningxia, qinghai, tibet, and xinjiang. as for the epidemic spread rate, there were 16 administrative units in the 'high-high' cluster, 0 in the 'high-low' cluster, 5 in the 'low-high' cluster, and 75 in the 'low-low' cluster. the high-high cluster areas were located in wuhan, huangshi, yichang, xiangyang, ezhou, jingmen, xiaogan, jingzhou, huanggang, xianning, suizhou, xiantao, qianjiang, tianmen, nanyang, and xinyang; the 'low-high' cluster areas were located in anqing, lu'an, jiujiang, shennongjia forest region, and changde; and the 'low-low' cluster areas were located in western china. the covid-19 epidemic first occurred in wuhan, and then spread to other parts of china. therefore, people have been the carrier, the transportation network has been the channel, and the social and economic connections have been the internal driving force in the process of the epidemic spread. thus, we selected the indicators reflecting the population distribution, population inflow from wuhan, traffic accessibility, economic connection intensity, average temperature, and medical facilities conditions j o u r n a l p r e -p r o o f as the detection factors (table 2) , and the epidemic spread rate as the detected factor to assess the formation mechanism for the spatial pattern of covid-19 epidemic. note: the gravity model was used to calculate the intensity of economic contact between each region and wuhan, and the distance was the time reachable distance (meng and lu, 2011). firstly, the classification method of natural discontinuities in arcgis10.2 software was used to divide detection factors into 6 categories, the classified maps of the detection factors were drawn (figure 3 ). according to formulas (3)-(8), the determination ability of detection factors was calculated by using the geodetector software to analyze the influencing factors of epidemic spread. j o u r n a l p r e -p r o o f (1) factor detection analysis the q values of all the detection factors passed the significance test at the 5% level, indicating that these factors have a significant determination ability of the spatial distribution of the covid-19 epidemic spread. specifically, the q (p) values of x1, x2, x3, x4, x5 and x6 were equal to 0.060 (0.003), 0.504 (0.000), 0.041 (0.000), 0.404 (0.000), 0.021 (0.028) and 0.078 (0.000), respectively. according to the size of q value, the inflow of population from wuhan was the primary factor affecting the epidemic spread, and its explanatory power reached 50.4%. the economic connection intensity was the secondary determinant factor, and its explanatory power was 40.4%. the availability of medical facilities was the third determinant factor, which accounted for a 7.8% of explanation power. the determination ability of population distribution was 6%, while the traffic accessibility and average temperature were both relatively weak, below 5%. it is worth noting that the differentiation and factor detection analysis discussed only the determination ability of single factor on the epidemic spread rate, and did not consider the interaction effect of factors. (2) interaction detection analysis the interaction detector analysis is used to identify the interactions between any j o u r n a l p r e -p r o o f two factors. table 3 shows the interactions detection results between factors. it can be seen from table 3 (3) ecological detection analysis according to table 4 , it could be found that the differences among the detection factors were statistically significant. specifically, the influence of the population distribution (x1) on the spatial distribution of the epidemic spread rate was significantly different from the population inflow from wuhan (x2), economic connection intensity (x4), and average temperature (x5), but not different from the traffic accessibility (x3) and medical facility conditions (x6). the influence of the population inflow from wuhan (x2) was significantly different from that of the traffic accessibility (x3), economic connection intensity (x4), average temperature (x5), and medical facilities conditions (x6). there was a significant difference between the influence of traffic accessibility (x3) and that of economic connection intensity (x4), but there were no significant difference with the average temperature (x5) and medical facilities conditions (x6). the influence of economic connection intensity (x4) was different from that of the average temperature (x5) and medical facility condition (x6). there was no significant difference between the average temperature (x5) and the medical facilities conditions (x6). generally speaking, the detection factors selected in this paper are reasonable, and the differences among them are statistically significant. note: y means the difference of the influence of the two factors is significant with the confidence of 95%, while n means no significant difference. (4) risk detection analysis table 5 showed that the epidemic had the fastest spread rate when the population density was 1,162-2,564 persons/km 2 . when the proportion of population inflow from wuhan was maintained at 6.94-14.25%, the epidemic spread rate was fastest. when the economic contact intensity with wuhan was kept in the range of 598,158.64-1,524,023.05, the epidemic spread rate was fastest. when the geographical distance from wuhan was 68.38-540.98 km, the spread rate was fastest. when the average temperature in winter was maintained at 11-16°c, the epidemic spread rate was higher. the epidemic spread rate was higher when there were between 9.58 and 14.49 beds for 1,000 persons. it can also be found that the population distribution, population inflow from wuhan, economic connection intensity, medical facilities, and the epidemic spread rate were significantly positively correlated, while the traffic accessibility was negatively correlated with the epidemic spread rate. this paper studied the spatial and temporal variation and the influencing factors of the covid-19 epidemic spread in mainland china, which can provide references for formulating the public health policies and promoting the resumption of production. however, there exist the following problems. in terms of data sources, although many countries or regions have published the epidemic announcements of covid-19 in real time, and the epidemic data was very convenient, virtually most of countries or regions had more people infected than registered, which could affect the accuracy of the evaluation results. then, the population density data in 2018 was used as a replacement due to a fact that the population density for the each administrative unit in mainland china during the epidemic period was unavailable. the treatment method hid the drastic changes in the data because the covid-19 epidemic happened during the chinese spring festival period, which had a characteristic that the scale and frequency of population movements were intensified. it's worth noting that the population density is an important indicator to explain the epidemic spread rate, so the alternative data inevitably weakened the explanatory power of current research from this perspective. in addition, the factors affecting the epidemic spread were complex, and involved both the quantitative and the non-quantitative indicators. this paper constructed an indicator system of the multiple factors influencing the epidemic spread based on the principle of data availability; the other non-quantitative indicators might be ignored, which increased the uncertainty of evaluation results. for the research method, the formula of epidemic spread rate was applicable to compare the epidemic spread rate of different administrative units at three time nodes, which actually did not conform to the exponential growth rule of infectious diseases (such as the covid-19, sars, and mers (middle east respiratory syndrome)) in the exposed population. how to accurately measure the actual spread rate of the epidemic in each region was the direction of future research. second, the exploratory spatial data analysis method investigated the spatial clustering characteristics of covid-19 epidemic in administrative units at prefectural level and above, and did j o u r n a l p r e -p r o o f not consider the agglomeration development situation at a finer spatial scale, which inevitably weakened the application value of the research results. third, the geodetector method was adopted to obtain the most favorable range of the covid-19 epidemic spread in this paper, which was developed from the perspective of statistics. the sample data directly affected the final evaluation result, and no epidemiological investigation on the residents' health status was implemented, so the conclusions drawn from current research were uncertain to some extent. finally, there might have multicollinearity between the strength of economic connection economic and other factors in this paper, and the geodetector method was not used to deal with it, which would weaken the persuasiveness of the research results. (1) the temporal changes of the covid-19 epidemic in mainland china are clear, and the epidemic spread rate has an evident spatial variation. in terms of temporal change, the epidemic quickly spread to most regions from january 24 to february 6. the epidemic spread rate slowed down from february 6 to february 20, although the epidemic situation in some cities worsened sharply. the areas where the epidemic spread quickly were mainly located in the hubei province, its surrounding areas, and some economically developed cities. the western part of china, as well as the remote areas of central and eastern china experienced a slow epidemic spread. (2) the global and local spatial correlation characteristics of the covid-19 epidemic were dominated by clustering situations. specifically, the global spatial correlation characteristics initially increased and then decreased, while the local spatial correlation characteristics tended to be stable with the passage of time, and were mainly composed of the 'high-high' and 'low-low' cluster types. the 'high-j o u r n a l p r e -p r o o f high' cluster areas were located in wuhan, huangshi, yichang, xiangyang, ezhou, jingmen, xiaogan, jingzhou, huanggang, xianning, suizhou, xiantao, qianjiang, tianmen, nanyang and xinyang. the 'low-low' cluster areas were located in parts of inner mongolia, gansu, ningxia, qinghai, tibet, and xinjiang. (3) the population distribution, population inflow from wuhan, traffic accessibility, economic connection intensity, average temperature and medical facilities conditions had significant effects on the epidemic spread rate. the population inflow from wuhan was the primary factor affecting the epidemic spread, followed by the economic connection intensity, and the medical facilities conditions. the population distribution, traffic accessibility, and average temperature also had different degrees of influence on the epidemic spread. from the perspective of action direction, the population distribution, population inflow from wuhan, economic connection intensity and medical facilities conditions played a positive role in the process of epidemic spread, while the traffic accessibility played a negative role. (4) detection factors interacted through mutual enhancement and nonlinear enhancement, and their influence on the epidemic spread rate exceeded that of single detection factors. the interaction between the population inflow from wuhan and medical facilities conditions, as well as that between the population distribution and population inflow from wuhan, that between the population distribution and economic connection intensity, and that between the economic connection intensity and medical facilities conditions had a great influence on the epidemic spread. the interaction between the population distribution and traffic accessibility, as well as that between the population distribution and average temperature, that between the traffic accessibility and average temperature, and that between the average temperature and medical facilities conditions had little impact on the epidemic spread. influencing factors are analyzed. 2) the global and local spatial correlation characteristics of the epidemic distribution present a positive correlation. 3) the population inflow from wuhan and strength of economic connection are the main factors affecting the epidemic spread. 4) the interaction influence of detection factors on the epidemic spread exceeds that of the single factor. 5) when the average temperature in winter is maintained at 11-16°c, the epidemic spread rate is higher. population movement, city closure and spatial transmission of the 2019-ncov infection in china analysis of the economic impact of the ncp and countermeasure study local indicators of spatial association-lisa early transmission dynamics of novel coronavirus pneumonia epidemic in shaanxi province incidence trend of novel coronavirus (sars-cov-2)-infected pneumonia in china the continuing 2019-ncov epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in wuhan exploratory spatial data analysis of the distribution of regional per capita gdp in europe nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modeling study evolution of patterns in the ratio of gender at birth in henan province transmission dynamics of 2019 novel coronavirus the diffusion characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in guangdong province analysis of the spatio-temporal characteristics and transmission path of covid-19 cluster cases in zhuhai impact of high-speed railway on accessibility and economic linkage of cities along the railway in henan province spatial differentiation patterns of carbon emissions from residential energy consumption in small and medium-sized cities: a case study of kaifeng geodetector: principle and prospective preliminary analysis on the early epidemic and spatiotemporal distribution of new coronavirus pneumonia in guangdong province when will be the resumption of work in wuhan and its surrounding areas during covid-19 epidemic? a data-driven network modeling analysis determinants and identification of the northern boundary of china's tropical zone modeling and prediction for the trend of outbreak of ncp based on a time-delay dynamic system quantifying the influence of nature and socioeconomic factors and their interactive impact on pm 2.5 pollution in china backtracking transmission of covid-19 in china based on big data source key: cord-338001-jig46hsk authors: ong, jacqueline s. m.; tosoni, alvise; kim, yaejean; kissoon, niranjan; murthy, srinivas title: coronavirus disease 2019 in critically ill children: a narrative review of the literature date: 2020-04-21 journal: pediatr crit care med doi: 10.1097/pcc.0000000000002376 sha: doc_id: 338001 cord_uid: jig46hsk coronavirus disease 2019 has spread around the world. in the 3 months since its emergence, we have learned a great deal about its clinical management and its relevance to the pediatric critical care provider. in this article, we review the available literature and provide valuable insight into the clinical management of this disease, as well as information on preparedness activities that every picu should perform. t he novel severe acute respiratory syndrome coronavirus 2 (sars-cov-2) originated in wuhan, hubei province in december 2019 and has now circumscribed the globe, involving 168 countries outside of china at the time of writing. as of this writing, 1,000,000 cases have been confirmed globally (1), with 50,000 deaths, giving rise to an estimated case fatality rate (cfr) of 4%, although that number is expected to change. there has been significant regional and global variation in cfrs, with hubei having a seven-fold increase of 2.9% versus 0.4% for the rest of china (2) . italy, the current epicenter of the european coronavirus disease 2019 (covid-19) outbreak, currently stands at a cfr of 7.2% (3). children do not appear to account for a large proportion of covid-19 disease. in the largest series to date from china (2) , pediatric patients less than 19 years old accounted for only 2% of confirmed cases. in italy, covid-19 cases in the pediatric cohort (0-18 yr old) account for only 1.2% (3) . in korea, children less than 19 years were 4.8% (4) . in a series of 1,391 pediatric patients from wuhan children's hospital who were screened from january 28, 2020, to february 26, 2020, sars-cov-2 was confirmed in 171 patients (12.3%) (5) . this is higher than a previously described cohort of 366 children from tongji hospital in wuhan that only found six positive cases (1.6%) (6) . in guangzhou, china, of 745 children who were in close contact with covid-19 infected adults, only 10 tested positive (1.3%), suggesting a great deal of variation (7) . children also appear to be relatively spared of severe disease. in the largest published covid-19 retrospective case review in children (n = 2,143) to date (8) , 94.1% of the children were either asymptomatic (4.4%) or had mild (50.9%)/ moderate disease (38.8%). this series was predominantly suspected, not-confirmed (65.9%), cases from winter with a variety of circulating viruses, and it is unclear what the true positive rate is in this series. in the case series of true positives from wuhan children's hospital (5), 15.8% (n = 27) were asymptomatic and 19.3% (n = 33) only had an upper respiratory tract infection. the most common symptoms were cough (48.5%) and fever (41.5%)-this is supported by several other smaller case series already in the literature (6, 7, 9, 10) . in adults (2, 3) , approximately 5% of patients will require intensive care. information on pediatric patients requiring intensive care is very limited. in the large nationwide pediatric series (8), 5.2% (n = 113) of the 2,143 children had respiratory distress or hypoxia and 0.6% (n = 13) progressed to acute respiratory distress syndrome or multiple organ dysfunction. however, infants under 1 year appear to have an increased risk of severe disease with 10% (n = 40 out of 379 cases) of the cohort fulfilling severity criteria, defined as an oxygen saturation less than 92%. the rate of severe or critical disease in the www.pccmjournal.org xxx 2020 • volume xx • number xxx other age groups was lower (7.3% in 1-5 yr, 4.2% in 6-10 yr, 4.1% in 11-15 yr, and 3% > 16 yr), with a death in a 14 yearold. the infant group had the highest proportion of clinically diagnosed disease, and there remains the possibility that other viruses such as influenza a/b and respiratory syncytial virus may have caused severe disease. in the cohort with 1,391 children from wuhan children's hospital (5) , only three children required intensive care. one child had preexisting immunosuppression (leukemia on maintenance chemotherapy) and the other two had preexisting though perhaps unrelated conditions (hydronephrosis and intussusception). unfortunately, the child with intussusception died of multiple organ failure 4 weeks after admission. in the small cohort from tongji hospital (6), wuhan, one out of the six children with covid-19 was admitted to intensive care. this child received antiviral therapy (ribavirin, oseltamivir), glucocorticoids, pooled immunoglobulin from healthy donors as well as supplemental oxygen. it is unclear if she required mechanical ventilation. there were no deaths in this cohort. other published small cohorts have also not had documented admission to the picu (7, 11, 12) . the published data and anecdotal evidence from picu colleagues globally supports the notion that most children do not exhibit severe disease. most children who tested positive in china were identified because of screening of household contacts and family clusters rather than because of signs and symptoms of disease (5) (6) (7) . this experience is in keeping with the previous coronavirus outbreaks of middle east respiratory syndrome coronavirus and sars cov where children had a milder manifestation of disease (10) . why children appear to be less severely affected, compared with adults, by sars-cov-2 is unknown. lessons gleaned from adults may provide some clues. in adults, the pathophysiology of covid-19 appears to be related to immune dysregulation and a resultant cytokine storm (13, 14) . adults with covid-19 presenting with progressive and/or severe lymphopenia and an increasing neutrophil count have been associated with higher disease severity (13) (14) (15) (16) . in addition, adults who have required icu care have had higher levels of circulating cytokines associated with the innate immune response (16) . clinical worsening in the adult population has been described to occur in the second week of illness, in keeping with the proposed pro-inflammatory pathophysiology, resulting in progressive lung injury (15) . it has been postulated that sars-cov-2 induces a delayed or suppressed interferon response during the initial phase, resulting in subsequent uncontrolled viral replication and a hyperinflammatory response by the body (13) . children, on the other hand, have not displayed a similar tendency toward immune dysregulation. lymphopenia was present in only 3.5% of pediatric cases in the wuhan children's hospital series (5), compared with 70.3% in hospitalized adults (17) . also, other markers of a pro-inflammatory response such as c-reactive protein, deranged liver function tests, and d-dimers are not common in children as compared with the adult population (5-7). children may be also less susceptible as a result of possible age-related differences in the expression of angiotensinconverting enzyme 2 (ace2) in humans (18) . sars cov and sars-cov2 both use ace2 as the cell receptor in humans, predominantly in type ii pneumocytes, and its presence appears to protect against lung injury (18, 19) . in rat lung, however, the expression of ace2 decreases with age which runs counter to the proposed mechanism of protection (20) . the variation of ace2 expression and activity with age and its impact on disease is a major knowledge gap in our understanding of pediatric covid-19. we have little data on the impact on sars-cov-2 on children with chronic illnesses. many children are likely to suffer these comorbidities with advanced treatment and hence will need to monitored closely for severe disease. the main method for detection for sars-cov-2 has been by real-time polymerase chain reaction (rt-pcr) testing on upper or lower respiratory tract secretions. as the majority of children have had mild symptoms, the vast majority of samples have been obtained via nasopharyngeal swabs. viral shedding via the fecal route has been detected in children, although implications for transmission are unclear (7). as compared with adults, children have also not consistently demonstrated abnormal chest radiographs on presentation. in a case series of 20 children from wuhan, ct scans of the chest were performed in order to support the diagnosis of covid-19, with 80% of the children (n = 16) showing some abnormality, including 60% with groundglass opacities and 50% with consolidation with surrounding halo sign (21) . however, given children have generally mild disease, and turnaround time for rt-pcr is generally improving, the use of ct scan as a diagnostic tool may have limited uptake. it is also worth noting that coinfection with other respiratory viruses has been described. forty percent of children in the same radiological case series above were noted to be coinfected with other pathogens such as influenza a/b, respiratory syncytial virus, and mycoplasma (21) . this is in keeping with prior studies showing that other viruses can be isolated from up to two-thirds of children with coronavirus infection (22) . to better understand their role, and trials should enroll children to better understand their safety and effectiveness in this population. despite likely small numbers, caring for children with covid-19 will require careful considerations in clinical care, staffing and isolation requirements, and all picus should be prepared for these possibilities. given that children appear to have mild disease and may have a clinical picture similar to that of viral bronchiolitis, the use of noninvasive ventilation (niv), and/or high-flow nasal cannula (hfnc) for respiratory support would likely be preferred amongst picu clinicians. some institutional guidelines would, however, suggest avoiding niv and hfnc in open wards to reduce the risk of aerosolization of droplets and move patients toward early intubation, if negative pressure rooms are unavailable. there are, however, concerns about balancing the potential morbidity of intubation for the pediatric patient with mild respiratory distress with the theoretical risk of increased aerosolization. at present, as rates of severe pediatric covid-19 remain low and the rates of other viral etiologies remain unchanged, individualized institutional practice in the use of niv/hfnc may be considered in appropriate pediatric patients. several guidelines about airway management for covid-19 have been made publicly available from icus and anesthesia societies (23) (24) (25) (26) . local guidelines are largely in place for many hospitals. the principles of maintaining safety for both patient and the intubating team remain paramount. prior to intubation, it is important to minimize the number of staff in the room and all staff to apply good hand hygiene and don full personal protective equipment (ppe). the patient should ideally be admitted to a negative pressure isolation room. a clear checklist for drugs and equipment should be in place and roles clearly delineated ( table 1) . most importantly is acknowledging the potential for aerosolization and ensuring that all staff present are familiar and comfortable with required ppe. communication is critical and made particularly challenging by the use of ppe during intubation, especially in units with powered air-purifying respirator use. closed-loop communication is crucial and members of the team should monitor each other for potential contamination. the most experienced practitioner should perform intubation. several centers do advocate the use of video laryngoscopy if available, and if the practitioner is trained in its use-this may reduce distance to the patient airway. rapid sequence induction with paralysis to avoid coughing is ideal. adult guidelines suggest apneic oxygenation and minimal bagging to reduce aerosol generation, but this will be challenging in infants and small children with a small functional residual capacity and limited space. as such, bag valve mask ventilation can be considered with great care, with a tight mask seal (two-handed technique might be required) and small tidal volumes. cuffed tubes can be selected to minimize significant air leaks during high-pressure ventilation and possibly minimize transmissibility. once the child is intubated, disruptions to the ventilator circuit should be minimized, with closed in-line suction. staff should don appropriate ppe and be prepared to clamp the tube if ventilator circuit breaks are anticipated. doffing ppe after the procedure requires equal care and is a high-risk period for contamination risks. given the complexity of the process, it is strongly recommended that hospitals and units run simulations to practice each step of the intubation and extubation process prior to having a real patient in the unit. the complex process of donning and doffing ppe, the need for anticipating far more than usual, and the challenges of communication cannot be over-emphasized. one or more caregivers usually accompany pediatric patients and this too needs to be taken into account when considering the care of covid-19 patients. caregivers are close contacts of the infected patient, although they may be asymptomatic at the time-in the wuhan children's hospital series with active case finding of close contacts, 90% of confirmed cases had family members who were either confirmed or suspect disease (5) . many centers have limited the number of caregivers at the bedside to one caregiver, restricting movement of the caregiver in the hospital, and ensure that staff maintains ppe when at the bedside. clearly, given the high rates of familial clustering, there is a high likelihood of these family members being similarly infected, and local public health guidance should be followed to ensure minimal risk of nosocomial spread. within this environment, the ability to deliver the same standard of family-centered care that is given during peacetime will be significantly compromised. the significant psychologic stress that may be experienced by a solo caregiver, coupled with staff time constraints, impaired communication potentially generated by full ppe, and the urgency of multiple sick patients create a perfect storm of challenges. in this scenario, the creation of a family liaison contact may alleviate some of the burden and allow a basic level of familycentered care to be delivered (27) . as point-of-care testing is unavailable, in the setting of widespread community transmission, it is currently recommended that hospitalized children who fit local case definitions for covid-19 be treated as a patient under investigation until tests come back negative. this implies using the same levels of infection prevention and control, speaking to the tremendous importance of rapidly and widely available testing, given the www.pccmjournal.org xxx 2020 • volume xx • number xxx resource and personnel requirements involved in this process. given the low rates of critical illness due to covid-19, this process will likely exert more impact on day-to-day processes in picus than sick patients with confirmed infection. although pediatric cases requiring critical care might be low, it is important to anticipate that exposures may occur and staff are quarantined for a period of time. it may be necessary to use a segregated roster where two or three groups of clinical staff are completely separated from each other such that if one group is exposed, the entire team may be quarantined together and the next team can take its place. in lean picu teams, this may be extremely challenging but the scenario needs to be considered carefully and backup plans established. identifying potential surge capacity in the form of extra beds, staff, and equipment should also be anticipated and published guidance on early planning for pandemics is already available (27, 28) . this may necessitate reducing elective work and anticipating the need for high dependency areas to be converted to intensive care space. identifying clinical staff who may be able to bolster the picu response, for example, pulmonologists, and anesthetists may be necessary at an early stage. nursing staff may need to look to up-skilling general ward staff to help look after the less critically ill patients, allowing the picu nursing staff to focus on the sickest patients. it is imperative that clear guidelines about the use of appropriate ppe are established and training done at all levels. this is to ensure appropriate usage and prevent ppe from being wasted unnecessarily. in a global pandemic, stocks of necessary items are likely to run low and hospital/national workflows should be established to maintain staff safety. given the burden of disease on adult icus, it is also possible that pediatric units may be called upon to help look after adult patients so as to increase covid-19 capacity in adult units. feasible options such as increasing the age limit for the picu to 25 years old or to consider accepting patients with shared picu diagnoses, such as diabetic ketoacidosis, overdose, trauma, or congenital cardiac disease might have to be considered. these arrangements should be made early and the decisions made must reflect local and regional capabilities and in line with appropriate standards of care for the patient (29) . setting up local and international communication groups over social media channels such as whatsapp, telegram, and twitter have also proved to be very helpful in disseminating information and education for this emerging infection with rapidly generated data. the hashtags #pedsicu and #covid19 have garnered high volumes of information for twitter users online. these social media channels, in combination with free open access medical education websites such as open pediatrics and the life in the fast lane blog (www.litfl.com) have also served as international covid-19 resources and facilitated knowledge sharing at a rapid rate and fostered a powerful sense of community amongst practitioners. this is a stressful time for all clinical staff and the sense of isolation and fear can be profound. social distancing has been implemented in several countries and regular hospital meetings, teaching sessions, and conferences have largely been canceled. anxiety about personal welfare as well as the safety of family and friends cannot be underestimated. hospital and icu leadership is critical during this time and communication about plans and workflows needs to be measured and wellpaced. it is wise to consider programs in the unit and hospital to encourage staff and to consider measures to cater to mental wellbeing of staff. at present, critically ill covid-19 pediatric patients remain rare, as the majority of pediatric cases have mild symptoms. the substantial rise in international numbers, however, necessitates early planning in consideration of a rise in pediatric cases. a comprehensive response will require cooperation at a local, regional, and national level. in addition, the international picu community should act together to share information rapidly given the limited amount of information we have on these critically ill children. johns hopkins coronavirus covid-19 resource center characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak coronavirus disease 2019 (covid-19) in italy korean society of infectious diseases; korean society of pediatric infectious diseases report on the epidemiological features of coronavirus disease 2019 (covid-19) outbreak in the republic of korea from sars-cov-2 infection in children detection of covid-19 in children in early characteristics of pediatric sars-cov-2 infection and potential evidence of persistent fecal viral shedding epidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in china clinical and epidemiological characteristics of 34 children with 2019 novel coronavirus infection in shenzhen coronavirus infections in children including covid-19 novel coronavirus infection in hospitalized infants under 1 year of age in china sars-cov-2 infection in children: transmission dynamics and clinical characteristics dysregulation of immune response in patients with covid-19 in wuhan, china immune responses in covid-19 and potential vaccines: lessons learned from sars and mers epidemic clinical course and risk factors for mortality for adult inpatients with covid-19 in wuhan, china: a retrospective cohort study the deadly coronaviruses: the 2003 sars pandemic and the 2020 novel coronavirus epidemic in china clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in angiotensin-converting enzyme 2 inhibits lung injury induced by respiratory syncytial virus are children less susceptible to covid-19? age-and gender-related difference of ace2 expression in rat lung clinical and ct features in pediatric patients with covid-19 infection: different points from adults human coronavirus in hospitalized children with respiratory tract infections: a 9-year populationbased study from norway staff safety during emergency airway management for covid-19 in hong kong the intensive care society, royal college of anaesthetists, uk: information, guidance and resources supporting the understanding and management of coronavirus (covid-19) the alfred icu guideline for intubation of critically ill patients paediatric intensive care society uk: pics guidance on management of critically ill children with covid-19 infection task force for pediatric emergency mass critical care: pediatric emergency mass critical care: focus on family-centered care paediatric intensive care society uk: pics and ics joint position statement on planning for the pandemic. available at introduction and executive summary: care of the critically ill and injured during pandemics and disasters: chest consensus statement the authors have disclosed that they do not have any potential conflicts of interest.for information regarding this article, e-mail: srinivas.murthy@cw.bc.ca key: cord-336963-evjmz49u authors: chen, dong; hu, chenchan; su, feifei; song, qifa; wang, zhen title: exposure to sars-cov-2 in a high transmission setting increases the risk of severe covid-19 compared to exposure to a low transmission setting? date: 2020-06-05 journal: j travel med doi: 10.1093/jtm/taaa094 sha: doc_id: 336963 cord_uid: evjmz49u nan reported in other provinces of china (who situation report, 27 february 2020). the striking difference in mortality between wuhan and other cities in china was partly attributed to insufficient medical services at the time when the health care system was overwhelmed in wuhan. 1 however, the higher mortality persisted in wuhan despite the fact that after the initial epidemic peak same clinical management guidelines were applied throughout china, and case fatality rates remained higher even when more medical personnel was deployed to wuhan. similarly, in the epicentre in northern italy, a very high case fatality rate was reported during the height of the outbreak. 6 the high mortality in northern italy was also initially attributed to the fact that hospitals were overwhelmed by the onstorm of cases. but maybe there is another factor inherent to high transmission settings that lead to a higher case fatality rate as observed in our study? in our study, we were able to exclude any differences in healthcare systems and clinical management as a confounding factor for severity. in conclusion, our study highlights that sars-cov-2 infection in a hotspot or epicentre with high transmission intensity may adversely impact mortality rates compared to infection in a low transmission area. we hypothesize that repeat or constant exposure to the widely circulating virus could explain this phenomenon. however, our study was only an observational study, and can only provide indirect ecological evidence. more studies in other settings and countries are necessary to elucidate to what extent repeat exposure may increase the risk of more severe covid-19 disease outcomes and relevant immunological mechanisms. u n c o r r e c t e d m a n u s c r i p t university and sixth people's hospital of wenzhou. oral consent was acquired from all patients. *these authors contributed equally to the article. all authors read and approved the final manuscript. all authors declare no conflict of interests. table 1 . comparison and multivariate analysis of epidemiological and clinical features between the group exposed to a high-epidemic area and the group exposed to a low-endemic area potential association between covid-19 mortality and health-care resource availability correlation between travellers departing from wuhan before the spring festival and subsequent spread of covid-19 to all provinces in china clinical features of patients infected with 2019 novel coronavirus in wuhan, china this study was supported by key scientific and technological innovation projects of wenzhou (zy202004) and natural science foundation of ningbo (2017a610273). key: cord-333226-o23da4x2 authors: wang, yuke; teunis, peter title: strongly heterogeneous transmission of covid-19 in mainland china: local and regional variation date: 2020-06-19 journal: front med (lausanne) doi: 10.3389/fmed.2020.00329 sha: doc_id: 333226 cord_uid: o23da4x2 background: the outbreak of novel coronavirus disease 2019 (covid-19) started in the city of wuhan, china, with a period of rapid initial spread. transmission on a regional and then national scale was promoted by intense travel during the holiday period of the chinese new year. we studied the variation in transmission of covid-19, locally in wuhan, as well as on a larger spatial scale, among different cities and even among provinces in mainland china. methods: in addition to reported numbers of new cases, we have been able to assemble detailed contact data for some of the initial clusters of covid-19. this enabled estimation of the serial interval for clinical cases, as well as reproduction numbers for small and large regions. findings: we estimated the average serial interval was 4.8 days. for early transmission in wuhan, any infectious case produced as many as four new cases, transmission outside wuhan was less intense, with reproduction numbers below two. during the rapid growth phase of the outbreak the region of wuhan city acted as a hot spot, generating new cases upon contact, while locally, in other provinces, transmission was low. interpretation: covid-19 is capable of spreading very rapidly. the sizes of outbreak in provinces of mainland china mainly depended on the numbers of cases imported from wuhan as the local reproduction numbers were low. the covid-19 epidemic should be controllable with appropriate interventions (suspension of public transportation, cancellation of mass gatherings, implementation of surveillance and testing, and promotion of personal hygiene and face mask use). in december 2019, several cases of severe pneumonia appeared in wuhan, the capital city of hubei province in china. the outbreak was caused by a novel coronavirus: severe acute respiratory syndrome coronavirus 2, or sars-cov-2 (1) and the disease (covid-19) started to spread rapidly (2) in wuhan. as of 28 may 2020, globally 5,593,631 cases have been confirmed with 353,334 deaths in 227 countries (3) . in the early outbreak in china, by 19 february 2020, 83.2% (62,031/74,576) of the confirmed cases were located in hubei province and 60.4% (45,027/74,576) were located in the city of wuhan, where the outbreak originated (4, 5) . the "pneumonia of unknown etiology" appeared in wuhan from 8 december 2019. many early cases have been reported to be linked to the huanan (southern china) seafood wholesale market (hereafter referred to as "the market") (6) . by 2 january 2020, 41 initial cases were confirmed as covid-19 (7) . as the novel coronavirus epidemic was spreading within wuhan, the chinese new year/spring festival (25 january 2020), the most important holiday in china, was approaching. in 2019, 2.99 billion of people traveled by bus, train, and plane during 40 days around chinese new year (8) . wuhan, with a population size of 11 million, is one of the four most important railway hubs in china. with billions of people traveling and lots of family and friends gathering, there was greatly increased risk of rapidly spreading this newly emerging infectious disease, nationally, and even globally. on 19 january 2020, the first confirmed covid-19 case outside of wuhan appeared in shenzhen, guangdong (9) . as of 23 january 2020, confirmed covid-19 cases have been reported in 29 provinces of mainland china and nine countries and areas outside of mainland china (10, 11) . on the same day, the central government of the people's republic of china initiated a lockdown in wuhan and two nearby prefectural cities, huanggang and ezhou, in hubei province, to prevent spreading of the covid-19 outbreak (12, 13) . however, as many cases had "escaped" from wuhan before the lockdown, covid-19 has spread to most provinces. the numbers of cases imported from wuhan for different provinces heavily depend on their connectivities with wuhan. at the same time, municipalities responded differently, regarding timeliness and adequacy of measures (including declarations of public health emergency, holiday extension, event cancelation, and surveillance using infrared thermometers in public spaces. in this study, we used a method for analysing transmission patterns based on the serial interval between clinical cases of covid-19 (14) . based on dates of symptom onset and contact various data with different levels of detail were collected from different sources. first, detailed data for 112 confirmed cases between 21 january 2020 and 12 february 2020 in tianjin province was obtained from the website of tianjin health commission, the website of tianjin centers for disease control and prevention, and the official weibo (china's twitter equivalent) of a local newspaper (15) (16) (17) . collected information included demographic information, travel history to wuhan/hubei, date of symptom onset, and any contact information that could be found. see table 1 for a summary. second, to evaluate the role of "the market" in wuhan and estimate the numbers of cases caused by contact with this source (its reproduction number) in early transmission, data for the first confirmed 425 covid-19 cases with date of symptom onset and exposure information to "the market" was extracted from a recently published report (6) . and in third place, we collected epidemic curve data: numbers of cases (total of 6941) by province and date of confirmation from the wikipedia page of covid-19 cases in mainland china (18) and combined these data with detailed information, wherever available, about travel history and location (city and district) extracted from announcements of the health commissions of the provinces. these data were used to compare transmission of covid-19 in different provinces and cities. since the travel figure 1 | the serial interval between linked cases. (a) when a subject is infected, there is a latency until they start shedding virus and become infectious to others, then they (may) become symptomatic and can be detected clinically. when subject j infects subject i the time between symptom onset in case j and symptom onset in their descendant case i is the serial interval for onset of clinical symptoms. (b) distribution of the serial interval for onset of clinical symptoms, estimated from covid-19 clusters with partially known links ( figure 2 ). shown are the prior and the posterior mode distribution (the most probable), with 90% predictive interval. history to wuhan is currently not available for all cases outside of wuhan, the probability that any confirmed cases were linked with wuhan was estimated using the 228 confirmed cases with known travel history between 20 january 2020 to 3 february 2020 in beijing. adopting terminology of teunis et al. (14) a transmission probability matrix v can be defined where element v i,j is the probability that subject i was infected by another subject j; v i is a vector of transmission probabilities linking case i to any other case. the total number of observed subjects is n. all observed cases could appear twice: as a descendant (infected subject) i and an ancestor (infecting subject) j. since any case can only have one ancestor the corresponding network must be sparse. elements of v can be estimated by utilizing a distance kernel κ i,j (x i,j |i ← j), that defines a pairwise likelihood that subject i was infected by subject j. the distribution of the serial interval ( figure 1a) : the distance in time between pairs of cases defines a practical distance kernel, translating the time intervals between symptom onsets in any two cases into a likelihood that these cases were linked as a transmission pair (19) . as outlined in teunis et al. (14) , the elements of the transmission probability matrix v may be estimated in a markov chain monte carlo procedure. the elements of the transmission matrix are subject to constraints. diagonal elements must be zero (subjects cannot infect themselves) and rows must add to 1 (unless the parent of the corresponding subject was not observed). additional constraints may be imposed, for instance by preventing links between subjects known to have not been in contact. a mask matrix m (n × n, like v) may be defined, with elements 1 where links are admissible, and 0 where they are not. this mask m may be applied to the matrix of kernels κ i,j () by elementwise multiplication. elements of v representing pairs of subjects with inadmissible links are thus excluded: the corresponding v i,j are set to zero, and they are not updated in mcmc estimation. the mask m can be used to define contacts: whenever subject i is known to have been in contact with another subject j element m i,j = 1. and perhaps more importantly: when subject i is known to not have had contact with subject k then m i,k = 0. when a sufficient number of infectious contacts is known, the serial interval distribution may be estimated from outbreak data. first, the elements of the transmission probability matrix v are estimated, using (plausible) starting values for the parameters of the serial interval distribution. then, v is fixed and the serial interval distribution parameters are estimated. then the serial interval distribution is fixed and v is estimated. this alternating procedure can be repeated until no more improvement (in posterior probability) is found (14) . in the present analyses a special node (0) was defined, that has a uniform kernel κ i,0 : any subject can be infected by node 0 at any time, within a given time range. outside that time range κ i,0 = 0. such a node could represent environmental transmission, i.e., from "the market" to anyone in contact with that environment, or contact with a pool of infectious subjects, i.e., from any infectious subjects within wuhan/hubei to subjects outside of wuhan/hubei. as the outbreak progressed, travel to wuhan became increasingly less likely, especially after the lockdown of the city of wuhan on 23 january 2020. however, contacts did not cease abruptly: travel records from the confirmed cases in beijing showed a gradually decreasing probability of contact with wuhan. therefore the probability of linking any confirmed cases outside hubei province to wuhan was modeled as a logistic function of the date of confirmation where t is the number of days after 20 january 2020. the parameters were estimated using the travel history records from the 228 confirmed cases in beijing ( figure a1 ). the fitted logistic relation was then used to impute contacts with wuhan sources for all cases outside hubei province with unknown travel history. once infection has been imported from wuhan, further transmission depends on local contacts: since these comprised relatively few cases it is unlikely that all local cases were equally connected. to simulate inhomogeneous transmission local contacts were imputed by distributing cases within a province or city into clusters. cases within a cluster were assumed fully connected while cases in different clusters were not connected, thus allowing only transmission within a cluster and not between clusters. cluster size was assumed random, with average size five people, and a high probability (88.8%) of small clusters (average 1-5 people) and a low probability (11.2%) of medium to large clusters (average 10-25 people). the transmission probability matrix may be used to estimate reproduction numbers by calculating the row sums that represent expected numbers of cases infected by infectious case j (its outdegree), or its reproduction number. reproduction numbers thus are calculated for individual subjects. therefore, they can be grouped in any way useful: by time, to illustrate the progression of transmission during the outbreak; by location, to illustrate spatial variation in transmission; or by other characteristics, like age or gender. in order to translate the transmission probability matrix into a transmission network a multinomial sample of size 1 and probability vector row v i reduces the vector v i to a binary vector with exactly one element 1 and the rest zero. this reduced matrix may be interpreted as an adjacency matrix, equivalent to a directed graph representing a transmission tree of the outbreak (14). for 112 confirmed cases in tianjin between 21 january 2020 and 12 february 2020, the transmission network could be estimated based on the dates of symptom onset, augmented by contact information between cases. table 1 shows some summary statistics of demographic and contact information for those cases in tianjin. as contacts between many of the cases could be identified, so that many elements of the transmission probability matrix were known, joint estimation of the remaining unknown contact probabilities and the serial interval distribution was feasible. with a prior for the serial interval distribution set as gamma(4,2), 1,000 updates were performed, alternating between probability transmission matrix and serial interval distribution parameters, with 100 iterations for each update and the best fit parameters were chosen as those with the highest posterior probability (14) . figure 2 shows an estimated (posterior mode) transmission network. using the available contact information, there appeared to be considerable variation in the sizes of clusters of cases. there were two major clusters: one among crew members of tianjin railway and another one among sales representatives and customers in baodi department store. figure 1b shows the posterior mode serial interval distribution as a gamma distribution (shape parameter 3.16, scale parameter 1.52), with a mean of 4.8 days. this best fit serial interval distribution has been used in all following analyses. figure 3 shows estimated reproduction numbers by day for the initial 425 confirmed cases in wuhan. "the market" node as an infectious source was linked to as many as 13.6 cases, on average. for those 425 initial cases, the mean reproduction number was 2.5 (until 31 december 2019). the estimated numbers of imported cases from wuhan varied among provinces in mainland china. provinces bordering hubei province include henan, hunan, anhui, and jiangxi (213, 175, 163, 146), and provinces with close economic ties with hubei province include zhejiang and guangdong (271 and 228, respectively). these provinces all had high estimated numbers of cases imported from wuhan by 3 february 2020 ( figure 4b) . outside hubei there was less transmission than within hubei province, with average reproduction numbers between 1 and 2 during the first 5 days after the first confirmed local case. the provinces guizhou, hebei, shandong, and guangdong had higher average reproduction numbers: 2.25, 2.14, 1.95, and 1.91, respectively ( figure 4a) . though the average reproduction numbers were not very high, there existed large variations in reproduction numbers of individual cases, which indicated some individual cases could have spread the disease to many people (figure 2) . within a province, there was also spatial variation in the amount of transmission. figure 5 shows the disease transmission in 21 cities within guangdong province. shenzhen and guangdong, the two largest and most affluent urban centers in guangdong, had the highest estimated numbers of cases imported from wuhan (127 and 124, respectively) by 3 february 2020. guangzhou, zhaoqing, shaoguan, shenzhen, and zhuhai had reproduction numbers slightly larger than 1 (1.35, 1.31, 1.30, 1.10, and 1.05, respectively) for first 5 days after the first confirmation of a local case in the city. figures a2, a3 show boxplots of estimated reproduction numbers for provinces in china and cities in guandong province, respectively. figure a4 shows reproduction number estimates by gender and age for beijing and tianjin. spreading patterns of covid-19 at different spatial scales, from local (railway department and department store) to regional (cities within guangdong province) to nationwide (provinces within china), appear similar: new cases arise from contacts with a reservoir, spreading to remote locations through travel from the origin outbreak region. there likely is some secondary spread locally, from cases infected from the reservoir, but local reproduction numbers are low, often insufficient to support sustained transmission. knowledge of the serial interval, for symptomatic cases in the outbreak, is essential for analysis of the transmission probabilities (14) . previous studies have estimated the distribution of serial intervals from a set of confirmed transmission pairs, where both the ancestor (who caused infection) and the descendant (who frontiers in medicine | www.frontiersin.org became infected) were known (19, 20) . as such information is mostly lacking (6) (and may be hard to obtain) in this covid-19 outbreak, we have estimated the serial interval distribution from a curated network, using whatever contact information was available. existing knowledge of contacts (and timing of those contacts) between cases was used to construct a matrix of prior probabilities, to restrict the transmission network to only those links that are possible. when all transmission links are known, the serial interval distribution can be easily estimated. however, at early stages of an outbreak, information on transmission links is usually incomplete. when a sufficiently large proportion of the transmission links is known, it is possible to estimate both the serial interval distribution, and the transmission probability matrix (14) . starting from a plausible serial interval distribution, the transmission probability matrix v is updated until convergence; then v is frozen and the serial interval parameters are updated, again until obtaining a new optimum; then the serial interval distribution is frozen and the transmission probability matrix is updated again, and so on, until no further improvement can be found. the estimated serial interval distribution, gamma(3.16, 1.52), has a mean of 4.8 days and good spread out (i.e., large scale parameter) to long serial interval. the variation of serial interval could caused by highly varied incubation period (21) . such a short serial interval, compared to sars (mean: 8.4 days) (22) and mers (mean: 6.8 days) (23), gives covid-19 ability to spread more rapidly. the rapid spread of covid-19 in south korea (from 31 cases on 18 february to 2,022 cases on 28 february) and italy (from 20 cases on 21 february to 650 cases on 28 february), shows how missed infectious subjects may cause rapid transmission within a very short period, due to the combination of a short serial interval and an occasionally high reproduction number (24) . as the incubation period seems to be highly variable, it may be possible that appearance of symptoms in any case precedes symptom onset in its ancestor. when that happens, the serial interval for symptom onset is negative. details of the negative serial interval can be found in the supplementary material. to check whether negative serial intervals would adversely affect analysis we used an alternative distribution, where the serial intervals were shifted leftward by a small amount. a shift of 1 or 2 days had no destructive effect on estimation of v, and the resulting estimates of the effective reproduction numbers did not change substantially. early transmission of a newly emerging infectious disease in a population lacking immunity could reveal the basic reproduction number as long as there is no intervention. currently, the source of covid-19 is still unclear but many of the early cases were reported to have had contact with the huanan seafood wholesale market. a recent announcement released by the chinese academy of sciences indicated that the source may not have come from this seafood market (25) . any patient zero would have occurred before the initial 425 confirmed cases, but lacking any specific information about early spread of covid-19, it can be assumed that a reservoir of infectious subjects could function as a super-spreading node causing new infections upon contact at any time within the outbreak. assuming such a source for the initial cluster in wuhan ("the market") led to an estimated basic reproduction number 13.6. it must be noted that this environmental "super-spreading node" is hypothetical, and represents the production of new cases by the joint presence of infectious subjects connected to the initial source. there was strong heterogeneity in disease transmission in different provinces of mainland china. the present analysis produces two relevant characteristics: the numbers of cases imported from wuhan, and the average reproduction number for the first 5 days after any confirmed imported case in each province. when there are many imported cases from wuhan, these constitute a large base number of cases to start local spreading of the disease. provinces geographically close to hubei province are expected to experience mass migration from wuhan, especially near the holiday season. provinces with big tier-1 cities like zhejiang and guangdong both have very high estimated numbers of cases imported from wuhan due to their economic connection with hubei. when early transmission has a high reproduction number, local growth rate in a province will be high. provinces geographically distant from hubei, like hebei, guizhou, and shandong, appear to have relatively high reproduction numbers during early local transmission. in provinces distant from wuhan, the central hub of the outbreak, inhabitants and local governments may have been less cautious (with few public and personal prevention measures) considering high costs of interventions and perceived low risk. since guangdong province has both large numbers of imported cases and high reproduction numbers for early transmission, we further examined the transmission inside of guangdong by city. shenzhen and guangzhou, two of the biggest cities in china, had many imported cases. this is expected considering intense economic connectivity: transportation links, for goods and people including enormous numbers of migrant workers working in those two cities. the numbers of cases imported from wuhan into other cities in guangdong province was smaller. this pattern matches the flow of people in public transport (by train and airplane) converging onto the main transportation hubs (shenzen and guangzhou) and diverging from there toward other destinations in guangdong province. for early transmission following import from wuhan, the reproduction number in most cities in guangdong had an average reproduction number around 1, during the first 5 days. with appropriate and sustained disease prevention and control measures (e.g., suspension of public transportation, cancellation of mass gatherings, implementation of surveillance and testing, and promotion of personal hygiene and face mask use), the outbreak is unlikely to spread out in those cities. among reported cases, gender differences seemed unimportant; most serious illnesses occurred among the elderly, in particular those with health problems prior to infection, while only a small proportion of cases were young of age (21) . in the present study, when reproduction number estimates were grouped by gender, no differences were found. similarly, estimates of transmission from different age groups showed that small children and elderly people were equally likely to transmit infection as any other age group (figure a4) . we also examined the effect of the size of clusters imputed on the results and the difference was trivial between average cluster size three and five. an important issue in analyzing transmission of covid-19 is the amount of silent transmission. as mentioned earlier, some infectious subjects may transmit their infection before they become symptomatic. as long as their descendant cases also go on to develop symptoms their transmission link may still be established. however, when infected subjects who remain completely asymptomatic could be infectious to susceptible contacts, the appearance of such contacts, when symptomatic, could not be linked to their immediate ancestors. given the fact that symptoms seem to be milder in those who are young, such unobservable transmission cannot be excluded (26) . silent transmission has been seen in other infectious diseases (27) where, notably, asymptomatically infected subjects appeared to cause fewer transmission. as asymptomatic infections would lead to an antibody response, serology could be a valuable tool to assess the importance of asymptomatic transmission. the datasets analyzed for this study can be found at github (https://github.com/ywan446/covid-19-transmission). severe acute respiratory syndrome-related coronavirus: the species and its viruses a statement of the coronavirus study group national health commission of the people's republic of china (2020) available online at early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features of patients infected with 2019 novel coronavirus in wuhan available online at available online at national health commission of the people's republic of china (2020) available online at available online at infectious disease transmission as a forensic problem: who infected whom? available online at available online at available online at available online at different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures enhanced hygiene measures and norovirus transmission during an outbreak clinical characteristics of 2019 novel coronavirus infection in china transmission dynamics and control of severe acute respiratory syndrome unraveling the drivers of mers-cov transmission how generation intervals shape the relationship between growth rates and reproductive numbers decoding the evolution and transmissions of the novel pneumonia coronavirus (sars-cov-2) using whole genomic data molecular and serological investigation of 2019-ncov infected patients: implication of multiple shedding routes nosocomial transmission of norovirus is mainly caused by symptomatic cases all authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication. we were grateful to the alumni of cohort b5 '08 at shijiazhuang no. 2 middle school, including di an, jiayi liu, xun li, menghan hou, yunpeng zhang, fan huang, and hongxu li for gathering and sharing information form various sources about covid-19. the supplementary material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmed. 2020.00329/full#supplementary-material conflict of interest: the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright © 2020 wang and teunis. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord-305054-4d84b2g6 authors: liu, yuan; yan, changhui title: the selection of reference genome and the search for the origin of sars-cov-2 date: 2020-08-11 journal: biorxiv doi: 10.1101/2020.08.10.245290 sha: doc_id: 305054 cord_uid: 4d84b2g6 the pandemic caused by sars-cov-2 has a great impact on the whole world. in a theory of the origin of sars-cov-2, pangolins were considered a potential intermediate host. to assemble the coronavirus found in pangolins, sars-cov-2 were used a reference genome in most of studies, assuming that pangolins cov and sars-cov-2 are the closest neighbors in the evolution. however, this assumption may not be true. we investigated how the selection of reference genome affect the resulting cov genome assembly. we explored various representative cov as reference genome, and found significant differences in the resulting assemblies. the assembly obtained using ratg13 as reference showed better statistics in total length and n50 than the assembly guided by sars-cov-2, indicating that ratg13 maybe a better reference for assembling cov in pangolin or other potential intermediate hosts. recently, the outbreak of sars-cov-2 (covid-19) has caused an ongoing global pandemic. as of july 21, 2020, the pandemic resulting in a total of 14,562,550 clinical cases and 607,781 deaths all over the world (www.who.int). with an effort of metagenomic rna deep sequencing, the genome of a sars-cov-2 isolate, wuhan-hu-1, was published in [11] . the genome showed high nucleotide similarity (89.1%) to a group of sars-like coronavirus that were identified in bats in china, which indicated the possibility of animal origin. to identify potential direct or intermediate host of sars-cov-2, coronavirus in several animals were studied and compared with sars-cov-2. bat and pangolin were the two mostly investigated species. a cov in bat, ratg13, showed 96% full-genome similarity with sars-cov-2 [14] . other virus isolates from bat, zxc21 and zc45 also shared 85% of similarity to sars-cov-2. these results led to the hypothesis that the progenitor of sars-cov-2 originated in bats and it spilled over to humans using another animal as intermediate host. many researchers believed that pangolins are a potential intermediate host and they attempted to characterize coronavirus in pangolin. liu, chen, and chen [8] constructed coronavirus contigs using de novo assembly method from organ samples of dead malayan pangolins rescued at the guangdong wildlife rescue center. of the 11 collected pangolins, coronavirus was detected in two. zhang, wu, and zhang [13] re-analyzed the rna-seq reads from two pangolins carrying coronavirus using reference-guided de novo assembly method, with wuhan-hu-1 as the reference genome. the resulting draft genome shared 91.02 and 90.55% whole genome similarity with wuhan-hu-1 and ratg13, respectively. xiao et al. [12] obtained 21 samples from pangolins rescued by guangdong customs and conducted reference-guided genome assembly, with wuhan-hu-1 as the reference genome. the derived viral genome showed 80 and 98% whole genome sequence identity to sars-cov-2 and ratg13, respectively. lam et al. [3] collected 43 samples from 18 pangolins from guangxi medical university, china, and six samples contained coronavirus sequences. the viral genomes of six samples were de novo assembled. they also performed rna sequencing in five archived pangolins samples from guangdong, and assembled the genomes using wiv04, another sars-cov-2 genome from human, as reference genome. the resultant draft genomes have 85.5% to 92.4% identity to the sars-cov-2 genome. they suggested two sub-lineages of coronavirus existed in pangolins. in terms of all coding sites, coronavirus identified in pangolins from guangdong is more closely related to wiv04 than bat-cov ratg13, whereas coronavirus genome of pangolins in guangxi showed lower genome similarity to wiv04 than bat-cov ratg13. liu et al. [8] took samples from three coronavirus positive pangolins rescued in guangdong and performed deep sequencing. using de novo assembly method, they obtained viral genome that showed 90.32% and 90.24% of whole genome identify to wuhan-hu-1and bat-cov ratg13, respectively. all of the pangolins involved in published coronavirus analysis were from either the guangdong collection or the guangxi collection. pangolins from the guangdong collection were investigated in most studies [3, 8, 9, 12] . the resulting viral genomes were derived from de novo assembly with or without a guided reference and further curated using blast annotation or pcr amplicon sequencing. all studies have showed that cov in pangolin was highly related to bat-cov and sars-cov-2. in all of the studies that used reference-guided de novo assemblies, a sars-cov-2 genome (wuhan-hu-1 or wiv04) was chosen as reference [3, 12, 13] . this choice was based on the assumption that sars-cov-2 was the closest neighbor of the pangolin cov in the phylogeny tree. however, this assumption may not necessary be true. therefore, choosing the sars-cov-2 genome as reference could inadvertently introduce bias in the genome assembly, leading to inaccurate or incomplete results. in this study, we assembled the pangolin cov genome using several different genomes as reference. we investigated how the reference genome impact the resulting genome and its phylogenetic relationship with others. the results from this study will provide guidance for future studies on how to accurately construct cov genomes from pangolin or other potential intermediate hosts. two rna-seq samples, lung07 and lung08, were downloaded from ncbi sra under bioproject sra: prjna573298. the two samples were originally published in [8] for viral metagenomics analysis. adaptor trimming and quality control were performed on the raw sequence reads using with the trimmonmatic program (verson 0.39) [1] . to eliminate host contamination, the remaining reads were aligned to the manis javanica genome (sra: prjna256023) using bwaaln (version 0.7.17) [6] and reads mapped to the host genome were discarded. reads unmapped to the host reference genome were used to construct genome in the subsequent de novo assembly. cleaned reads were used to assemble genome using reference-guided de novo assembly. to investigate how the results were influenced by the choice of reference genome, we explored a few representative virus genomes on the phylogeny tree (table 1) as the reference genome. these genomes were selected based on previous studies [3, 9, 11, 13] . once a reference genome was picked, the cleaned reads were aligned to the reference genome using bwa-mem [5] , and the mapped reads were assembled de novo using meghit (version 1.1.3) with meta-sensitive mode [4] . the resulting contigs were concatenated into an assembly by aligning them to the reference genome. phylogenetic distance analysis was performed using mega x (version 10.1.8) [2] .the whole genome was used in phylogenetic and distance analysis, and phylogenetic trees were constructed in the best-fit dna/amino acid substitution mode with 1000 bootstrap replications. the whole genome nucleotide identity analysis was performed in simplot 3.5.1 [10] . a total of eight viral genomes were tested as the reference genome in reference-guided de novo assembling. numbers of mapped reads ranged from 2 to 3,060, and length of the resulting draft assemblies varied from 5,969 to 22,419 bp (table 2) . two reference genomes, merscov and bat hp-betacov zhejiang2013, failed in reads assembling due to the limited number of remaining reads. less than 1,000 reads were mapped to three reference genomes, bj01, bm48_31, and longquan140, resulting in shorter assemblies. a total of 1,061 reads were mapped to zc45 and subsequently assembled into a 21,819-bp assembly with 67.8% of coverage. ratg13, which is a bat cov, had 1,287 reads mapped to it, and the resulting assembly has total length of 21,925 and n50 of 1,428. a total of 3,060 reads were mapped to wuhan-hu-1, a human sars-cov-2 strain, which was the highest number among all genomes we surveyed. the assembly guided by ratg13 and wuhan-hu-1 showed similar coverage at about eighty percent. however, the resulting assembly had shorter total length (21,819) and n50 (1, 195 ) than those of the assembly that used ratg13 as reference. to understand this seemly contradiction, we investigated the reads coverage and depth on ratg13 and wuhan-hu-1. the results (figure 1) show that there were an excessive number of reads mapped to distal regions of wuhan-hu-1, which could indicate artifacts or contaminations during the sequencing. after removing these tail regions (with > 200x depth), 62 more unique reads were mapped to wuhan-hu-1. figure 2 shows the overlap of between the unique reads mapped to ratg13 and wuhan-hu-1. unique reads were used to construct venn diagrams. all reads mapped to italy strain were also mapped to wuahn-hu-1 genome (figure 2 ). the additional 1516 unique reads were mapped to wuhan-hu-1. most reads were mapped to both ratg13 and italy strain, but a total of 45 reads were aligned to either one. bat-cov, zc45 and ratg13, shared 999 reads in alignment, and ratg13 genome guided over two hundred more reads into assembly. the two assemblies that used ratg13 and wuhan-hu-1 as reference genomes respectively, were aligned with the eight reference viral genomes in table 1 in a multiple alignment. the multiple alignment result was used for similarity analysis and phylogenetic analysis. in terms of the whole genome nucleotide, the ratg13-guided assembly showed 85.8% and 85.2% identity to ratg13 and wuhan-hu-1, respectively, and the wuhan-hu-1-guided assembly showed 88.6 and 88.8% identity to ratg13 and wuhan-hu-1 respectively. the difference between wuhan-hu-1-guided assembly and ratg13-guided assembly was not always consistent with difference between ratg13 and wuhan-hu-1 (table s1 ). the differences between ratg13-guided and wuhan-hu-1-guided assemblies in the regions of 18,431-18,601 bp were probably due to references between the reference genomes (table s1 ). however, the differences in some regions including 4,761-5,021 bp and 10,121-11,321 bp, were not due to differences in the reference genomes. we further investigated phylogenetic relationship between the two assemblies and eight reference viral genomes using mega x with 1000 bootstrap tests. the two assemblies positioned between ratg13 and zc45 with strong statistical evidence (figure 3) . the sars-cov-2 genome, wuhan-hu-1, and bat-cov, ratg13, clustered closely together. the two assemblies from this study consistently positioned between this cluster and other covs ( figure 4 ). among other covs, zc45 is the closest neighbor to the assemblies. currently, very few samples of coronavirus-positive pangolins have been sequenced. pangolins-cov obtained from the guangdong collection and the guangxi collection represent two lineages of coronavirus [3] . after outbreak of sars-cov, thousands of bat samples were collected and sequenced to identify coronaviruses that bat may carry. we can expect that in near future more pangolin samples will be collected and studied for better understanding of coronavirus in pangolin. in a reference-guided assembling, the resulting assembly may show bias towards the reference genome [7] . successful decoding a complete viral genome usually require deep sequencing and further manual curations to fix the gaps. inaccuracies in assembling the sequencing reads could mislead the subsequent curation step. the whole genome identity between bat-cov ratg13 and sars-cov2 wuhan-hu-1 is about 96%, which corresponds to a total difference of about 1,500 nucleotides. our results have shown that observable difference could be found in the resulting assemblies when these genomes were used as reference separately. particular, when ratg13 was used as reference, the resulting assembly had a longer total length and higher n50 value than when wuhan-hu-1 was used. this points to the possibility that pangolin-cov is more closely related to ratg13 than to wuhan-hu-1. therefore, in order to decode the coronavirus sequence accurately, ratg13, and possibly other sars-cov-2 isolates, should also be considered as reference in future studies of coronavirus in pangolin or other potential intermediate hosts. in addition to using one reference genome to guide the assembling, we also attempted to assemble all reads that mapped to either ratg13 or wuhan-hu-1 genomes. the resulting twogenomes-guided assembly has a total length of 22,707 bp, which is slightly longer than that of the ratg13-guided assembly. however, the n50, 1,388bp, is slightly shorter. the authors have no conflict of interest. table s1 . the whole genome nucleotide similarity from ratg13, wuhan-hu-1, and resulting assemblies. trimmomatic: a flexible trimmer for illumina sequence data mega x: molecular evolutionary genetics analysis across computing platforms identifying sars-cov-2-related coronaviruses in malayan pangolins megahit: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph aligning sequence reads, clone sequences and assembly contigs with bwa-mem fast and accurate short read alignment with burrows-wheeler transform reference-guided de novo assembly approach improves genome reconstruction for related species viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (manis javanica) are pangolins the intermediate host of the 2019 novel coronavirus (sars-cov-2)? full-length human immunodeficiency virus type 1 genomes from subtype c-infected seroconverters in india, with evidence of intersubtype recombination a new coronavirus associated with human respiratory disease in china isolation of sars-cov-2-related coronavirus from malayan pangolins probable pangolin origin of sars-cov-2 associated with the covid-19 outbreak a pneumonia outbreak associated with a new coronavirus of probable bat origin key: cord-284376-plwyjhl8 authors: fu, xinmiao; ying, qi; zeng, tieyong; long, tao; wang, yan title: simulating and forecasting the cumulative confirmed cases of sars-cov-2 in china by boltzmann function-based regression analyses date: 2020-05-31 journal: journal of infection doi: 10.1016/j.jinf.2020.02.019 sha: doc_id: 284376 cord_uid: plwyjhl8 • cumulative confirmed cases in china were well fitted with boltzmann function. • potential total numbers of confirmed cases in different regions were estimated. • key dates indicating minimal daily number of new confirmed cases were estimated. • cumulative confirmed cases of 2003 sars-cov were well fitted to boltzmann function. • the boltzmann function was, for the first time, applied to epidemic analysis. in this journal, zhu et al. recently reported the results of their genomic analysis of multidrug-resistant klebsiella pneumoniae isolates from individual patients before and after colistin treatment highlighting the rapid emergence and multifaceted molecular mechanisms of colistin resistance in k. pneumoniae. 1 this work highlights the therapeutic and public-health challenges of colistinresistance (cr), which is increasingly used as a large resort antibiotic, despite its unattractive toxicity profile and narrow therapeutic window. 2 oral non-absorbed colistin has been proposed as a decontamination strategy in intensive care units and for patients carrying multidrug resistant enterobacterales (mdr-e). 3 , 4 the impact of decolonization strategies in terms of emergence of cr has rarely been monitored because no reliable selective medium existed and cr was not considered a public-health problem. recently, reliable universal culture media have been developed to screen for cr. 5 here, we studied the impact of non-absorbed oral colistin on the emergence of cr in the gut microbiota of patients from the rgnosis-wp3 randomized controlled trial. 6 thirty-nine subjects colonized with mdr-e were randomized to receive oral colistin sulfate 2 miu 4 times a day + neomycin sulfate 500 mg bid for 5 days followed by a fecal microbiota transplant (fmt) from healthy donors, or no intervention. stool samples were collected on visit v0 (screening sample), v2 (after 5 days of oral decontamination and before fmt for the intervention group), v3, v4 and v5, respectively 5-10 days, 30-40 days and 150-210 days later. 6 stool samples from donors and 15 subjects from the intervention group and 15 from the control group were available for this work and plated on drigalski plates (control) and superpolymyxin r plates. 5 colony forming units (cfu) counts of all gram-negative rods were determined. isolates growing on superpolymyxin r plates were identified by maldi-tof; cr was confirmed by the culture-based rapid polymyxin np test and mic determined by the microdilution method. the limit of detection was 10 2 cfu/g of stool. cr-e. coli were sequenced using the illumina hiseq technology. to determine whether cr isolates were present before the intervention, a specific mcr-1 pcr was performed on patients stool prior to intervention (v0) and on the donor's stool. 7 electroporation of plasmids was performed to localize the gene conferring resistance to colistin and neomycin and molecular typing of the electroporants was performed using pcr based replicon typing (pbrt). ✩ université de paris, iame, inserm, umr-1137 no patient or donor included in the trial carried cr isolates on v0. among the 15 patients in the intervention group two (13.3%, [ic90 −1; 3], p = 0.24) carried cr isolates at least at one visit after the intervention ( fig. 1 ) . no cr-enterobacterales was detected in the stools of subjects from the control group. among both subjects with cr-enterobacterales, one carried 10 log cfu/g of hafnia paralvei , a species which is intrinsically resistant to colistin (mic = 8 mg/l), also resistant to neomycin (mic = 32 mg/l) on visit 4 and the other carried 1 log cfu/g and 3 log cfu/g cr-e. coli at visits 4 and 5, respectively, with a colistin mic at 8 mg/l. relative abundance of cr-e. coli increased between v4 and v5 from 0.01% to 1% of the total enterobacterales population. the cr-e. coli recovered at v4 and v5 both belonged to phylogroup c st23 group and carried the serotype o176:h9. a plasmid-borne mcr-1.1 gene encoding for cr as well as a aph(3 )-ia gene conferring resistance to neomycin were identified, both being co-located on the same inchi2 plasmid. in addition, resistance genes conferring resistance to hygromycin b ( aph(4)-ia ), sulfonamides ( sul2 ), tetracyclines ( tet(a) ) and phenicols ( flor and cata1 ), all antibiotics used in veterinary medicine, were evidenced. for both subjects, cr strains could not be retrieved in the initial stool of the subject or in the donor's stool. pcr experiments performed with specific primers to detect mcr-1 gene directly on the pre-therapeutic stool were also negative. to our knowledge, this is the first report of the in-vivo selection of cr-enterobacterales in the gut microbiota of patients after oral decontamination by colistin. the selection of cr strains (a naturally-resistant h. paralvei and a mcr-1 producing e. coli ), both resistant to colistin and neomycin, may be the result either of the enrichment process by sod of preexisting cr strains that had not been initially detected because of very low abundances, or of an exogenous acquisition, either from other individuals or through fmt. 8 indeed the transmission from fmt of mdr strains from positive donors is a potential risk. 8 despite our efforts to decrease the limit of detection of mcr producers by using a pcr technique directly on the pre-therapeutic stool sample and the donors' stools, we failed to detect the parental strain, either because cr strains were in intestinal niches, the limit of detection remained too high, or the strain was acquired exogenously. however, the mcr-1 -positive e. coli is likely of animal origin according to its genetic features and its co-resistance profile. 9 indeed, phylogroup st23 is frequently encountered among avian pathogenic e. coli (apec) and co-resistances to many antibiotics used specifically in veterinary medicine is striking. 10 furthermore, the aph(3 )-ia gene confers resistance to neomycin and paromomycin, the latter commonly used in cattle and pigs. the selection of the mcr-1 producer is an illustration of the "one health" problem of resistance: a strain likely to have been selected by veterinary antibiotics among animals ended up in a patient's gut, later enriched by the use of colistin and neomycin as decontaminant. although the small number of subjects is a clear limitation, this observation is a "proof-of-concept" of the risk of selection of cr-enterobacterales after oral colistin treatment and fmt, at a time when colistin is one of the last resort antibiotics to treat mdr-enterobacterales infections. the selection of commensal cr-e. coli is especially worrying, given the pathogenic potential of e. coli and its ability to widely colonize animals and humans. given the controversial results of oral decontamination by colistin, we believe it should only be used with precautions and with thorough monitoring of cr. we read with interest a recent paper in this journal by luzatti and colleagues, 1 who explored the significance of the presence of herpes simplex virus (hsv) dna in lower respiratory tract (lrt) specimens for the diagnosis of hsv pneumonia in immunocompromised patients. the authors underlined the difficulty in gauging the clinical relevance of such a laboratory finding in the absence of histopathological data, as hsv shedding in the lrt may occur in the absence of disease. the interpretation of real-time pcr results for diagnosis of pneumocystis jirovecii (pj) pneumonia (pjp) faces an analogous challenge, since the presence of pj dna in lrt may reflect colonization (carriage) rather than infection. 2 there is limited information on the clinical value of pj real-time pcr in diagnosing pjp in patients with hematological diseases; 3-6 this is exceedingly challenging as the sensitivity of direct examination procedures is suboptimal due to low fungal burdens. 3 here, we report on our experience on this matter. a total of 219 episodes of pneumonia occurring in 192 consecutive patients with hematological disorders in which pjp was considered in the differential etiological diagnosis were included. of these, 127 episodes developed in patients undergoing either allogeneic hematopoietic stem cell transplantation-allo-hsct-( n = 86) or autologous-hsct ( n = 19), and 92 in non-transplant patients (acute leukemia, n = 61; lymphoma, n = 16; chronic leukemia, n = 8; others, n = 2). the patients were attended at the hospital clínico universitario-hcu-( n = 100) or at the hospital universitario politécnico "la fe" -hlf-( n = 92) between june 2014 and august 2019. no patients in the cohort tested positive for hiv. this study was approved by the respective hospital ethics committee and informed consent was obtained from all patients. a single specimen per episode was available for diagnosis (bal fluids, n = 179; sputa, n = 22; ta, n = 17 and bronchial biopsy, n = 1). the realcycler pjir kit r (progenie molecular, spain) was used at hcu, and the pneumocystis jirovecii real time pcr detection (certest biotech; zaragoza, spain) was employed at hlf (see footnote in table 1 ). both assays target the large sub-unit of ribosomal (mtlsu) rna gene. preliminary experiments using 5 bal specimens indicated that both assays yield comparable pcr cycle thresholds (c t s) (median, 28.2, range, 26.4-32.3 vs. median 27.5; range, 26.3-33.1, respectively; p = 0.89). all specimens tested negative by direct examination for pj, whereas 27 were positive by real-time pcr (bal, n = 18; sputa, n = 7, and ta, n = 2); following stringent clinical, microbiological and imaging criteria ( table 1 ) , pjp was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. no histopathological confirmation of pjp was available for any patient. pcr c t values inversely correlate with fungal burden in the sample. 6 which is higher in patients with pjp than in colonized individuals. 2 here, overall, pj pcr c t s in specimens from patients with pjp tended to be lower than in pj carriers ( p = 0.39); when only bal fluid specimens were considered, the difference reached statistical significance (median, 29.0; range, 26.4-34.7 vs. median 34.6; range, 30.0-41.0; p = 0.04). this finding is likely related to use of more standardized procedures for bal fluid sampling. receiver operating characteristic (roc) curve analysis showed that a threshold c t value of 30.0 in bal specimens displayed a sensitivity of 85.7% (95% ci, 45.0-100%) and a specificity of 80% (95% ci, 40.8-100%) for pjp diagnosis. a number of studies have established different c t s cut-offs for that purpose, [6] [7] [8] [9] . in our view, however, the variability in the performance of different pcr assays and sampling conditions, heterogeneity of patient populations, and in particular the lack of a pj international standard material for pcr result normalization precludes defining a consensus universal threshold nowadays. the absence of anti-pj prophylaxis, treatment with corticosteroids and serum ldh levels ≥400 u/l have been shown to be associated with pjp. 3 here, patients not undergoing anti-pj prophylaxis were more likely to display a clinically significant pj pcr result ( table 1 ). in turn, roc curve analysis indicated that a cut-off ldh value ≥400 u/l had a sensitivity of 81.8% (ci 95%, 59.0-100%) and specificity of 67% (95% ci, 34.0-99.3%) for pjp diagnosis. in univariate regression logistic models, serum ldh values ≥400 u/l were associated with a clinically significant positive pcr pj result (or, 9.0; 95% ci, 1.2-63.8; p = 0.02). in contrast, corticosteroid use within the month before sampling was not different between the probability of pneumocystis jirovecii (pj) pneumonia (pjp) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented pj presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-pjp treatment; (v) absence of alternative diagnosis. the efficacy of therapy was assessed on a daily basis. pjp was ruled out if real-time pcr for pj tested negative, or if clinical recovery occurred in the absence of pj-targeted antimicrobial therapy. pj colonization (carriage) was the most likely possibility when patients did not meet the above criteria and an alternate diagnosis was made. b frequencies were compared using the χ 2 test (fisher exact test) for categorical variables. two-sided exact p values were reported and p values ≤ 0.05 were considered statistically significant. the data were analyzed with the spss (version 20.0) statistical package. c respiratory tract specimens were obtained following conventional procedures. specimens were examined for presence of ascus or trophic forms of pj by microscopy following blue toluidine, calcofluor white or grocott's methenamine silver staining. cytospin preparations were prepared from bal specimens for direct examination. sputa and ta samples were mixed v/v with sputasol (oxoid, uk) and vortexed for 5 min. all samples were centrifuged at 30 0 0 g for 10 min, and the pellets were resuspended 1/10 in 0.9% nacl for further processing. for real-time pcr, dna was extracted from 200 μl of specimens using the qiaamp dna blood mini kit (qiagen, hilden, germany) on either qia symphony or ez-1 platforms (qiagen), following the manufacturer's instructions. at hcu, a commercially-available real-time pcr assay previously evaluated by others, the realcycler pjir kit r (progenie molecular, spain), which targets the mitochondrial large sub-unit of ribosomal (mtlsu) rna gene, was used according to the manufacturer's instructions ( http://www.progenie-molecular.com/pjir-u-in.pdf ). at hlf, the commercially-available pneumocystis jirovecii real time pcr detection. (certest biotech; zaragoza, spain), which also targets the large sub-unit of ribosomal (mtlsu) rna gene, was employed following the manufacturer instructions ( https://www.certest. es/wpontent/uploads/2019/02/viasure _ real _ time _ pcr _ pneumocystis _ jirovecii _ sp1.pdf ). at both centers pcr were performed in the applied biosystems 7500 fast real-time pcr platform (applied biosystems, ca, usa). pcr results were reported as positive or negative. for positive samples, threshold cycle (c t ) values were also recorded. no standard curve was generated with a positive control for quantitative estimations. d antimicrobial prophylaxis for pjp was performed with trimethoprim-sulfamethoxazole (tmp/smx), one double-strength tablet (160 mg tmp/800 mg smx) given 2 (in allogeneic hsct patients) or 3 times a week with oral folic acid (15, 16) . patients with suspicion of pjp according to the attending physician were treated with tmp/smx 15-20 mg/kg (tmp) 75-100 mg/kg (smx) per day for 2-3 weeks. e in all these cases, death was attributable to pjp. patients with clinically significant pj detection and pj carriers ( table 1 ) . detection or recovery of other microbial agents (one or more) was documented in 17 of the 27 specimens testing positive by pj pcr ( table 2 ). in line with a previous report, 9 this microbiological finding was significantly less frequent ( p = 0.001) in specimens from patients with pjp than in colonized patients; in fact, microbial co-detection was inversely associated with pjp in univariate logistic regression models (or, 0.024; 95% ci, 0.002-0.26; p = 0.002). strengths of the current study are the following: (i) clinical categorization of pjp was based upon stringent criteria defined by a multidisciplinary team; (ii) only hematological patients were included; (iii) a comprehensive routine investigation of microbial causes of pneumonia other than pj was conducted; (iv) the experience of two centers was collected. in addition to its retrospective nature, our study also has some limitations: (i) we cannot completely rule out that some patients categorized as being pj carriers did in fact have pjp, as most of these patients received full courses of tmp/smx in combination with antimicrobials targeting other microbial agents. the lack of standardized criteria for pjp diagnosis makes clinical misclassification of patients a potential drawback in studies such as ours, particularly when no positive microscopy or histopathology findings are available; (ii) although we evaluated bal, bronchoalveolar lavage; pjp, pneumocysis jirovecii pneumonia; ta, tracheal aspirate. a as per our routine protocol, all specimens were examined by gram and acid-fast bacilli stain. samples were also examined for presence of respiratory viruses (rvs) using either the luminex xtag rvp fast assay (luminex molecular diagnostics, austin, tx,usa) at hcu, or the clart® pneumovir assay (genomica, coslada, spain) at both centers, as previously reported. 10 semiquantitative (sputa) and quantitative (bal and ta) cultures for bacteria were performed on conventional media: bacterial loads > 10 4 cfu/ml or > 10 5 cfu/ml were deemed to be clinically relevant on bal fluids and ta samples, respectively. specimens were cultured on bcye-alpha agar, bd (becton dickinson) mgit® ( mycobacteria growth indicator tube)/lowenstein-jensen agar slants and sabouraud agar for recovery of legionella pneumophila, mycobacterium spp., and other fungal organisms, respectively. the platelia tm aspergillus ag kit (bio-rad, hercules, ca, usa) was used for quantitation of aspergillus spp. galactomannan in bal fluid and serum specimens. all bal fluid specimens underwent cytomegalovirus (cmv) pcr testing using the realtime cmv pcr assay (abbott molecular) at hcu or the cmv r-gene® assay (biomerieux) at hlf, as previously reported. 10 over 200 patients, only 12 presumptively had pjp; (iii) two different commercially-available pcr assays were used across centers. nevertheless, we found them to yield rather comparable c t s. in summary, we found that a positive pj pcr result in respiratory specimens from transplant and non-transplant hematological patients with pneumonia frequently reflects colonization rather than infection; pcr c t values in bal fluids, serum ldh levels and lack of co-detection of other microorganisms potentially involved may be helpful in clinical categorization in the absence of positive by pj microcopy results. we have no conflict of interest to declare. dear editor , poller et al., in this journal, provided a useful consensus for use of personal protective equipment for managing high consequence infectious disease 1 . although this was driven largely by recent ebola virus disease emergencies, we should remind your readers of the continuing problem of lassa fever (lf) in west africa. lf is a febrile infectious disease caused by lassa virus. the clinical presentation of the disease is nonspecific and includes fever, fatigue, hemorrhage, gastrointestinal symptoms, respiratory symptoms, and neurological symptoms 2 . the observed case fatality rate among patients hospitalized with severe lf is 15-20% 3 , 4 . the disease is mainly spread to humans through contamination with the urine or faeces of infected rats 2 . human-to-human transmission can occur through contact with the body fluids of infected per-sons. therefore, health care workers are at high risk for infection when the standard precautions for infection prevention and control including appropriate personal protective equipment are inadequate 5 . it is estimated that there are approximately 30 0,0 0 0 lf cases annually, resulting in approximately 50 0 0 deaths in west african countries 4 . in 2018, nigeria had a large lf outbreak, and we previously reported epidemiological characteristics of the outbreak, analyzing data collected between january and may 2018. 6 however, information on laboratory-negative suspected cases was not enough to conduct a case-control study to fully determine the risk factors and clinical characteristics of the disease. nigeria had a lf outbreak in 2019 as well. 7 here we report the epidemiological and clinical characteristics of the outbreak including case-control analysis against laboratory-negative suspected cases using data collected between 1st january 2018 and 6th october 2019. from january to december 2018, there were 3498 suspected cases, including 633 laboratory-confirmed lf cases. in 2019, there were 4019 suspected cases reported by 6th october, including 721 laboratory-confirmed lf cases. details on the case definition, laboratory test, surveillance, and data collection have been described previously. 6 of the confirmed lf cases, there were 171 fatalities (case fatality rate, 27.0%) in 2018 and 154 fatalities (case fatality rate, 21.4%) in 2019. the number of laboratory-confirmed lf cases and positivity rate peaked in the dry season (january-march) in both 2018 and 2019 ( fig. 1 (a) ). the largest number of laboratory-confirmed lf cases were reported from the neighboring edo and ondo states in both 2018 and 2019 ( fig. 1 (b) ). there were laboratory-confirmed lf cases in states such as kebbi and zamfara that had no reported cases previously, in 2019. during the study period, the detailed demographic and clinical information was collected for 1305 laboratory-confirmed lf cases (of 1354 cases, 96.4%) and 3350 laboratory-negative suspected cases (of 6163 cases, 54.4%). chi-square tests were conducted to compare the distribution of age, sex, and each symptom between the laboratory-confirmed lf cases and laboratory-negative suspected cases ( table 1 ). the proportion of children was significantly lower in laboratory-confirmed lf cases compared with that in laboratory-negative suspected cases. the proportion of males was significantly higher in laboratory-confirmed lf cases than that in laboratory-negative suspected cases. fever was the most prevalent symptom in both laboratoryconfirmed lf cases and laboratory-negative suspected cases, followed by headache ( table 1 ) . gastrointestinal symptoms, such as abdominal pain, vomiting, and diarrhea, were observed in more than 30% of laboratory-confirmed lf cases, whereas hemorrhaging was observed in 21.1% of laboratory-confirmed lf cases. while the prevalence of face/neck edema was low even in laboratoryconfirmed lf cases (6.4%), nonetheless, the odds ratio of having face/neck edema was 6.0 times high for laboratory-confirmed lf cases. we here reported the lf outbreak in 2018-2019 largest recorded in history. while previous studies have focused on laboratory-confirmed lf cases and mainly compared fatal cases and survived cases, 6 , 8 , 9 our observation revealed the difference between laboratory-confirmed lf cases and laboratory-negative suspected cases. the age and sex distribution differed significantly between laboratory-confirmed lf cases and laboratory-negative suspected cases. fever, headache, and gastrointestinal symptoms were the most common symptoms in laboratory-confirmed lf cases, which are similar to those reported previously. 6 , 8 however, these symptoms were also prevalent in laboratory-negative suspected cases. clinical guidelines for lf state that edema in the face and neck is a specific sign of the disease. 10 the present study found that the symptom had a significantly high odds ratio for confirmed lf although the prevalence of this symptom was low. unfortunately, we did not determine the differential diagnosis for the laboratory-negative suspected cases. laboratory tests for the differential diagnoses are now underway for the lf-negative samples collected during the outbreak. the results would provide us further insight for better clinical management of patients with febrile illnesses in lf-endemic areas. in addition to the standard precautions for infection prevention and control including appropriate personal protective equipment pointed out by poller et al., 1 it is important to know epidemiological and clinical characteristics of high consequence infectious diseases such as lf. that would help healthcare workers and public health officers increase an index of suspicion of the diseases, further leading to better clinical management and surveillance. the authors have declared that no conflicts of interest exist. this work was partially supported by the leading initiative for excellent young researchers from the ministry of education , culture, sport, science & technology of japan and the japan society for the promotion of science (grant number, 16809810 ). the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 1 these authors contributed equally to this article. accepted 31 december 2019 available online 15 january 2020 https://doi.org/10.1016/j.jinf.2019.12.020 © 2020 the british infection association. published by elsevier ltd. all rights reserved. recently, several studies in this journal have demonstrated the threat of animal-derived viruses to humans. [1] [2] [3] since 2018, an increase in human pseudorabies virus (prv) infection cases has been reported in china, indicating a new animal-derived virus threat to human health. porcine pseudorabies (pr), also known as aujeszky's disease, is one of the most economically important viral diseases in pigs globally. its causative agent is prv, which is classified into the genus varicellovirus of subfamily alphaherpesvirinae , family herpesviridae . prv is almost always fatal in newborn piglets, is frequently accompanied by neurological symptoms, and may cause abortions and/or stillbirths in pregnant sows. prv primarily infects members of the suidae family and can also infect other domestic and wild mammals, including horses, cattle, sheep, goats, dogs, cats, etc. currently, vaccination is the most effective strategy for pr prevention and control in pigs worldwide. in china, prv infections in pigs were first recorded in 1947. in the 1970s, an inactivated vaccine consisting of the bartha-k61 vaccine strain was imported into china. since then, this vaccine has been widely used in pig vaccination for pr prevention and control. before 2011, no large pr outbreaks were reported in pigs in china. however, after late 2011, novel prv wild-type variants emerged in nearly all regions of china and affected a number of swine herds vaccinated regularly with the bartha-k61 vaccine, resulting in significant economic losses. 4 subsequent animal experiments indicated that the bartha-k61 vaccine could not provide complete protection for pigs against a challenge with novel prv wild-type variants in china. for control and eradication of pr, the disease was listed in the "mid-and long-term animal disease prevention and control program in china (2012-2020)" by the chinese government, with the aim of eliminating pr in china by 2020 ( http://www.gov.cn/zwgk/2012-05/25/content _ 2145581.htm ). however, vaccination for prv is still voluntary and not required in china. a nationwide epidemiological investigation in 2014 demonstrated a high prevalence of 23.26% of prv among swine herds in china. 5 humans were previously regarded as refractory for prv infection, although serological prv antibody positivity was found in three cases. in 2018, the first human prv infection case with direct molecular evidence was reported in china (case 1, table 1 ). 6 in this case, the eyes of a 46-year-old woman were directly exposed to sewage on a hog farm. in the following two weeks, symptoms of fever, headache, coma, and endophthalmitis were observed in the patient. next-generation sequencing (ngs) indicated that prv dna was detected in her vitreous humor samples but not in her cerebrospinal fluid (csf). after surgery, the patient was discharged, but her vision remained impaired. in a subsequent study, zhao et al. table 1 clinical characteristics and other information on the twelve human prv infection cases in china. analyzed csf samples from four patients with encephalitis of unknown etiology using ngs (cases 2-5, table 1 ) and found molecular evidence of prv infection. 7 in addition, retinitis and blindness was observed in two cases (cases 2, 5, table 1 ), and the patient in case 3 died. the occupation of the four patients was all associated with pork production/sale/cooking. in 2019, six other human prv infection cases involving encephalitis were reported in china, and all patients were pork/pig handlers or veterinarians. [8] [9] [10] it was noted that all patients still suffered from various sequelae after discharge, except for in one case where the patient died. increasing reports on human prv infection cases in china have recently indicated that prv poses a significant threat to public health in china, especially in people in close contact with sick pigs and/or related pork products/contaminants. to reduce the risk of prv infection in susceptible workers, it is necessary to promulgate relevant policies by the chinese government to promote pr vaccine development to protect pigs from infection with novel prv wild-type variants currently circulating in china. in addition, relevant policies should be updated by the chinese government to monitor vaccination status and virus variation in pigs nationwide. moreover, it seems that prv can infect humans via injury to the skin or eyes. until now, no effective drugs to prevent the progression of the disease caused by prv infection have been reported. therefore, it is necessary to improve biosafety and self-protection awareness in susceptible populations that have contact with sick pigs and work in jobs related to handling pork products/contaminants. promoting drug development for curing prv-related disease in infected patients may also help reduce the currently increasing threat of prv to human health in china. all authors declare that they have no competing interests. dear editor, the emergence and spread of gram-negative bacteria, for example, klebsiella pneumoniae , co-producing carbapenemases and mobilized colistin resistance ( mcr ) genes limit our choice for treating multidrug-resistant infections, posing significant threats to public health. herein, we reported the discovery of mcr-9 gene in 28 k. pneumoniae strains isolated from patients in eight european countries, including belgium ( n = 2), denmark ( n = 1), montenegro ( n = 13), poland ( n = 1), romania ( n = 1), serbia ( n = 1), slovenia ( n = 1), and spain ( n = 7). notably, the co-existence of mcr-9 and the carbapenemase-encoding genes, ndm-1, vim-1, and oxa-48 were confirmed in k. pneumoniae isolates of human origin. phylogenetic analysis suggested that mcr-9 -carrying k. pneumoniae isolates, including 23 carbapenem-resistant and five susceptible k. pneumoniae strains, show a highly geographically clustered pattern. genetic environment analysis revealed the presence of insertion element is903, is1 or a cupin fold metalloprotein, wbuc, in the mcr-9 flanking. taken together, these findings indicated that mcr-9 has existed for a long time and already spread among crkp isolates of human origin in europe since 2013, further increasing the significant threat of public health through either the nosocomial spread or environmental routes. the mobilized colistin resistance ( mcr ) gene mcr-9 was detected in 28 human gut microbiomes, which has been disseminating across three continents, including asia, europe and america, recently published in the journal of infection. 1 the rapid increase in carbapenem resistance among gram-negative bacteria worldwide has greatly compromised the efficacy of carbapenem antibiotics, which has gotten renewed attention to the importance of polymyxin antibiotics for multidrug-resistant (mdr) infections. recently, sophia david and colleagues 2 reported the epidemic of carbapenem-resistant klebsiella pneumoniae (crkp) in europe, which raised concern that mobile carbapenemase resistance determinants were widely spread in european hospital settings, and inter-hospital spread is far more frequent within, rather than between, countries. however, limited information regarding the co-occurrence of carbapenemases and mcr genes in the klebsiella pneumoniae ( k. pneumoniae ) isolates have been provided. plasmid-mediated resistance genes mcr as well as tet (x3/x4) have been widespread in bacterial species of animal, human, and environment origin as well as human and animal gut microbiomes worldwide, where is a huge arg reservoir with a high horizontal gene transfer possibility. 1 , 3 -5 several studies 6 -8 illustrated that the newly described mcr-9 has spread beyond the united states into europe and asia, and into other enterobacteriaceae species. of clinical concern is the inevitable spread of a plasmid harboring the mcr-9 gene into a crkp isolate, which has been listed by the world health organization as a critical priority antibiotic-resistant bacterial pathogen for which new antibiotics are urgently needed. 9 in response to this potential clinical problem, we download > 1717 k. pneumoniae genomes isolated from 244 hospitals in 32 european countries 2 and the 14,764 complete bacterial genome sequence (accessed 26 july 2019), and explored the distribution of plasmid-mediated resistance genes mcr and tet (x3/x4). we are surprised to find that the complete mcr-9 gene (nucleotide = 100%) was present in 28 k. pneumoniae isolates of 1717 k. pneumoniae strains from belgium ( n = 2), denmark ( n = 1), montenegro ( n = 13), poland ( n = 1), romania ( n = 2), serbia ( n = 1), slovenia ( n = 1), and spain ( n = 7) (table s1 ). additionally, 23 of the 28 k. pneumoniae isolates of human origin were crkp strains and only five were carbapenem-susceptive isolates (table s1 ). as reported, these mcr-9 -harbouring strains were isolated from patients in europe between 2013 and 2014. these results suggest that mcr-9 gene might have been presented in europe for a long time and already spread to the crkp isolates, which is a major cause of both hospital-and community-acquired infections. 2 to further analyze these mcr-9 -positive k. pneumoniae isolates, the resistome of the draft genome was analyzed using the comprehensive antibiotic resistance database. 10 interestingly, the mcr-9 gene was co-existed with various carbapenemase-encoding genes: in eleven isolates with ndm-1, eight with vim-1, and two with oxa-48 ( fig. 1 (a) ). it should be noted that the mcr-9 -and ndm-1-carrying isolates were distributed in denmark ( n = 1), montenegro ( n = 8), romania ( n = 1), and serbia ( n = 1), as well as several other beta-lactam resistance determinants (for example, tem-1, cmy-16, oxa-10 and shv-11) ( fig. 1 (a) and table s1 ). moreover, the mcr-9 -and vim-1-harbouring isolates were dominant in spain ( n = 7) and slovenia ( n = 1), as well as two beta-lactamase-encoding genes (non-carbapenemases) (ctx-m-9 and shv-11) ( fig. 1 (a) and table s1 ). it is worrying that a crkp isolate from spain in 2014 was carrying mcr-9 , vim-1, and oxa-48 genes simultaneously. the presence of mcr-9 in crkp isolates from patients is of critical importance as mcr-9 could be present in hospital-borne outbreaks cre strains in the future. from whole-genome shotgun (wgs) data of the 28 mcr-9 -positive k. pneumoniae isolates, sequences types (sts) were extracted and assigned to nine different types, i.e. , 274, 461, 15, 16, 416, 1890, 37, 1942, and 147 ( fig. 1 (a) ). phylogenetic analysis suggested that mcr-9 -carrying k. pneumoniae isolates show a highly geographical clustering pattern 2 ( fig. 1 (a) ). isolates from patients in the same hospital were clustered into one clade, for example, in spain and montenegro. overall, the k. pneumoniae isolates from different countries were genetically diverse, suggesting that the mcr-9 -positive k. pneumoniae isolates were also genetically diverse and that mcr-9 could disseminate among different k. pneumoniae isolates, mainly by nosocomial transmission. 2 nowadays, all known mcr genes have been detected in various gram-negative bacterial species, whereas a small number of studies have shown the presence of mcr-1, mcr-3, mcr-7 , and mcr-8 in k. pneumoniae isolates from animal and human origin at relatively low detection rate. 11 -14 the presence of mcr-9 in the crkp isolates indicated that this novel mcr gene may already be widely spread among k. pneumoniae isolates of human origin in europe. we subsequently searched mcr-9 gene in 14,764 complete bacterial genome sequence and ncbi-nr database (14 october 2019) in the ncbi, to fully understand the prevalence of mcr-9 gene in klebsiella species isolates. interestingly, the mcr-9 gene (identity > 99% and 100% query coverage) was present in various bacterial genomes, including three klebsiella species isolates consisting of k. pneumoniae ( n = 4), k. quasipneumoniae ( n = 1), and k. oxytoca ( n = 3) (table s3) . therefore, further studies focusing on the epidemiology and transmission mechanism of mcr genes, in particular mcr-9 in klebsiella species of human origin are warranted to better understand the public health threat of emergence of antibiotic resistance among clinical k. pneumoniae . contigs carrying mcr-9 in 28 k. pneumoniae isolates could be classified into two groups (for example, gca_900513855.1 and gca_900501685.1) (table s2) . genetic environments analysis indicated that the presence of insertion element is903 and wbuc (a cupin fold metalloprotein), in the mcr-9 (gca_900513855.1, ∼28 kb) upstream and downstream flanking, respectively, similar to (identity > 99%) the plasmid sequences of pme-1a, pctxm9_020038, and pmrvim0813, and contigs from of e. coli isolate 68a and nz_naan010 0 0 063 from salmonella 15 ( fig. 1 (b) ). additionally, mcr-9 in another contig ∼8.7 kb was in the upstream of two insertion element is1 and is30 0 0, as well as a beta-lactamase-encoding resistance gene ctx-m-9, which similar to the plasmid sequence of pmrvim0813. we did not detect the downstream regulatory genes (qsec and qseb) found in the isolates that harbor mcr-9 . 8 , 16 moreover, we were unable to determine whether a complete is903 element is upstream due to a short mcr-9 -bearing contig that is available for comparison ( fig. 1 (b) ). therefore, a long-read sequencing coupled with a hybrid assembly method is needed to fully evaluate and monitor the transfer and development of args, especially mcr-9 among crkp isolates. although two unique plasmid-mediated tigecycline resistance genes firstly discovered in bacteria of animal origin in china and subsequently identified in many bacterial isolates of human, animal and environment origin, including klebsiella species, as well as human and animal gut microbiomes, 1 , 4 , 5 none of them was detected in the 1717 k. pneumoniae strains in europe. in summary, we reported the discovery of mcr-9 gene in 28 clinical k. pneumoniae strains of human origin in eight european countries. importantly, the mcr-9 gene was co-existed with different carbapenemase-encoding genes in the same strains. the spread of mcr-9 , ndm-1, vim-1, and oxa-48 and other beta-lactam resistance determinants (non-carbapenemase) carrying by crkp appears likely to be by plasmid dissemination, as the genes identified in isolates belonging to a diverse set of sts distributed in different hospitals in europe. it is noteworthy that all these mcr-9 -positive crkp strains were isolated between 2013 and 2014, highlighting an earlier presence of mcr-9 among crkp around the world than previously known. these findings raise the likelihood of ongoing undetected mcr-9 gene spread among cre strains. therefore, further study is urgently needed to understand the prevalence and dissemination of mcr-9 , especially in cre and crkp strains, and effective measures should be taken to control its spread. g.f.g. designed the study. y.n.w. and f.l. collected and downloaded the datasets. y.n.w., f.l., y.f.h., b.l.z., g.p.z., and g.f.g. analyzed and interpreted the data. y.n.w. and g.f.g. wrote the draft of the manuscript. all authors discussed, reviewed and approved the final report. supplementary information is available for this paper. correspondence and requests for materials should be addressed to g.f.g. the authors declare no competing interests. the interesting systematic review by amin-chowdhury and colleagues provides information about outbreaks of severe pneumococcal disease (spd) in closed settings that occurred in the conjugate vaccines era 1 . it shows that vaccine-type spd outbreaks are still occurring and it highlights the lack of consensus on how to manage such outbreaks. in the following, we will describe how we managed a recent outbreak of spd in norway. in march 2019, møre and romsdal hospital trust notified the norwegian institute of public health (niph) about a cluster of spd amongst men working in shipyards in møre and romsdal county. serotype data from niph were available for nine of the cases -all were serotype 4. the majority of cases had been working at one specific shipyard. municipal medical officers (mmo), the norwegian labour inspection authority (nlia), and niph formed a multidisciplinary outbreak team to investigate and control the outbreak. we formed specific case definitions: each case had to have resided in møre and romsdal county in the period from 1. january 2019 onwards and: confirmed : had invasive pneumococcal disease (ipd) with serotype 4 isolated from a normally sterile site. probable : worked at the specific shipyard and had a clinical presentation compatible with lower respiratory tract infection or ipd, but without microbiological confirmation or serotype 4 isolated from a non-sterile medium (e.g. nasopharyngeal swab or sputum culture). we identified 20 cases, ten confirmed and ten probable in the period between 28. january and 3. april ( fig. 1 ). all available isolates were serotype 4 (10 confirmed, 7 probable) and were susceptible to penicillin. fifteen isolates were sequence type (st) 801, while two were a single locus variant of 801, st 15,063. all cases were men between 20 and 60 years, with a mean age of 47 years. fifteen were hospitalized. four were norwegian citizens, the remaining came from other european countries. seven cases smoked. one case had an underlying medical risk condition. immunization history against pneumococci were unknown for all. the cases had several professions; mostly related to interior outfitting and metal welding. approximately 1800 individuals worked at the shipyard in the time period. many of them lived in temporary accommodation. at an on-site inspection of the shipyard, nlia observed a polluted atmospheric work environment and little use of personal protective equipment. several measures were put in place to control the outbreak, including information and advice to raise symptom awareness and to reinforce hand and respiratory hygiene, vaccination and occupational corrections. local medical clinics and hospital were alerted about the outbreak and advised to have a low threshold to admit and treat suspected cases. mmo held information meetings with shift leaders, and written information about spd in several languages was distributed to workers to increase spd awareness. intensified hygiene measures were implemented at the ship yard and housing quarters. nlia ordered immediate occupational corrections related to controlling the atmospheric work environment. niph recommended vaccination with the 13-valent conjugate vaccine (pcv13) to interrupt transmission and prevent disease. both the pcv13 and the 23-valent polysaccharide vaccine provide protection against serotype 4, but pcv13 was preferred as this may also affect colonization. as several work tasks were conducted in parallel process in confined spaces with suboptimal ventilation, we were unable to identify a single target group for vaccination. hence, the shipyard offered vaccination to all workers. occupational health service promptly vaccinated all workers during a four-day period. contrary to the majority of studies included in the systematic review, niph did not recommend chemoprophylaxis. as the workers were otherwise healthy (i.e. no high risk group like old age, immunocompromising conditions etc.), and since it was impossible to target a specific group of workers, niph deemed it undesirable to distribute antibiotics to 1800 asymptomatic workers, with the possibility of inducing antimicrobial resistance and possible side effects. due to high turnover of personnel it was not possible to calculate an attack rate. we did not find any new cases after control measures were implemented. no deaths have been reported in relation to the outbreak. this outbreak closely resembles one of the outbreaks described in the systematic review; between april and june 2015, an outbreak with serotype 4, st 801 occurred at a shipyard in belfast 2 . we are also aware of an outbreak this fall, 2019, at a shipyard in finland with serotype 4 (st 801), 8 and 12f 3 . although welders are a known risk group for spd, 4 in all these three outbreaks, people who worked closely alongside welders were also infected. in addition to exposure to welding fumes, the crammed and poorly ventilated working conditions, and possibly housing conditions, may have increased the risk of developing spd and facilitated the transmission of pneumococci in this closed setting. overall, this norwegian outbreak extends the knowledge about how to manage and control outbreaks of spd in closed settings. none. in this journal brunet and colleagues 1 discussed reactivation of latent infections in the context of chronic disease, solid organ transplantation or long-term immunosuppressive treatment. we recently observed the reactivation of leishmania infection in a 46-year-old patient receiving methotrexate for psoriasis, who was diagnosed with visceral leishmaniasis (vl) showing a mucocutaneous involvement. we analyzed the epidemiologic and clinical characteristics of all cases of leishmaniasis in patients with psoriasis found through a review of the literature. our patient was admitted into the infectious disease unit of paolo giaccone hospital, in palermo, with a painless and ulcerated lesion onto the oral mucosa ( fig. 1a ) , two nodular ulcerated lesions on the right knee and another one on instep of the right foot appeared one month before ( fig. 1b ) . the patient did not travel outside italy during the last year. he had been suffering from lowgrade fever in the last month. considering the above findings leishmaniasis was suspected and a needle aspiration of oral and cutaneous lesions was arranged in order to perform microscopy and leishmania-pcr, which were positive for leishmania. laboratory tests exhibited: wbc 4970/mmc, hb 13.9 g/dl, c reactive protein, 26.9 mg/l; positive serology for leishmania (igg 1/3200) and positive leishmania-pcr test on peripheral blood. abdominal us examination revealed splenomegaly (14 cm); methotrexate was suspended and liposomal amphotericin b, 4 mg/kg per day for 10 days, followed by two further administrations two weeks later was started. cutaneous and mucosal lesions improved at the end of the first 10 days of therapy and completely vanished after two further administrations, 40 days from the beginning of treatment. leishmania-pcr on peripheral blood after 10 days of therapy was negative. table 1 shows the literature data about characteristics, therapy and outcome of patients with psoriasis and leishmaniasis. leishmaniasis is a vector-born chronic infectious disease caused by protozoa of the genus leishmania and transmitted to humans by the bite of phlebotomine sandflies. in europe, the mediterranean countries are the most affected areas. leishmania parasite establishes chronic intracellular parasitism, survives for an infected person's lifetime and, in the event of major immune deficiency, may be reactivated from sites of latency. leishmaniasis can present with a spectrum of clinical manifestations and three patterns of infection are described: cutaneous (cl), mucosal or mucocutaneous (ml or mcl) and visceral leishmaniasis (vl). the infecting species of leishmania is very important in determining the clinical manifestations and the host immune response is crucial in determining the clinical outcome of infection 2 . today, non-hiv related immunosuppressive conditions are becoming increasingly prevalent, mainly because of better medical care of patients with chronic illnesses and the therapeutic use of immunosuppressive drugs. in the field of rheumatology, leishmaniasis has been reported in association with the use of various immunosuppressive drugs. 3 the introduction of tumor necrosis factor-alpha (tnf-α) antagonist drugs has received much attention recently and several cases of vl have been reported in rheumatic patients who do anti-tnf α drugs. 4 psoriasis is a chronic inflammatory autoimmune disease affecting 2-3% of the world's population and characterized by an aberrant hyper-proliferation of keratinocytes. the pathogenesis of psoriasis is complex. genetic susceptibility, environmental triggering factors and an over-reaction of local innate immune response initiate inflammation. subsequent involvement of adaptive immune response with production of th 1 cytokines, chemokines and growth factors lead to epidermal hyperplasia. 5 recently, a functional role of interleukin-17-producing t helper cells (th17) in psoriasis has been suggested by their reduction during successful anti-tnf treatment. 6 it is also known that th17 lymphocytes play an essential role in protecting against intracellular protozoa and in the successful clearance of leishmania by strengthening the th1 response. 7 in view of this, it could be argued that psoriasis may represent a protective factor for leishmania infection. indeed, in our review we did not found any case of leishmaniasis in psoriatic subjects who were not under immunosuppressive therapies. biological agents, which are powerful immunosuppressive drugs, have been more and more used in rheumatic patients and leishmania infections have been reported among anti-tnf-agents users. 8 recently maritati et al. found higher prevalence of subclinical leishmaniasis in patients with inflammatory rheumatic diseases receiving biological drugs than those treated with other immunosuppressive drugs. 9 however, leishmaniasis has also been reported in psoriatic patients not receiving biological drugs, as occurred to our patient ( table 1 ) . diagnosis of cl in psoriatic patients is challenging, as it mimics many other infections or a flare-up of psoriasis itself that can lead to ineffective and harmful changes of therapy. immunosuppressive therapies cause atypical manifestations of leishmaniasis with large lesions spread over large cutaneous areas and associated to a possible mucosal involvement. ml by l. infantum is very rare and only sporadically described in patients receiving powerful immunosuppressive therapies or in hiv-coinfected patients. mcl is mostly observed in latin america where l. braziliensis accounts for most cases, but l. panamensis, l. guyanensis, and l. amazonensis have also been implicated. only rarely cutaneous lesions extend to areas of skin distant from the mucosa involved, as in our case in which two lesions on the foot and knee were associated with the oral lesion. in the context of impaired immunity, it is also advisable to rule out vl by pcr-leismania on peripheral blood so as to establish the most appropriate therapy: intralesional or intravenous. finally, there is no agreement on appropriate screening for leishmaniasis before immunosuppressive treatments and on the strategy to be followed after the diagnosis of leishmaniasis in rheumatic patients taking immunosuppressive drugs. 10 molecular methods are highly sensitive and specific tools for the diagnosis of visceral leishmaniasis and a screening with leishmania-pcr in immunosuppressed patients living in endemic areas could be useful to identify patients at highest risk of reactivation. 9 specific leishmaniasis treatment followed by suspension of the immunosuppressive therapy was adopted by most of the authors. overall even if the treatment response is not as good as seen in the immunocompetent population, our review reports a good outcome in all cases and patients remained relapse-free without maintenance therapy and despite the ongoing use of immunosuppressive medication. in conclusion physicians must be alert to the possibility of development of leishmaniasis in immunosuppressed rheumatic patients. adequate screening for vl should be incorporated into the list of baseline studies to carry out before initiating biologic therapies, at least in endemic areas. the authors declare that there is no conflict of interest. as demonstrated in several studies in journal of infection , herpesviruses pose an increasing threat to human health. [1] [2] [3] according to international committee on taxonomy of viruses (ictv), equine herpesviruses (ehvs) belong to the family herpesviridae . until now, a total of 9 ehv species types have been determined in equines, viz. ehv1-ehv9. 4 among them, ehv1 and ehv4 are the most relevant herpesviruses affecting equines. both ehv1 and ehv4 infection are associated with upper respiratory tract disease, but only ehv1 infection could cause abortion and myeloencephalitis. ehv1 and ehv4 are prevalent in equines on all continents and have considerable economic impact on the horse industry. 5 in china, the number of equines is very large, reaching to be ∼ 6.8 million in 2018 ( http://www.stats.gov.cn/tjsj/zxfb/ ). ehv infection in equines was first reported in china in 1980, and the epidemiological investigation since then indicated ehv was prevalent in the equine population in all the studied 16 provinces in mainland china, with a seroprevalence ranging 8% −92%. [6] [7] [8] vaccination is commonly used to prevent and control ehv. however, china has not developed a commercially available ehv vaccine so far. ehv vaccine has a limited market application potential in china currently. due to the lack of relevant knowledge on ehv, most of the chinese horse owners always erroneously identified it as other common pathogen of equine respiratory diseases, and didn't realize its potential threat to equine health and reproduction. although the number of equines in china is large, most of them are labor/farming horses. to the best of our knowledge, even for racehorses, vaccination with ehv vaccine has not been performed in mainland china. considering the wide distribution and high prevalence of ehv in china, it is urgently to popularize knowledge on ehv in horse owners and promote market application prospects of ehv vaccine. in china, few veterinary researchers are currently investigating equine virus, including ehv. this is mainly caused by the change of equines' historical role. in the last century, a great number of equines were used for military in china. however, there is only one military equine farm in mainland china at present. considering a more important economic role of other domestic animals (e.g., pigs, chickens, and cattle) compared with equines, investigating equine virus (including ehv) is not a priority in the related guide policies issued by the chinese government. though epidemiological studies on ehv in china are limited, it still could be concluded that epidemic status of ehv is very complicated in china, which increases the difficulty in ehv vaccine development. in most provinces, ehv1 and ehv4 were co-circulating in equines with a high seroprevalence. 8 until now, a total of 7 ehv1 strains have been isolated from tissue samples of aborted equine fetuses (5 from farming horses in northeast china in 1980, 1 from asian wild horses in western china in 1999, 1 from farming horses in western china in 2016). 6 , 8 in addition, a novel ehv8 strain was isolated from one horse with serious respiratory disease in northern china in 2010. 9 recently, our laboratory firstly determined the molecule evinces for ehv4 and ehv5 in racehorses in sothern china (data not shown). however, a more large-scale and surveillance of ehv in equines is necessary to fully understand epidemic status of ehv in china, which could establish a foundation for updating the composition of ehv vaccine developed in china in future. in other countries, much effort has been made to develop ehv vaccine, and modified-live and inactivated virus vaccines have been registered for sale. 10 before an ehv vaccine is developed successfully in china by itself, it is necessary to vaccinate the susceptible equine population with an ehv vaccine commercially available from other countries to prevent and control ehv in china. however, a well-designed case-control animal challenge study still needs to estimate the protective efficacy of different vaccines against the field prevalent ehv strains in china. all authors declare that they have no competing interests. a recent review article on the treatment of hepatitis c with directly-acting antiviral (daa) drugs, makes numerous recommendations for baseline drug resistance testing. 1 in our local practice, we have been performing baseline drug resistance testing for some years now, prior to the publication of these guidelines. we present a recent retrospective hcv kinetics analysis of these patients' changing viral loads in response to daa therapy below. such studies have been used previously to compare viral suppressive responses in different hcv genotypes and treatment regimens. 2 , 3 the patients were a mixture of treatment-naive and treatment-experienced (including with interferon-based, ns3 protease inhibitor-based and daa-based regimens) cases. the current standard of care for hepatitis (hcv) patients is a combination of direct acting antivirals (daas), for which there are three different hcv viral protein targets (ns3, ns5a and ns5b). table 1 ns3, ns5a, ns5b resistance associated substitutions (ras), by hcv genotype, found in this patient cohort at baseline drug resistance testing (viral sequencing performed at imperial college, london, uk). the patients included a mixture of treatment-naïve and treatment experienced (i.e. interferon-based, ns3 protease inhibitor-based and more recent daa-based regimens) cases. resistance associated substitution (ras) by hcv genotype treatment with daas cure the vast majority of hcv-infected patients, with oral regimens having > 95% efficacy in most patient groups. 1 , 4 , 5 treatment failure currently affects approximately 5% of treated patients and is often associated with the selection of resistance associated substitutions (ras). 1 we performed hcv drug resistance testing both retrospectively (following treatment failures) and prospectively (prior to treatment) in our cohort of hcv genotype (g) 1-3-infected patients, during march 2015-june 2018. viral extraction, pcr and sequencing were performed at imperial college, using qiagen viral rna mini kits (qiagen pn:52906, qiagen ltd., manchester, uk), and inhouse pcr and sanger sequencing methods on an abi prism 3100-avant genetic analyser (thermo fischer scientific, loughborough, uk). the prediction of hcv genotype and drug sensitivities is derived from the geno2pheno algorithm [ www.geno2pheno.org ]. 6 treatment regimens used during this period complied with contemporaneous nhs rate cards: for non-cirrhotic or compensated cirrhotic patients: g1-treatment-naive: omb/par/rit + das + r; g1-treatment-experienced: elb/grz + /-r; g2-treatmentnaive/experienced: gle/pib; g3-treatment-naive/experienced: gle/ pib; g1-decompensated cirrhotic patients sof/led + r; g2/g3decompensated cirrhotic patients: sof/vel + r. we assessed the impact of any ras across g1-g3 on hcv rna kinetics by analysing viral load (realtime hcv viral load, abbott m20 0 0, abbott molecular uk, maidenhead, england) decline rates. we applied linear mixed regression to model the viral loads and assumed a linear decline (log 10 scale) over time, using sas statistical software (sas institute inc., nc, usa). in this cohort of 54 patients (n: g1 = 21, g2 = 6, g3 = 27), hcv ras were found as shown in table 1 . hcv rna viral load decline rates were found to be similar and not statistically different ( p = 0.760) at: −2 log 10 and −1.8 log 10 per month, respectively, for g1 and g2/g3 ( fig. 1 ). this suggests that these viral load decline rates were similar across g1-g3 infections despite baseline differences in viral load, ras profile, or a history of any previous treatment (i.e. interferon-based, older ns3 protease inhibitor-based, or more recent daa regimens). these results demonstrate similar hcv rna clearance efficacies of the various daa treatment regimens for g1-g3, in this patient cohort. although other studies on hcv kinetics have been published, they do not usually compare multiple hcv genotypes. 7 similar studies on patients infected with g4-6 viruses, and/or undergoing other daa treatment or retreatment combinations, 8 , 9 will be with great interest we have read the report of zhang et al. concerning the increased susceptibility to pertussis in chinese adults at childbearing age, as determined in a comparative seroprevalence study using samples collected from 2010 to 2016. 1 the authors describe that about 5% of the individuals had pt-igg antibodies, which is indicative of a recent infection. in the adults 20-39 years of age, 29.1% subjects had undetectable pt-igg antibodies in 2010 but 57.4% in 2015/2016. it is well known that adolescents and adults have become the reservoir of pertussis and an important source of transmission to vulnerable infants. bordetella pertussis is commonly associated with atypical pneumonia as determined in hospitalized children. 2 several seroprevalence studies conducted in different regions of china indicate that the incidence of pertussis is most likely underestimated. 3 , 4 this may be due to the use of insensitive diagnostics. at present, the diagnosis of pertussis in china is mainly based on culture. however, both the cdc and the world health organization (who) use pcr as the gold standard for diagnosis, in addition to culture. 3 oropharyngeal or nasopharyngeal swabs were obtained from 17,104 inpatients aged between 10 days and 14 years of age with clinical suspicion of pertussis, enrolled from march 2014 to february 2018 in shenzhen children's hospital. more than 50% of all patients were younger than 6 months of age. the hospitalized patients included 10,894 males and 6210 females (sex ratio, 1.75). all patients recovered after the treatment. a real time pcr assay targeting ptxa-pr was used to detect b. pertussis . of the 17,104 samples, 772 (4.51%) tested positive for b. pertussis by rt-pcr. our results indicate that despite vaccination pertussis remains a major health problem in china, since the prevalence of infection by b. pertussis in hospitalized children was high. the majority of patients were admitted because of pneumonia. the detection rate in hospitalized patients was lower than the rates reported earlier in shanghai and ji'nan. 3 , 4 this may be due to lower number of samples collected in these studies and due to the use of serology or culture methods. the overall prevalence rates were 3.97% and 5.48%, respectively. however, b. pertussis infection in female patients was significantly higher than in male patients (x 2 = 20.913, p < 0.001). this has earlier been reported by the ecdc 5 and haberling et al. 6 and may point to a genetic association with susceptibility to b. pertussis . the detection rates were dependent on age in patients (x 2 = 139.8, p < 0.001). the prevalence decreased with age: 8.71% newborns, 5.33% in infants, 2.39% in toddlers, 1.28% in (pre-) schoolers ( fig. 1 ) . the high vulnerability of newborns and young infants for b. pertussis infection may be related to a combination of insufficient herd immunity and suboptimal protection against b. pertussis infection in children too young to be fully vaccinated. since vaccination rates in infants are already at 99%, it will be difficult to improve this further. therefore, other measures must be considered, including booster vaccination at pre-school age and vaccination during pregnancy. because young infants are mainly cared for by mothers and other adults, the most important cause of infection with b. pertussis is their close contact with parents and siblings. 7 in general, b. pertussis was detected more often during seasonal changes, especially from late summer to early autumn. in hospitalized children the number of b. pertussis infections increased in march and september as compared to other months ( fig. 2 ) . the seasonal infection rates were 4.66% in spring, 4.75% in summer, 4.62% in autumn and 4.00% in winter, respectively. the prevalence in the winter season was lower but not statistically different than in other seasons (x 2 = 3.388, p = 0.336). in this study, we used real-time pcr, the most accurate method to detect b. pertussis . the detection rate may be significantly lower than the actual level, because oropharyngeal samples in most patients were collected instead of nasopharyngeal samples, and the pcr target gene was ptxa-pr instead of is4 81. is4 81 is present in high-copy numbers in b. pertussis whereas ptxa-pr is a single-copy target. however, the ptxa-pr pcr is more specific and will not detect b. parapertussis , which contributes to more than 5% of pertussis cases. 8 many studies have shown that adolescents and adults with b. pertussis infections, causing chronic cough, are an important reservoir for transmission, putting newborns at high risk. 9 maternal pertussis immunization prevents infant pertussis, as recently shown by amirthalingam et al. vaccine effectiveness against infant deaths was estimated at 95%, and disease incidence in infants < 3 months of age has remained low. 10 according to our results, vaccination of pregnant women and adults, especially those in close contact with infants and young children, may help to prevent pertussis in infants and young children in china. the authors have declared that no competing interests exist. this study was supported by the sanming project of medicine in shenzhen ( szsm201512030 ) and by the shenzhen science and technology project ( jcyj20170303155012371 ). tang and colleagues reported in this journal their experience with covid-19 disease 1 , the outbreak of which began in december 2019 in wuhan, hubei province, china 2 , 3 with spread to 33 additional countries 4-8 as of the 21st february 2020. here we report the clinical features and outcome of the first two cases of disease caused by sars-cov-2 infection in the united kingdom (uk) -the first imported and the second associated with probable person-toperson transmission within the uk. public health management will be reported separately. the index case (a) entered the uk on 23/01/20 from hubei province in china. initially asymptomatic, this individual, a 50 year-old female with no past medical history and on no regular medications, developed symptoms of fever and malaise on 26/01/20, accompanied by sore throat and dry cough. she had travelled with her partner and reported no infectious contacts prior to travel. on 28/01/20, a close household contact of the index case, a resident of the uk, developed symptoms of fever (38.5 °c), followed the next day by diffuse myalgia and a dry cough. this patient (case b) is a previously fit and well 23 year-old male. he had returned to the uk from hubei province on 06/01/20. case b promptly sought advice via the national health service (nhs) self-referral service nhs 111, and he and case a were assessed as being possibly at risk of covid-19, and were admitted to the regional infectious diseases unit at castle hill hospital, hull university teaching hospitals for isolation, assessment and diagnostic sampling. they were managed in separate negative pressure cubicles with anterooms. nursing and medical staff donned personal protective equipment (ppe) as recommended by public health england (phe). the clinical observations of each of the patients, together with their initial blood tests, are shown in table 1 . ( fig. 1 ) . clinical examination findings were unremarkable. initial investigations revealed only mild lymphopenia and elevation of crp, with mild neutrophilia in case b. periodic fever of 38-38.5 °c was observed in case b until d3 of admission. repeat blood tests in this individual on d3 demonstrated mild acute kidney injury (aki, serum creatinine 144 μmol/l). the aki was thought most likely due to dehydration, and resolved within 24 h with administration of intravenous infusion of crystalloid at 125 ml/h. cxr was normal. empirical oral antibiotic therapy (co-amoxyclav 500/125 mg p.o. t.d.s.) was administered on d3, to cover the possibility of secondary bacterial infection, but was subsequently discontinued. symptoms resolved in case a by d3 and in case b by d4 of admission. pcr testing of sars-cov-2 from nose and throat swabs taken daily was negative from d2 onwards in case a and from d5 in case b (throat swabs from this individual were negative throughout). there was no clinical indication for the use of experimental antiviral therapies. patients were deisolated according to current phe guidance, based on complete resolution of symptoms and two sequential negative respiratory pcr tests at least 24 h apart. rooms were decontaminated with 0.1% hypochlorite followed by uv light treatment. the contact of these individuals remained asymptomatic throughout the 14 days incubation period but was isolated as a precaution and to be close to family these first cases of sars-cov-2 are informative for clinicians caring for suspected and confirmed cases in the uk and elsewhere. reassuringly, illness in both individuals was relatively mild and short-lived, with no evidence of parenchymal lung disease (reflected by normal oxygenation and the absence of radiological infiltrates) or of the late-stage deterioration that has been reported in case series 9 , possibly due to the absence of comorbidities. experimental antiviral therapeutic options for severe disease were not considered necessary given the mild clinical nature of the illness. clinical illness correlated with the presence of viral rna in upper airway samples ( fig. 1 ) , with no evidence of prolonged asymptomatic shedding, although discordance between nose and throat samples in case b highlights the need to sample both areas. it was reasonably assumed that the source of infection in case b was close contact with symptomatic case a, given that the time from travel to china to onset of symptoms in case b was 22 days, although this cannot be proven. based on this assumption, the period from exposure to disease onset appeared short, at approximately 48 h, consistent with recent reports of the incubation period of sars-cov-2 6 . co-occurrence of respiratory viral infection, as we observed in case b with rhinovirus, has been described in the context of sars-cov-2 ( https://www.medrxiv.org/ content/10.1101/2020.02.12.20022327v1 ) as it has with many other respiratory viruses spread by similar routes, and may have contributed to the increased symptomatology in case b. interestingly the partner of case a, who was a close household contact, remained asymptomatic throughout and had negative tests for sars-cov-2 shedding. it will be of interest to investigate the serological responses in this individual to ascertain evidence of subclinical infection. isolation, minimisation of contacts and use of appropriate ppe is a cornerstone of management of high consequence respiratory viral infection. in the cases reported here, phe recommendations for ppe were followed 10 and there were no breeches in ppe or nosocomial transmission. this should provide reassurance to healthcare workers managing patients with suspected covid-19 in the uk that current ppe is both feasible and effective. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. dear editor , as reported in this journal 1 and elsewhere, 2 an outbreak of atypical pneumonia caused by the zoonotic 2019 novel coronavirus (sars-cov-2) is on-going in china and has spread to the world. as of feb 16, 2020 (24:00, gmt + 8), there have been 70,548 confirmed patients and more than 1700 deaths from sars-cov-2 infection in china, and 58,182 confirmed patients and 1696 deaths in the most affected province, hubei province. much research progress has been made in dissecting the evolution and origin of sars-cov-2 and characterizing its clinical features. [3] [4] [5] [6] [7] while the outbreak is on-going, people raise grave concerns about the future trajectory of the outbreak, especially given that the working and schooling time has been already dramatically postponed after the chinese lunar new year holiday was over (scheduled on jan 31). in particular, a precise estimation of the potential total number of infected cases and/or confirmed cases is highly demanding. earlier studies based on susceptible-exposed-infectious-recovered metapopulation and susceptible-infected-recovered-dead models revealed the number of potentially infected cases and the basic reproductive number of sars-cov-2. 3 , 8 , 9 these traditional epidemiological models apparently require much detailed data for analysis. 3 , 8 here we explored a simple data-driven, boltzmann functionbased approach for estimation only based on the daily cumulative number of confirmed cases of sars-cov-2 (note: the rational for boltzmann function-based regression analysis is presented in supporting information (si) file). we decided to collect data (initially from jan 21 to feb 10, 2020) in several typical regions of china, including the center of the outbreak (i.e. wuhan city and hubei province), other four most affected provinces (i.e., guangdong, zhejiang, henan, hunan) and top-4 major cities in china (i.e., beijing, shanghai, guangzhou, shenzhen). during data analysis on feb 13, 2020, the number of new confirmed cases on feb 12 in hubei province and wuhan city suddenly increased by 14,840 and 13,436, respectively, of which 13,332 and 12,364 are those confirmed by clinical features (note: all the number of confirmed cases released by feb 12 were counted according to the result of viral nucleic acid detection rather than by referring to clinical features). we thus arbitrarily distributed these suddenly added cases to the reported cumulative number of confirmed cases from jan 21 to feb 14 for hubei province by a fixed factor (refer to table s1 ), assuming that they were linearly accumulative in those days. it is the same forth with the data for wuhan city. regression analyses indicate that all sets of data were well fitted with the boltzmann function (all r 2 values being close to 0.999; figs. 1 a, b, s1 , and table 1 ). the potential total number of confirmed cases for mainland china, hubei province, wuhan city, and other provinces were estimated as 72,80 0 ±60 0, 59,30 0 ±60 0, 42,10 0 ±70 0 and 12,80 0 ±10 0; respectively; those for provinces guangdong, zhejiang, henan and hunan were 1300 ±10, 1170 ±10, 1260 ±10, 1050 ±10, 1020 ±10 and 940 ±10, respectively ( table 1 ) ; those for beijing, shanghai, guangzhou and shenzhen were 394 ±4, 328 ±3, 337 ±3 and 397 ±4, respectively. in addition, we estimated the key date, on which the number of daily new confirmed cases is lower than 0.1% of the potential total number as defined by us subjectively (refer to table 1 ). the above analyses were performed assuming that the released data on the confirmed cases are precise. however, there is a health commission, the state administration of traditional chinese medicine, the academy of chinese medical sciences, 29 provinces and cities, as well as the army ( fig. 1 ) . huoshenshan hospital is a specialized hospital established in the wuhan staff sanatorium. patients with confirmed coronavirus pneumonia have been admitted to our hospital. it has a total of 10 0 0 beds, and includes an intensive care unit, an ordinary care unit, a laboratory, and radiology and other auxiliary departments. according to the national health commission of the people's republic of china, the related design scheme of the institute was completed on january 24, 2020. construction of the hospital began on january 29th, and the hospital was completed and put into use on february 2nd. the chinese people's liberation army has transferred 1400 medical personnel to undertake the task of helping people infected with the virus. we firmly believe that chinese medical 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www.gov.uk/government/publications/wuhan-novelcoronavirus-infection-prevention-and-control/wuhan-novel-coronavirus-wncov-infection-prevention-and-control-guidance accessed 3rd emergence of a novel coronavirus causing respiratory illness from wuhan a novel coronavirus outbreak of global health concern epidemiological and clinical features of the 2019 novel coronavirus outbreak in china a new coronavirus associated with human respiratory disease in china a pneumonia outbreak associated with a new coronavirus of probable bat origin genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding clinical characteristics of 2019 novel coronavirus infection in china nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study data-based analysis, modelling and forecasting of the novel coronavirus (2019-ncov) outbreak a data driven time-dependent transmission rate for tracking an epidemic: a case study of 2019-ncov emergence of a novel coronavirus causing respiratory illness from wuhan early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features of patients infected with 2019 novel coronavirus in wuhan the novel coronavirus originating in wuhan. china: challenges for global health governance emergence of sars-like coronavirus poses new challenge in china we are indebted to all colleagues who contributed to this substudy in paris and geneva. in particular, we would like to thank no public or private funds were used for the current study. eliseo albert holds a río hortega research contract from the carlos iii health institute (ref. cm18/00221 ). estela giménez holds a juan rodés research contract from the carlos iii health institute (ref. jr18/0 0 053 ). we thank all the staff of the domestic and international organizations who fought against this outbreak, including those at the various health care facilities, lassa fever diagnostic laborato-ries, nigeria centre for disease control, world health organization, african field epidemiology network, public health england, ehealth africa, pro health international, university of maryland baltimore, us centers for disease control and prevention, alliance for international medical action, médecins sans frontières, and numerous other partners. we also express our sincerest condolences to the families and friends of those who died during the outbreak. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2019.12.016 . this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sector. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2020.01.019 . this work was supported by the national natural science foundation of china ( 31702271 ), and the guangdong provincial natural science foundation ( 2017a030310367 ). we are grateful to the patients for providing their written informed consent to publish this report. our thanks go to nursing, laboratory and medical colleagues in hull university teaching hospitals nhs trust and the newcastle upon tyne hospitals nhs foundation trust who contributed directly and indirectly to patient care, and to many colleagues in public health england and across the hcid network who contributed their time and expertise to the management of these cases. cjad is supported by a clinical research career development fellowship from the wellcome trust ( 211153/z/18/z ). we thank graduate students (boyan lv, zhongyan li, zhongyu chen, yu cheng, mengmeng bian, shuang zhang, zuqin zhang, and wei yao; all from prof. xinmiao fu's research group at fujian normal university) for data collection. this work is support by the national natural science foundation of china (no. 31972918 and 31770830 to xf). the reported cumulative number of confirmed cases may have uncertainty. assuming the relative uncertainty follows a single-sided normal distribution with a mean of 1.0 and a standard deviation of 10%, the potential total number and key dates were estimated at 95% ci. for detail, refer to the methods section and figs. 1 c, d, s2 and s3.b key date is determined when the number of daily new confirmed cases is less than 0.1% of the potential total number. tendency to miss-report some positive cases such that the reported numbers represent a lower limit. one typical example indicating this uncertainty is the sudden increase of more than 14 0 0 0 new confirmed cases in hubei province on feb 12 after clinical features were officially accepted as a standard for infection confirmation.another uncertainty might result from insufficient kits for viral nucleic acid detection at the early stage of the outbreak. we thus examined the effects of such uncertainty using a monte carlo method (for detail, refer to the methods section in si file). for simplicity, we assumed that the relative uncertainty of the reported data follows a single-sided normal distribution with a mean of 1.0 and a standard deviation of 10%. under the above conditions, the potential total numbers of confirmed cases of sars-cov-2 for different regions were estimated ( figs. 1 c, d, s2 and s3 ) and summarized in table 1 16 ,092), respectively, indicating that overall the outbreak may not be so bad as previously estimated. 9 such uncertainty analysis also allowed us to estimate the key dates at 95% ci. as summarized in table 1 , the key dates for mainland china, hubei province, wuhan city, and other provinces would fall in (2/28, 3/10), (2/27, 3/10), (2/28, 3/10) and (2/27, 3/13), respectively.finally, the ongoing sars-cov-2 outbreak has undoubtedly caused us the memories of the sars-cov outbreak in 2003. we thus collected the data from the who officiate website for analysis, and found that the cumulative numbers of confirmed cases of 2003 sars-cov both in china and worldwide were fitted well with the boltzmann function, with r 2 being 0.999 and 0.998, respectively ( figs. 1 e and f) .in summary, we found that all data sets, including both the on-going outbreak of sars-cov-2 in china and the 2003 sars-cov epidemic in china and worldwide, were well fitted to the boltzmann function ( fig. 1 and s1 ). these results strongly suggest that the boltzmann function is suitable for analyzing the epidemics of coronaviruses like sars-cov and sars-cov-2. one advantage of this model is that it only needs the cumulative number of confirmed cases, somehow as simple as the recently proposed model. 10 in addition, the estimated potential total numbers of confirmed cases and key dates may provide valuable guidance for chinese central and local governments to deal with this emerging threat at current critical stage. none. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2020.02.019 . we appreciate the work tang et al. have report emergence of a novel coronavirus in china. 1 the 2019-ncov broke out in wuhan, china at the end of 2019, and has attracted worldwide attention. [2] [3] [4] although the chinese government has taken active measures to control this epidemic, the virus is very infectious. according to the real-time data of the national health commission of the people's republic of china up until february 5, 2020, within a short period of half a month, the number of confirmed cases and the number of deaths were 24,443 and 493, respectively. the epidemic is progressing rapidly. 2019-ncov poses new public health challenges in china. 5 in wuhan, china, the number of local medical staff is insufficient for the demand resulting from the explosive increase in the number of infected patients. therefore, many medical personnel are needed to devote themselves to the front line of combating the virus.medical personnel throughout the country are led under the unified leadership of the chinese government. although the epidemic in wuhan is serious, a large number of medical staff rushed to wuhan to supplement the shortage of manpower in wuhan hospitals. this is a battle without smoke, the heroes of which are our medical staff. according to the national health commission of the people's republic of china, as of january 30, 2020, hubei province opened 11,0 0 0 isolated patient beds, and about 170,0 0 0 healthcare professionals from all kinds of medical institutions are working on the front lines and providing care for patients with fevers, and for suspected or confirmed patients. in this time of emergency, under the unified deployment of the chinese government, there are 52 medical teams including 6097 medical personnel from the national key: cord-325032-3x5wklr4 authors: jiang, shanhe; zhang, dawei; irwin, darrell d. title: semiformal organizations and control during the covid-19 crisis in china date: 2020-10-30 journal: asian j criminol doi: 10.1007/s11417-020-09334-z sha: doc_id: 325032 cord_uid: 3x5wklr4 scholars often compare china and western societies in terms of dichotomous forms of control—formal and informal. recent research indicates a nuanced form of social control—semiformal. using a survey data collected during the 2020 covid-19 pandemic in china, this study investigated the prevalence and importance of semiformal organizations, formal organizations, and informal groups participating in social control and social service and the predictors of the perceived importance of these three forms of social control mechanisms. findings from this study revealed that formal organizations, the semiformal organizations, and informal groups all participated in community control and service. semiformal organizations had the highest level of participation. this study found that education and age are the two major predictors of the views on the importance of formal, informal, and semiformal control and control mechanisms. order. on january 24, hubei invoked a class 1 response to public health emergency (han 2020) . under the lockdown order and class i response, the city's public transportation services including bus, metro, and ferry services were suspended. the city's airport and railway stations were also suspended except for exceptional circumstances. residents were first advised and then ordered to shelter in place and only allowed to leave their residence for essential activities (china cdc 2020; hubei.gov 2020) . during the period of lockdown, the local community played an essential role in food supplies, health screening, collecting and distributing the covid-19-related information, supplying personal protective gear, setting up checkpoints to monitor people who enter and exit communities, made drug purchases for those who faced difficulties obtaining medicines on their own, and carried out duties of community sanitization. other major cities and provinces quickly followed suit to launch a lockdown or issue a class 1 response to public health emergency. by january 29, all 31 provinces (or equivalents) in mainland china had launched a class 1 response (caixin 2020) and followed similar measures as wuhan and the other cities in hubei province. starting on march 13, cities in hubei province, except for wuhan, rescinded strict travel restrictions, and the citizens' daily lives began to gradually return to normal. on april 8, wuhan lifted its lockdown, being the last city in hubei and china to remove such strict controls (mao et al. 2020 ). traditional classification of social control is dichotomous: formal and informal (black 1976 (black , 1993 rose and clear 1998) . formal social control is a control imposed by law and implemented by government or government agencies such as courts, police, and prisons, while informal social control is a control carried out by informal groups such as neighborhood watches and kin mediation based on moral rules (huang 1993a; jiang et al. 2007; liu et al. 2001; rosenbaum 1988) . however, when this dichotomous classification of social control is applied to china, it overlooks an important form of social control-semiformal social control (huang 1993a (huang , 1993b (huang , 2010 jiang 2014; jiang et al. 2015; jiang et al. 2019) . during the early period of china's economic reform, researcher ronald troyer visited china five times from 1982 to 1987 to observe the chinese responses to crime and deviant behavior. his visitations, observations, and conversations with chinese officials and citizens, along with his examination of news media and academic literature review impressed upon him that two grassroots organizations-the residents' committee and the residents' groups-played an important role in social and crime control. he noted, however, that "they are not voluntary association in the u.s. sense; they are government organized and controlled entities" (troyer 1989: p. 27) . although troyer did not use the terms such as semiformal governance or control, he implied that these grassroots organizations are different from those informal groups and informal control in the usa. in their article published in 1996, zhang and his associates examined the importance of tiao-jie and bang-jiao in social control and crime prevention in china. according to xiong (1999) , tiao-jie is a form of mediating disputes that is carried out by the people's mediation committee, which is under the leadership of the residents' committee in urban areas and of the village committee in rural areas. another form, "bang-jiao means assisting, helping, guiding, and directing offenders, especially juvenile offenders" (zhang et al. 1996: p. 208 ). both tiaojie and bang-jiao groups are neither completely formal nor informal control devices. they are mass-roots organizations, both imposed and heavily influenced by the government, with rules for social behavior. chen (2004) compared and contrasted chinese and western social and legal control. he found that "some informal institutions such as neighborhood committees do not form a part of the formal criminal justice system, yet they are established based on certain legal regulations and often are trained by local justice organs or police" (chen 2004: p. 524 ). thus, informal groups or organizations such as neighborhood committees in china are "quasi-formal." huang (2008) reported similar forms of social control and control mechanism. using his archival research of documents from different periods of history in china, huang (2008) revealed a form of governance in dispute resolution which differs from that in the west; he called it semiformal governance. through his archival research of the qing dynasty's (1644-1911) approach to civil justice or minor matters, huang (2008) found that many small disputes such as arguments over land, debt, inheritance, and marriage were usually resolved by interventions by the local community or kin mediation. for minor matters, only when disputes could not be resolved by the local community, the court got involved. xiangbao (乡保) played an important role in handling local issues and was the liaison between the court and the community mediation. xiangbao was an unsalaried quasi-official recommended by the local community and confirmed by the state. the court heavily relied on xiangbao's work for its decisions on dispute cases and preferred to use informal and semiformal processes to resolve them. the widespread use of an unsalaried quasi-official in the process of disputes is semiformal governance. huang (2008) also found that the semiformal governance in the late qing not only existed in civil justice but also was frequently utilized in tax administration and educational administration. in fact, semiformal governance continued to exist in the republic period and the people's republic of china (1949-present) of today. in their test of the generalizability of social disorganization theory, jiang et al. (2013) also used social and crime control carried out by residents' committees as semiformal control and examined its impact on crime. based on the survey data, they revealed that semiformal control did decrease the perceived neighborhood property crime in guangzhou, china. in 2014, jiang reviewed the conceptual and empirical articles which pertain to the forms of social and crime control and stated that semiformal control is one of the chinese characteristics in social and crime control (jiang 2014) . in 2015, jiang and his associates expanded the review of the forms of social and crime control and concurred with huang (2008) that traditional research of the forms of formal and informal social and crime control overlooked an important form of control-semiformal. semiformal control is the integration of formal and informal controls (huang 1993a (huang , 1993b (huang , 2010 jiang et al. 2015) . semiformal control positions features underlying formal control and informal control but uniquely has features neither found in informal nor formal control. control carried out by semiformal organizations is the core part of semiformal control. according to jiang et al. (2015) , "semiformal organizations integrate formal and informal organizational features; they are grassroots organizations but are marked by the government; they are nongovernmental organizations but have official power and responsibilities; they are a bridge between the state and society." (p. 290). jiang et al.'s study (2015) not only described the semiformal control features of chinese community corrections but also empirically compared and contrasted correctional staff workers (representing formal control) and community committee members (representing semiformal control) in terms of individual characteristics, views of the criminal justice system, and the supervision strategies. encompassing a number of direct observations and studies, jiang et al. (2019) summarized three forms of social control: formal, informal, and semiformal. formal social control is a "control imposed by law and/or implemented by official controlling organizations" (jiang et al. 2007, p. 262) . policing and corrections are typical examples of formal social and crime control. informal social control is a "control carried out by unofficial controlling groups based on moral rules" (jiang et al. 2007, p. 262) . shaming by family members and neighbors is an example of informal social control. collective efficacy proposed by sampson et al. (1997) is another example of informal social control acting to mediate social problems. semiformal social control is the mix of formal and informal controls (huang 1993a (huang , 1993b (huang , 2010 . based on both controlling actor and rules of control, jiang et al. (2019) defined semiformal control as controlling action that is carried out by (1) semiformal organizations based on sentiment, reason, and law, and (2) government agencies or other formal organizations based on sentiment and reason. although government agencies and other formal organizations may use sentiment and reason to help their controlling action, their primary or basic action rules are laws, policies, and formal regulations. in addition, using jiang et al.'s (2019) definition would be difficult to classify or decide whether government agencies as formal or semiformal. thus, the current study uses controlling actors as a criterion and defines semiformal control as controlling action that is implemented by semiformal organizations. semiformal social control can be manifested in diverse ways in china. for example, when a community corrections group, consisted of local justice officers, community committee members, volunteers, and family members, employs the law and regulations to re-educate and reform an offender, semiformal control occurs (jiang et al. 2015; jiang et al. 2019) . when the mediation team within a community or a grid, which is usually composed of the communist party organization building, resident's committee administration, and residential volunteers, resolves disputes between residents based on laws and local norms (tang 2020) , semiformal control occurs. more broadly speaking, when social or crime control is carried out by semiformal organizations, semiformal social control occurs (jiang et al. 2015; jiang et al. 2019 ). communities (shequ) in china are large and widespread semiformal organizations. every local residential community is administered by a resident's committee in urban areas while it is managed by a village committee in rural areas (jiang et al. 2015) . accordingly, the last type of semiformal control is the most commonly used in china's social and crime control (jiang et al. 2019) . thus, a body of literature has emerged regarding the important role that semiformal organizations play in china's social control and social services. important semiformal organizations such as residents' committees and village committees bridge government and individual citizens. the government provides services to citizens and supervises citizens through community committees. semiformal organizations and controls make it possible for the chinese government to effectively deal with emergencies or crises such as the covid-19 outbreak. however, there is limited quantitative research on the investigation of the prevalence and importance of semiformal organizations in social control and service. this study was undertaken as an academic project to glean data on the use of social control during the covid-19 pandemic. the study also intended to quantitatively explore what stated and unstated factors explain the perceived importance of control. this research formulates the first effort to search for the predictors of the importance views. since there were no clear theoretical guidelines for the predictor selection, the previous literature on the importance of social control forms were used for the variable selection employed in this study. he variables gender, age, and education are often included as demographic characteristics in the extant studies (jiang et al. 2010a; jiang et al. 2010b; jiang et al. 2012; jiang et al. 2014; lambert et al. 2012a; lambert et al. 2012b) . following suit, this study also included them. the study additionally included another characteristic-political affiliation-whether the respondent is a communist party member. this variable is essential since the party membership is expected to be in favor of formal control mechanisms such as government agencies/officers and the police. living area is another commonly examined correlate of the views of forms of social and crime control jiang and lambert 2009; jiang et al. 2012; jiang et al. 2014) . since the outbreak of covid-19 in wuhan, the virus subsequently spread across china and around the world at different points. thus, this study also included two dummy variables (wuhan; hubei) to examine whether wuhan and hubei differed from other areas in china in the views of three forms of social control and social service. as for gender, in the west, particularly in the usa, women are encouraged to think independently. due to different socializations, especially during childhood, women are more likely to use a "care voice" reasoning for their response to many social and criminal justice issues, while men are more likely to use a "justice voice" reasoning to express their opinions (gilligan 1982) . women are often linked to an empathic, caring attitude toward criminal justice issues, while men are more likely to be impartial and justice oriented ). in china, women occupy different cultural, political, and social environments. on the one hand, when china progressively becomes modernized, women receive more education and become more economically independent, and they are encouraged to think more independently. on the other hand, patriarchal tradition, collectivism, and the one-party political system all encourage, promote, or even pressure different genders to think similarly . it is uncertain whether gender affects the views of different forms of social control and social service. in the past studies about the views of formal and informal control in china, results are mixed. most studies did not find an association between gender and the views of forms of social control. when lambert et al. (2007) examined whether gender differed in 15 statements (some of them measured formal or informal control), gender did show differences in some statements but not for others. jiang et al. (2010a) reported men were more likely than women to believe that formal control such as police, courts, and incarceration is deterrent to crime. however, the sample used in jiang, lambert, and jenkins' analysis included respondents from china and the usa. clearly, more research on gender and the views of forms of social control is warranted. age is commonly believed to be positively associated with the views of social control and social service. in other words, younger people are less likely to value social control than their older counterparts are. two possible reasons behind this assumption are that younger people are freer from constraints, and younger people are more likely to self-support and be self-sufficient. three studies quantitatively examined whether age is associated with the views of informal and formal social control in china. two studies jiang et al. 2010b) revealed no relationship existed between them. one (jiang et al. 2010a ) reported a positive relationship. when a specific formal agency was evaluated, age sometimes was found to be related to the views of formal control or formal control organizations. for example, sun et al. (2017) found that age was positively related to perceived police legitimacy and cooperation with police. inconsistent findings in the previous studies invite more research on age as a variable. education is also used to predict the views of formal and informal social control but in the lesser degree, relative to gender and age. generally, education leads to more critical and independent thinking that in turn results in the less favorable assessment of the importance of formal organizations in social control and more favorable attitudes toward the importance of informal groups in social control. two empirical studies reported mixed results concerning informal social control. one study conducted by jiang et al. (2010b) found that education was not associated with the perceived importance of informal control in neighborhoods in guangzhou, china. another study conducted in hubei by jiang and lambert (2009) reported that more educated people perceived more importance of informal groups in social control but perceived less importance of formal organizations. during the covid-19 crisis, governments in each nation have played a leading role in social control and social services. at the community level, the importance of government in social control and social services may vary from society to society. political affiliation could affect the perceived importance of government and other control mechanisms in china. furthermore, chinese communist party members may have more favorable ranking of the importance of formal control mechanisms such as government agencies and police than non-party members may. in contrast, non-party members may believe that semiformal organizations such as residents' committee/village committee and volunteers are more important in social control and service at the community level. thus, this study included party affiliation to examine whether the party membership affects respondents' views of forms of social control and service mechanisms. people who grow up in rural areas are socialized differently from those who grow up in urban areas. the cultures of rural areas have more traditional values with more personal interactions and thus are more cohesive than the culture of large urban areas. people who grow up in rural areas are more likely to use and believe in informal mechanisms such as family, neighborhood, and peers in maintaining community order and providing or obtaining mutual support. jiang et al. (2007) found that compared to people from urban areas, people from rural areas were more likely to rank the importance of informal control in crime prevention higher and the importance of formal control lower in china. however, jiang and lambert (2009) did not find the connection between living areas and ranking of the importance of formal and informal mechanisms in social control or crime prevention. this study further examined whether urbanization affects people's views of the importance of forms of control mechanisms in social control and services. our research anticipated that, relative to respondents from urban areas, respondents from rural areas rank the importance of community organizations and informal groups higher in terms of social control and service. for the importance of formal organizations in social control and service, the urbanization impact may be murkier. people from rural areas have more traditional values and may have high trust and confidence in government (irwin et al. 2016) . they may be more likely or equally likely to value the importance of government agencies in social control and service relative to their urban counterparts. the last two variables included in this study are based on the unique situation of the covid-19 crisis. covid-19 was first reported in wuhan and then spread throughout china and the world. wuhan experienced the most severe public health crisis in china. accordingly, social control and service needs in wuhan and surrounding areas in hubei may also differ. people from different areas may also view the role of government agencies, police, community, volunteers, and regular citizens in maintaining community order and providing service differently. thus, this study created two dummy variables to see whether people from wuhan, hubei, outside wuhan, and other provinces have different views of the importance of three forms of social control. based on the reported covid-19 cases in china, there is clear ranking order of severity of the outbreak among these three areas: wuhan, the capital of hubei province; hubei excluding wuhan; and other 30 provinces. the research team planned to collect data from approximately 200 people from each of the three regions. semiformal control and semiformal organizations are prevalent and play an important role in china's governance including social control and social service (jiang et al. 2019) . to quantitatively verify the prevalence and the importance of semiformal control and semiformal organizations, the research team in china designed the survey instrument and conducted the surveys. the questionnaire used in the survey was designed based on the semiformal control theory proposed by jiang et al. (2019) and additional literature on formal and informal control. the first questionnaire draft was completed in march 2020 and then pretested in hubei and eight other provinces at the end of march. in the early april, the revised questionnaire was pretested again in hubei including wuhan. considering memory will be gradually lost with time, the survey organizer in china recruited 48 interviewers from wuhan, hubei, and other regions to speed up the pace of the surveys. these interviewers were a mixture of current graduate students or graduates from the organizer's school and had experience in conducting previous surveys. all the interviewers were trained on how to conduct this survey in early april. the survey began on april 3 and ended on april 18, 2020. during this period, although china lifted its lockdown orders in all areas except in wuhan, many places still had restrictions on travel or person to person interactions. thus, to collect valid data and improve the response rate, two data collection methods were employed. one method was to send the survey instrument to the interviewees via the chinese social media wechat app or other digital portals where respondents were to answer the questions by themselves. using this method, the interviewers were required to be available to answer any questions when a respondent was completing the questionnaire. doing so aimed at helping improve the completion rate for the entire survey instrument as well as each individual question. the second survey method used to collect data was via an online platform such as zoom or wechat or in face-to-face interviews. using this method, the interviewers asked questions and recorded the interviewees' responses. all the respondents were informed (1) who the survey team were; (2) the survey participation was voluntary; and (3) the data from the survey would be confidential. through this process, respondents were assured if the collected data are used for publications or reports, no individual respondents would be identified. seven hundred questionnaires (online or in print) were distributed, and 632 valid questionnaires were used in this study. successful response rate was slightly more than 90%. one of the survey's purposes was to collect data on the prevalence of formal, informal, and semiformal control or organizations in maintaining community order and providing service during the covid-19 lockdown. government agencies or officials and community police or police officers are the indicators of formal control mechanisms. volunteers and regular citizens are the indicators of informal control groups or individuals. community committees or committee members are the indicators of semiformal control mechanisms. thus, questions pertaining to the prevalence of three forms of control ask whether each of these actors participated in community control and service during the lockdown period. related to the prevalence, the respondents were also asked to judge how important each of these organizations or their representatives was in six essential community control and service activities during the covid-19 lockdown: checkpoint inspection, health screening, food supplies, drug supplies, sanitization, and information distribution. importance here refers to an appraisal of the level of involvement of a given actor. the response categories for these questions were not important at all (= 1), not important (= 2), between not important and important (= 3), important (= 4), and very important (= 5). the score summation of these six activities formed the five dependent variables for five-control-service mechanisms: community, government, police, volunteer, and citizen. independent variables in this study refer to those predictors of the views of forms of community-control-service mechanisms. they include age, sex, education, party, locationurban or rural-and two dummy variables for region: hubei and wuhan; the reference group is other regions. age was measured in years. sex was measured by male (= 1) and female (= 0). education was measured by the highest degree completed or was studying for at the interview time. the answer categories were elementary or less (= 1), junior high (= 2), high school (= 3), technical school (= 4), 3-year college (= 5), bachelor's (4-year) degree (= 6), and graduate school (= 7). party was measured by whether a respondent was the communist party member with yes = 1 and no = 0. location was measured by whether a respondent came from an urban area or rural area. the two dummy variables are hubei (= 1) and wuhan (= 1). table 1 is constructed to meet the first goal of this study: investigate the prevalence of semiformal organizations participating in social control and service during the covid-19 lockdown. the table is based on the data from the respondents' answers to this question: "during the covid-19 lockdown period, who participated in the following activities: checkpoint inspection, health screening, food supplies, drug supplies, sanitization, and information distribution." the choices included residents' or village committee, government agencies or officers, community police or police officers, volunteers, regular citizens, and no action. the respondents could make multiple choices for each activity item. in this survey, volunteers were those who registered with a residents' committee in urban areas or a village committee in rural areas to volunteer their time to help the community control and service activities. regular citizens refer to any citizens who voluntarily helped the community control and service activities but did not register with the community. visual inspection of table 1 revealed several points. first, relative to other activity items, demand for food and drug supplies via community was lower. this finding makes sense because only a small portion of people need drugs. in addition, citizens who were not infected by the virus or their neighbors in a same multi-story building who were not infected by the virus were usually allowed to go out to buy life necessities by themselves, though they were limited to one person per family at certain time periods. second, community (resident's or village) committee had the highest participation in all the activities. this finding is not surprising. according to china's residents' committee act of 1989, a community is a self-governing unit. each community has a residents' or village committee, in which members are local citizens and elected by local citizens and approved by the government (jiang et al. 2010b) . the committee has many neighborhood functions, including but not limited to "distributing and promoting laws and policies from the central government and local government, settling disputes, assisting the local police department to maintain public order, …, household registration, local sanitation and cleanliness activities, encouraging residents to practice birth control, and a variety of other services to the local residents, such as establishing senior centers" (jiang et al. 2010b, p. 462) . during the covid-19 lockdown, the residents'/village committee was instructed by the government to participate in the activities listed in table 1 . third, overall, volunteers had the second highest participation in the table 1 activities. china is a collective society, and things or activities are usually organized and done by the local community and government. however, during these lockdown times, many people volunteered their time, resources, and vehicles to help needy people in the community. this voluntary outpouring was a particularly good thing happening in this challenging time. table 1 showed that volunteers actively participated in all activities except distributing the healthrelated information. a relatively low level of participation in the activity is understandable because this information is more likely from the government. the government mobilized to address the covid-19 health crisis at multiple levels, most prominently flying in thousands of nurses and doctors from around china to wuhan and other hubei cities (xinhua news 2020). fourth and the last, the participation of community police officers in table 1 activities was not high. there were at least two reasons behind the low level of the participation. first, a community usually has one officer so their participation was not easily observed. second, the officer's major role is to assist the community committee to maintain community order. during the lockdown, outdoor activities were reduced to a minimum, and as a result, deviant or criminal behavior was also greatly decreased. thus, the officer's social control action was also lessened. in sum, formal organizations, government agencies and police, the semiformal organizations, residents' committee in urban areas and village committee in rural areas, and informal groups or individuals, volunteers, and regular citizens, all participated in community control and service. semiformal organizations had the highest level of participation during the lockdown period. table 2 is constructed to meet the second purpose of the study: investigate the importance of semiformal organizations in social control and service, compared to formal organizations and informal groups. the table presents the perceived importance of five types of actors in the six activities. consistent with the level of participation in the activities, the importance of the community committee was the highest while that of regular citizens was the lowest. in addition, community police officers were ranked relatively high in mandatory controlling items such as a checkpoint inspection and health screening and low in-service items such as helping shop for necessities and medicine. next, the importance of government agencies or officers was relatively low in shopping for necessities and medicine and relatively high in other items such as health information distribution and health screening. this finding makes sense because the governmental role at the community level was more focused on directing and supervising action implementation rather than specific action. although the government sent one or more officials to each community, their visibility to citizens was low. in contrast with government agencies or officers, the importance of volunteers in shopping for necessities and medicine was very high. their high participation or action in these activities may be the reason behind this. examining table 2 , government services acted as the superstructure providing guidance with the volunteers acted informally to meet daily needs. the findings from table 2 confirmed the importance of semiformal organizations in maintaining community order and providing community service during the lockdown period. the reported importance of semiformal organizations is higher than that of formal organizations and informal groups. tables 3, 4, and 5 meet the third purpose of the study: discover the predictors of the views of forms of social control and service. table 3 presents the descriptive statistics of the dependent and independent variables in this study. the mean score for each dependent variable in the table was created from the simple summation of scores in the six community activity items. as revealed in table 2 , the summarized mean scores in table 3 confirmed that community had the highest score, government the second, volunteer the third, police the fourth, and citizen the last. for the independent variables, about 33% of the respondents were members of the chinese communist party. almost 50% of the respondents were from rural areas while the other 50% from urban areas. more females (56%) participated in the survey. the mean age of the respondents was approximately 26. most respondents had a bachelor's degree or were studying at a 4-year college. table 4 presents the results from bivariate regression analyses of all independent and dependent variables. table 5 shows the findings from multiple regression analyses of the each of the actors in this table was ranked in terms of their importance in the six activities. the answer categories concerning the importance are not important at all (= 1), not important (= 2), between not important and important (= 3), important (= 4), and very important (= 5) effect of all the independent variables on each dependent variable. several significant relationships in table 4 disappeared in table 5 . visual inspection of tables 4 and 5 shows that education is the strongest predictor of the views of all the five control and service mechanisms: communities, governments, police, volunteers, and regular citizens. it is the only predictor that is statistically significant for all the five control and service mechanisms. one possible reason behind the finding is that people who are more educated are more critical and have higher expectations about the role each control and service mechanism should play. thus, relative to those with lower education, the respondents with higher education were more likely to give control and service mechanisms lower rankings of their level of involvement in control and service activities. next, age is a significant predictor for the views of government agencies/officials and community policing officers. furthermore, younger people had more favorable views. this is surprising. the findings are neither consistent with the expectations in this study nor the (1) the two dummy variables hubei and wuhan were entered into the regression model together. (2) results from independent t tests for comparing two means showed the same patterns as in this table regarding whether a relationship between two variables (one nominal independent variable with importance view scores) is statistically significant *p < .05, **p < .01, *** p < .005 findings in the previous studies of formal and informal control jiang et al. 2010b; jiang et al. 2010a) . do these findings suggest that younger people have more trust and confidence in government in community control and service? a further examination reveals that the mean age of the respondents is about 26. many of them have grown up at the time when china's economy developed quickly and has improving international visibility. relative to older people, they may be fortunate with no experiences of economic hardship in their life. they may be still in school and have been educated to hold a positive view of the government and china. acknowledging different lived experiences, it is worth further examining the linkages between respondents' ages and views of control mechanisms and support for government policies. another surprising finding from table 4 is that party membership was negatively associated with the importance views of government and police. that is, the communist party members ranked the importance of government and police in maintaining community order and providing community service during the lockdown lower than non-party members did. in order to explore the reason behind these unexpected findings, this study used the forward selection method to control other variables in multiple regression analyses or multi-factor anova tests. results (not shown here but available upon to request) reveal that when education was controlled for, the relationships between party and the views of government and the views of police disappeared. these findings suggest that party members had less favorable views on the importance of government and police because they were more educated. the educated party members may recognize that disasters tend to disrupt bureaucratic goals and tasks when predictable social harmony and stable growth have been put forward as party goals to the public (irwin and willis, 2013) . table 4 also shows that respondents from urban areas ranked the importance of government and regular citizens in community control and service lower than those from rural areas. a further examination (results not shown here but available upon to request) reveals that when education was controlled for, city dwelling became statistically insignificant for government, and when both education and age were controlled for, city dwelling was no longer a predictor of the views of regular citizens. a further examination also showed that education and urban life intervened in the relationship between wuhan and volunteers and partially explains the relationship between hubei province and volunteers. furthermore, when the variables education and city were controlled for, the relationship between wuhan and volunteers disappeared, findings reported in the last section are constrained; first, the sample used in this study was not randomly selected and findings cannot be generalized to the larger population with a known error, and second, due to the covid-19 pandemic, people in china had limited interpersonal interactions during the survey time period. the online questionnaire survey and interviews were important methods to collect this purposive data while the response to covid-19 was still ongoing. internet access and a certain education level were required to participate in the surveys/interviews. as a result, the respondents surveyed in this study are younger and more educated than the general population. in addition, the proportion of the chinese communist party members (33%) in this study is higher than that (8%) of the general population aging 18 and older, suggesting that party members, not intentionally, were oversampled. these sampling biases can result in the over-or underestimation of the corresponding population values. in this regard, the nature of this study is exploratory. findings from this study are preliminary rather than conclusive. nonetheless, this study contributes to the research on forms of social control and social governance in several ways. this is the first to quantitatively investigate the prevalence of formal, informal, and semiformal control and control mechanisms simultaneously. thus, the study was able to provide us with comparative results of the participation level of each organization or group and their levels of control employed in maintaining community order and providing community service during the unique covid-19 lockdown conceived in china. results from this study provide complementary evidence that semiformal organizations and control are prevalent in china's social control and governance (jiang et al. 2019 ). this study on the covid-19 response in china is also the first to quantitatively evaluate the importance of formal, informal, and semiformal control and control mechanisms in maintaining community order and providing community service. the findings regarding the conceived importance allow us to not only compare the relative importance of each form of social control and service in china but also eventually find commonalities and differences with other nations in terms of covid-19 control mechanism using the survey methods described herein. the findings regarding the conceived importance also help us understand why semiformal organizations such as residents' committee and village committee play such a prevalent part in china's social control and services. finally, this study found that education and age are the two major predictors of the views on the importance of formal, informal, and semiformal control and control mechanisms. the findings confirmed the expectation that more educated people were more critical and expected more from all forms of control mechanisms in social control and service so they ranked the importance of all forms of control mechanisms lower than less educated people. findings from this study are inconsistent with our expectation that older people are more likely to have a favorable ranking of the importance of government agencies/officials and police in social control and service. some possible reasons are explored in the "findings" section, but more research is required to examine the age-importance view linkage. with a current focus fixed on the covid-19 pandemic, these findings from citizen respondents in china, though an important contribution, are preliminary, and more relevant research is needed in the future. the behavior of law 中国内地31省份全部启动突发公共卫生事件一级响应 (thirty one provinces or equivalents in mainland china lunched a class i to public health emergency social and legal control in china: a comparative perspective notice of tightening the prevention and control covid-19 crime and crime prevention in china: a challenge to the development-crime nexus in a different voice: psychological theory and women's development 武汉时间:从专家组抵达到封城的谜之20天 (wuhan 20 days between informal mediation and formal adjudication: the third realm of qing civil justice public sphere"/"civil society" in china? the third realm between state and society centralized minimalism: semiformal governance by quasi officials and dispute resolution in china chinese civil justice, past and present notice of further tightening restrictions amid the covid-19 crisis success or sorrow: the paradoxical view of crime control campaigns in china china's social transformation and the development of rural community corrections social and crime control with chinese characteristics views of formal and informal crime control and their correlates in china correlates of formal and informal social/crime control in china east meets west: an empirical comparison of formal and informal crime control among chinese and the u.s. students correlates of informal social control in guangzhou, china neighborhoods university students' views of formal and informal control in japan: an exploratory study formal and informal control inchina social ties, collective efficacy and perceived neighborhood property crime in guangzhou semiformal crime control and semiformal organizations in china: an empirical demonstration from chinese community corrections semiformal control: a paradigm from chinese society a preliminary study of gender differences on views of crime and punishment among chinese college students correlates of formal and informal social control on crime prevention: an exploratory study among university students formal and informal crime control views in bangladesh and the united states crime and social control in a changing china 武汉解封 (wuhan lifted the lockdown order chinese social control: from shaming and reintegration to "getting rich is glorious incarceration, social capital, and crime: implications for social disorganization theory community crime prevention: a review and synthesis of the literature neighborhoods and violent crime: a multilevel study of collective efficacy procedural justice, legitimacy, and public cooperation with police: does western wisdom hold in china? grid governance in china's urban middle-class neighborhoods social control in the people's republic of china how does china combat #coronavirus: more than 20,000 medics across the country came to wuhan criminal justice systems in china crime prevention in a communitarian society: bang-jiao and tiao-jie in the people's republic of china bicycle-theft victimization in contemporary urban china: a multilevel assessment of risk and protective factors publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the authors declare that they have no conflict of interest. informed consent yes key: cord-309478-yhmgopmr authors: jin, ying-hui; huang, qiao; wang, yun-yun; zeng, xian-tao; luo, li-sha; pan, zhen-yu; yuan, yu-feng; chen, zhi-min; cheng, zhen-shun; huang, xing; wang, na; li, bing-hui; zi, hao; zhao, ming-juan; ma, lin-lu; deng, tong; wang, ying; wang, xing-huan title: perceived infection transmission routes, infection control practices, psychosocial changes, and management of covid-19 infected healthcare workers in a tertiary acute care hospital in wuhan: a cross-sectional survey date: 2020-05-11 journal: mil med res doi: 10.1186/s40779-020-00254-8 sha: doc_id: 309478 cord_uid: yhmgopmr background: many healthcare workers were infected by coronavirus disease 2019 (covid-19) early in the epidemic posing a big challenge for epidemic control. hence, this study aims to explore perceived infection routes, influencing factors, psychosocial changes, and management procedures for covid-19 infected healthcare workers. methods: this is a cross-sectional, single hospital-based study. we recruited all 105 confirmed covid-19 healthcare workers in the zhongnan hospital of wuhan university from february 15 to 29, 2020. all participants completed a validated questionnaire. electronic consent was obtained from all participants. perceived causes of infection, infection prevention, control knowledge and behaviour, psychological changes, symptoms and treatment were measured. results: finally, 103 professional staff with covid-19 finished the questionnaire and was included (response rate: 98.1%). of them, 87 cases (84.5%) thought they were infected in working environment in hospital, one (1.0%) thought their infection was due to the laboratory environment, and 5 (4.9%) thought they were infected in daily life or community environment. swab of throat collection and physical examination were the procedures perceived as most likely causing their infection by nurses and doctors respectively. forty-three (41.8%) thought their infection was related to protective equipment, utilization of common equipment (masks and gloves). the top three first symptoms displayed before diagnosis were fever (41.8%), lethargy (33.0%) and muscle aches (30.1%). after diagnosis, 88.3% staff experienced psychological stress or emotional changes during their isolation period, only 11.7% had almost no emotional changes. arbidol (umifenovir; an anti-influza drug; 69.2%) was the drug most commonly used to target infection in mild and moderate symptoms. conclusion: the main perceived mode of transmission was not maintaining protection when working at a close distance and having intimate contact with infected cases. positive psychological intervention is necessary. infection in medical institutions happens easily when a new epidemic occurs. according to who daily situation report, after the coronavirus disease 2019 (covid19) outbreak, 22,073 covid-19 cases among healthcare workers have been reported to the who as of wednesday, 8 april 2020 [1] . the number of healthcare workers infected by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) reached 1716 china wide on february 11, 2020; among them, 1502 cases were in hubei province; with 1102 in wuhan [2] . as of early march, the infected number increased to 3300 and at least 22 died in china, and there were over 2600 infected with 13 died in italy as of 20 march, 2020 [3] [4] [5] . reports from medical staff describe physical and mental exhaustion, the torment of difficult triage decisions, and the pain of losing their patients and colleagues, all in addition to the infectious risk. healthcare workers are the pillar for fighting against this pandemic; hence, preventing them to be infected is a big challenge for maintaining a strong fighting force, high morale, and energy for fighting. now to protect healthcare workers away from infection has aroused great concern, many experts published opinions [3, 4, [6] [7] [8] [9] [10] to appeal to worldwide for paying attention to protect health care workers from woefully unprepared status. on 2 march 2020, lai et al. [11] reported mental health of 1257 healthcare workers treating patients exposed to covid-19 in 34 hospitals in china. results showed that they experienced psychological burden, especially nurses, women, those in wuhan, and frontline healthcare workers directly engaged in the diagnosis, treatment, and care for patients with covid-19. another qualitative study released 18 february 2020 suggested that maintains healthcare workers' mental health is essential to better control infectious diseases [10] . obviously, there is no study concerned about the infected healthcare workers with covid-19 and their mental health. therefore, we conducted this epidemiological investigation and aimed to explore the route of sars-cov-2 infection, influence, and management procedures of healthcare workers. we also believe our work will provide factual evidence and lessons learned can be used to prevent such infections in the future. this is a cross-sectional and single center study, using data of all 105 infectious healthcare staff from zhongnan hospital of wuhan university. 105 healthcare staff became infected before january 30, 2020, our study period was from february 15 to 29, 2020; and no new staff became infected until now. this study was reviewed and approved by the committee for ethical affairs of this hospital. all 105 healthcare professionals who were recorded in the division of medical affairs of confirmed covid-19 diagnosis were invited to finish the questionnaire. confirmation diagnosis was according to the diagnostic criteria of the national health committee of the people's republic of china (cnhc) [12] . we divided the departments represented in this study into two groups: high risk of nosocomial infection departments (hrds) and low risk of nosocomial infection departments (lrds) according to general principles for the management of nosocomial infection control of cnhc [13] and infection control expert opinion from this project group. hrds included departments of respiratory medicine, infectious diseases, emergency, clinical laboratory, anesthesia surgery, operating room, and intensive care unit; all other departments were categorized as lrds (fig. 1a) . all staffs were working in their normal departments and no one had been redeployed to other areas at the time of the survey. we employed a self-administered electronic tool to collect data using our validated questionnaire which included informed consent (see additional file 1). after readability and content validity test, the testretest reliability coefficient of our electronically administered questionnaire was 0.82 (1 = perfect repeatability) [14] . we also cross-checked information was from other sources. epidemiologic data were confirmed through phone calls to all participants, and we checked electronic patient records for collecting treatment information. additionally, our investigators also held tele-interviews with the department directors of infected ones where necessary, to determine exposure status of all staff in the week before sars-cov-2 infection. we conceptualized a research framework initially based on the following: 1) online interview or a free response set of questions to explore infection prevention and control experiences of covid-19 among frontline clinicians from the office of nosocomial infection control. 2) policy documents, guidelines or consensus for this epidemic or general prevention of infectious disease, such as notice on the issuance of a program for prevention and control of sars-cov-2 infection from the cnhc. samples presented were all from zhongnan hospital of wuhan university. zhongnan hospital of wuhan university is a 3500 bedded tertiary acute teaching hospital which has more than 800 doctors and 1800 nurses. this hospital is equipped with 46 clinical and medical technology departments, 17 teaching and research departments and 1 laboratory. zhongnan hospital of wuhan university is one of the key hospitals at the epicentre of this outbreak, and had treated 952 hospitalized patients with covid-19 between january 1 and march 12. samples selection in this study was not limited by departments of professional staff. we contacted all infected professional staff according to the hospital's records (n = 105). electronic questionnaires were sent to all infected staff member and send a message by mobile phone to reminder, and they were free to choose whether take part in or not; if unwilling, the can click "do not agree to participate in this research" bottom (see additional file 1). categorical variables were described as frequencies and percentages, continuous variables were showed as mean ± standard deviation (sd) or median (25-75% percentile) as appropriate. to assess the changes before and after covid-19 outbreak, mcnemar tests were performed for the change of training level, wilcoxon signed rank sum tests were conducted for the mastery level for knowledge of protective procedures which were measured using a likert scale. all analyses were carried out using the sas software (version 9.4 ts1m6, sas institute inc., cary, nc, us). twosided p values less than 0.05 were considered statistically significant. the data were visualized by microsoft 2019. all 105 infected medical staff with covid-19 in our hospital was invited, finally 103 cases agreed with the consent and finished our questionnaire was included for analysis (response rate: 98.1%), table 1 presented their basic characteristics. of them, 71 worked in lrds and 32 in hrds (fig. 1a) , the median age was 35.0 years, 41 were doctors (39.8%), 55 were nurses (53.4%), and 7 were medical technicians (6.8%). 39 (37.9%) were males and 64 (62.1%) were females. figure 1b presented the perceived routes of infection. among the 103 responders, 87 (84.5%) cases thought they were infected by the working environment in hospital, one (1.0%) thought infection was due to the laboratory environment with biological specimens of suspected or confirmed patients, and 5 (4.9%) thought they were infected in daily life or community environment. of the 87 staff who thought they were infected by the working environment in hospital found, 64 (73.6%) had close contact with confirmed patients, 15 (17.2%) had close contact with suspected patients, and 36 (41.4%) were exposed to their confirmed colleagues (fig. 1c) . among 103 infected staff, 46 (44.7%) had worked more than seven hours a day in an environment that posed a risk of them becoming infected (fig. 1d ). the top three perceived infection routes were: droplet transmission, contact transmission, and aerosol transmission (fig. 1e ). for nurses, the top three perceived infection causing procedures were sputum suction care, basic nursing, and pharyngeal swab collection (swab of throat) (fig. 1f ). for doctors, the top three procedures were physical examination, tracheal intubation, and manual ventilation before intubation (fig. 1g ). forty-three staff perceived protective equipment problems as the cause of their infection. of them, 44.2% believed infection was caused by inadequate provision of protective equipment, and another 32.6% considered it was due to insufficient protection provided by the personal protective equipment (ppe) they had (wearing only surgical mask to contact confirmed cases). use of protective equipment before covid-19 outbreak table 2 shows healthcare staff's retrospective account of the level of use protective equipment in their routine work before this outbreak. 77.7% staffs always strictly followed hand hygiene, and 53.4% always strictly followed the procedure for wearing and removing of protective equipment. among 103 staff, 66.0% always wore masks and 51.5% wore gloves in their routine work. the utilization of more sophisticated protective equipment in routine work was no higher than that of common protective equipment. we found there were table 2 also demonstrated the use of protective equipment in lrds and hrds. in routine work, utilization of masks (96.9% vs. 52.1%) and gloves (78.1% vs. 39.4%), strict hand hygiene procedure (81.3% vs. 76.1%), and wearing and removing protective equipment (84.4% vs. 39.4%) in hrds were much higher than those in lrds. for more sophisticated protective equipment, the utilization in routine work in hrds was also much higher than those in lrds. figure 2a and b presented types, layers, and length of masks and gloves usage by all participants (frequency), lrds and hrds (percentage). in their routine work, medical surgical masks were more often used than other types, and staffs in lrds were more likely to use medical and disposable surgical masks. however, those in hrds tended to use kn95 and n95 respirators. medical rubber examination gloves were used frequently. single layer and one-time use of both mask and glove were the main choices. of the 103 responders, symptoms were fever (48.5%), lethargy (42.7%), muscle aches (35.9%), and dry cough (34.0%) with a few of them having gastrointestinal symptoms (such as diarrhea, nausea and vomiting). in addition, the top three initial symptoms displayed before diagnosis were fever (41.8%), lethargy (33.0%), and muscle aches (30.1%), see fig. 3a . as shown in fig. 3b , among the infected cases who knew their results, 39.5% had decreased lymphocytes and 24.1% reported decreased white blood cell, but 31.8% reported increased c-reactive protein. platelet, alanine aminotransferase, aspartate aminotransferase, creatine kinase, and d-dimer remained almost normal. a total of 102 (99.1%) staff had ct chest examination, of which 82 were abnormal. all the 103 (100%) infected ones had nucleic acid test and 82.0% had at least one positive result or at least one suspected positive result; however, 18.0% of them had negative results. when confirmed as covid-19, all the 103 cases were divided into 2 classes, of which 98 cases presented with mild/moderate clinical stages and 5 were severe clinical stages, we had on one presenting as a critical stage. in mild/moderate cases, 12 of them received oxygen therapy, 86 received antiviral therapy, 23 received traditional chinese medicine (tcm) treatment, three developed into severe or critical stages after admission, but none were transferred to icu before the study closed. among the 86 staff receiving antiviral treatment, the most common antiviral drug was oseltamivir; some also received interferon, lopinavir / ritonavir and ribavirin, but none received peramivir. the majority of them received arbidol (umifenovir; an anti-influza drug used in china; 69.2%), followed by immunoglobulin (19.2%) and vitamin c (16.4%). all eight severe/critical stage cases received hormone and antibiotic treatment, three received interferon, three received antiviral therapy, one received noninvasive mechanical ventilation, and none of them received tcm treatment, extracorporeal membrane oxygenation (ecmo), or endotracheal intubation. all of 103 cases were isolated immediately after diagnosis: 47 were in the designated hospital, 38 at home, six at centralized isolation points, and 12 in other places (hotel, infection department in hospital and a mixture). of the 38 who isolated at home, 76.3% wore a mask at home, 89.5% did not go out during the isolation period, and 71.1% changed their masks in less than 8 h, 68.4% of them lived alone during home isolation, most took their temperature regularly at home, washed and disinfected their hands frequently, and had independent eating utensils. of the 65 who were not isolated at home, 95.4% received medical treatment immediately after diagnosis, and 98.5% were not accompanied by their family members during hospital isolation; 96.9% of them thought their quarantine location was disinfected daily, and 98.5% were satisfied with the isolation environment. prevention and control knowledge training before and after the outbreak before the outbreak of the 103 responders, 78 knew the covid-19 transmission route; and knew most of prevention and control information of covid-19 (with a correct rate > 90%), whereas the accuracy rate for "the window should be closed tightly in the general ward" (usually more than one patients in one sickroom in china) was only 57.3% (table 3) . compared with before outbreak, there was a focus on "wearing protective clothing", "wearing goggles or face shield", "isolation of suspected infectious patients", and "wearing isolation clothes". the training in these areas was significantly intensified (p < 0.05). conversely the training intensity of "hand hygiene" (98.1% before vs. 92.2% after) and "wearing gloves" (96.1% before vs. 90.3% after) was significantly decreased somewhat after outbreak. (table 4) . compared with before outbreak, the level of awareness of information related to "isolation of suspected infectious patients", "environmental cleaning and disinfection", "wearing goggles or face shield", "wearing protective clothing", and "wearing isolation clothes" has been significantly increased since the outbreak (p < 0.001), while the high level of awareness of "hand hygiene" and "wearing gloves" were only slightly enhanced (table 5) . results of these staffs' opinions regarding improvements needed for fighting nosocomial infection showed that: 84.5% chose "medical staff protection", followed by "emergency plan and work flow" (68.0%) and "pay attention to the health of medical staff" (66.0%); more than half believed further attention was needed in "infection outbreak management", figure 4 presents their psychological status. before they were diagnosed with infection, 49.5% said that they were fully aware of the seriousness of the situation, 64.1% remained neutral, 31.1% were anxious, 20.4% maintained an optimistic attitude, and only a few were fearful or pessimistic. after diagnosis, 88.3% staff experienced psychological stress or emotional changes during their isolation period, only 11.7% had almost no emotional changes. of the 88.3% ones, their psychological stress or emotional fortunately, they all took effective measures to control their emotions or stress, 75.8% staffs had actively expressed their psychological stress. the ways they used include self-regulation, communicating with others on wechat, and video call with family or colleagues. protecting medical professionals from infection is crucial to success in fighting covid-19. however, cluster outbreaks occurred in many departments in this study, for 9 departments had more than five cases. more than half of the infected staff had close contact with confirmed or suspected patients in their department or work environment before they knew the true status of sars-cov-2. during early january 2020, patients having fever and coughs were scatted throughout many hospitals across wuhan, just when influenza and common pneumonia rates are high and they were all treated in the same way. at that time most medical staffs usually used ordinary medical masks without any other medical equipment during these patients' diagnosis and treatment [15] . reports showed human-to-human transmission of sars-cov-2 was confirmed by the infection of 15 healthcare professionals after close contact with infected patients in a wuhan hospital [16] . for nearly a month, neither the public nor healthcare professionals were clear about all the characteristics of covid-19. during that time many medical staffs were not taking enhanced personal protective measures. our results were confirmed repeatedly by cross-checking information from the departments' directors of infected hospital workers and participants. lack of effective protective measures during the early stage is an important risk factor, and the main reason for transmission was failure to protect people working at a close distance and having intimate contact with infected patients. the prevention and control plan before diagnosis can help to explain this. only a fifth of infected staffs were routinely equipped with protective face shields, clothing or shoe covers. most of them just wore the usual protective equipment. in addition, improper use of ppe (e.g., repeated use of masks) is also a factor involved in increasing the infection risk [4] . with the continuous occurrence of confirmed infections during january 2020, the hospitals and government of wuhan introduced strategies and policies to improve the management of patients and protection of medical staff. the personal protection awareness of medical staff increased rapidly and the number of confirmed cases decreased rapidly during february 2020. we conducted an in-depth telephone interviews for cases confirmed in february 2020. for infected healthcare professionals beyond the concentrated outbreak period in january 2020, we cannot rule out that they may have experienced a longer incubation period before they were diagnosed as covid-19. in addition, some confirmed cases had worked in the frontline for a long time maybe leading to a lowered resistance to infection. the interview information showed that the last case we included is a frontline nurse who had been engaged in combating covid-19; she claimed that she was fully equipped by uniform standards at work, and she had frequently conducted cpr for confirmed patients before her own infection was confirmed. she believed that she was infected by confirmed patients, but was not sure about exactly when or which patient was involved. moreover, the first group of infected medical staff also forms part of the chain of transmission of nosocomial infections. 39 cases in our study suggested that their route of infection may be "close contact with colleagues who were subsequently", but they were infected during the early stage of epidemic. generally, we believe that physical examination poses a relatively lower infection risk than tracheal intubation or tracheotomy, but physical examination was selected by the highest proportion of infected doctors. in our study, nine infected doctors in the hepatopancreatobiliary surgery department, which is a lrd for nosocomial infection, reported that physical examination is the most likely cause of their infection. from tracking their questionnaire data we found that inadequate protective equipment and insufficient protection of protective equipment were frequently selected. the percentage of staff selecting "personal protective equipment used more often" was higher in hrds than lrds in routine work. this is maybe the reason why more infected cases appeared in lrds. however, we can only hypothesize why this occurred, because normally people don't use sophisticated infection control procedures routinely in lrds and to do so would be poor use of resources and also frightening for the public. as the above emphasizes, the main mode of transmission was failure to maintain protection when working at a close distance and having intimate contact with infected cases. for epidemics, like covid-19, protection for low exposure risk procedures should be upgraded, and medical protective masks, protective face shield/ screens and protective clothing are also needed especially in the emergency or infectious diseases department or when caring for high risk patients [12] . training in knowledge and skills for prevention and control covid-19 for healthcare providers is important [10] , especially as professor chen wang believes that sars-cov-2 may turn into a chronic disease and coexist with humans like the flu [17] . therefore, in order to cope with the long-term existence of sars-cov-2 and possible public health emergencies in future, health care workers should receive annual training on the use of personal ppe and additional education during surge events [4] . the learning and dissemination of epidemic prevention knowledge and skills should be increased not only for medical areas but for all the public. the areas of personal protection, emergency planning and work flow should be improved. shortages of ppe that intensify fears of coronavirus exposure at work contribute to the psychological distress or other illness. stable and adequate ppe supply is highly recommended even the time without pandemic. administrators in hospital mustensure that their staff feel safe, respected, prepared, and supported [4] . in addition, basic rules should be stressed, such as emphasizing hand hygiene, installing barriers to limit contact with patients at triage, prioritizing respirators for aerosol generating procedures and self-monitoring for signs of illness and self-isolating and reporting illness to managers, if it occurs [18, 19] . to sustain and restore frontline health care workers, health care organizations need to monitor the mental health outcomes of healthcare personals over time and prioritize the mental and physical health needs and recovery of first-line healthcare professionals [20] . understanding how workers are exposed to the virus will be essential to protect frontline healthcare staff. but, little knowledge is known about the presence of the virus contamination on surfaces in hospitals and concentration of virus in the air. this lack of evidence means we are using a precautionary approach which often results in our applying all available controls all the time. it also means that resources are used unnecessarily, possibly leading to shortages for workers in particular e. willingness to express psychological stress or emotional changes; f. methods to regulate their stress or mood changes; a-b, psychological status before diagnosis; c-f, psychological status after diagnosis environments where they could provide protection [21] . research about better ways of protecting workers from the virus is still needed. the major limitation of this study is estimating the exact reason of infection for some cases is not an easy thing, and some memory biases maybe exist among participants. participants usually pondered over the causes of infection. they could overstate the protection measures they were using before their diagnosis because they are reluctant or unwilling to believe that this is how they got infected. effective protective measures were generally lacking in hospitals in the early stage of covid-19. the main factor affecting transmission was not using protecting equipment when working at a close distance and having intimate contact with infected persons. most staff experienced psychological stress or emotional changes during their isolation period a after diagnosed. protective equipment should be upgraded in hospital at the onset of a new disease especially for staff conducting procedures involving close contact and caring for high risk patients. also, learning from these lessons is expected to help the chinese government and other parts of the world to better respond to future unexpected infectious disease outbreaks. supplementary information accompanies this paper at https://doi.org/10. 1186/s40779-020-00254-8. over 22,000 healthcare workers infected by covid-19: who xi: protection, care for health workers a priority covid-19: protecting health-care workers protecting health care workers against covid-19-and being prepared for future pandemics li wenliang, a face to the frontline healthcare worker. the first doctor to notify the emergence of the sars-cov-2, (covid-19), outbreak protecting health care workers during the covid-19 coronavirus outbreak -lessons from taiwan's sars response how to train the health personnel for protecting themselves from novel coronavirus (covid-19) infection during their patient or suspected case care managing mental health challenges faced by healthcare workers during covid-19 pandemic covid-19 and the risk to health care workers: a case report mental health care for medical staff in china during the covid-19 outbreak factors associated with mental health outcomes among health care workers exposed to coronavirus disease 2019 national health commission of the people's republic of china. accreditation regulation of control and prevention of healthcare associated infection in hospital development and preliminary validation of questionnaire for infection process and prevention of 2019 novel coronavirus infection in medical staffs reflections on the present response to the pneumonia associated with a novel coronavirus (2019-ncov) emergence of sars-like coronavirus poses new challenge in china covid-19) outbreak: rights,roles and responsibilities of health workers, including key considerations for occupational safety and health interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease 2019 (covid-19) in healthcare settings mental health needs of health care workers providing frontline covid-19 care protecting workers from covid-19 we extend special thanks for the contribution of consultant experts and healthcare practitioners from all hospitals for their participation.authors' contributions xhw, xtz had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis; yhj, xtz designed this study; yhj, qh, lsl, bhl hz, td and yw collected all questionnaire data and conducted qualitative research; qh, zyp, yfy, zmc, xh and zsc analysed and interpreted data of this study; yhj, qh, lsl and yyw drafted the manuscript; xhw, yfy, nw, mjz and llm made critical revision of the article for important intellectual content; xhw got the funding for this study; xhw, xtz and yw gave administrative, technical or logistic support for conducting this study; all authors agreed with the results and conclusions of this article. all authors read and approved the final manuscript. this work was supported by the emergency science and technology project in hubei province (2020fca008). the authors had complete control over the design, conduct, and analysis of the study and the decision to submit the manuscript for publication. the datasets used and/or analyzed during the current study are available from the corresponding author on request.ethics approval and consent to participate written informed consent was obtained from each participant (see additional file 1). this study was reviewed and approved by the committee for ethical affairs of zhongnan hospital of wuhan university. not applicable. the authors declare that they have no competing interests. key: cord-312399-7oaerpee authors: park, joo-hyun; jang, wook; kim, sang-woo; lee, jeongjun; lim, yun-sung; cho, chang-gun; park, seok-won; kim, bo hae title: the clinical manifestations and chest computed tomography findings of coronavirus disease 2019 (covid-19) patients in china: a proportion meta-analysis date: 2020-05-01 journal: clin exp otorhinolaryngol doi: 10.21053/ceo.2020.00570 sha: doc_id: 312399 cord_uid: 7oaerpee objectives: the objectives of this study were to identify the clinical features and chest computed tomography (ct) findings of coronavirus disease 2019 (covid-19) patients and to compare the characteristics of patients diagnosed in wuhan and in other areas of china by integrating the findings reported in previous studies. methods: we conducted a proportion meta-analysis to integrate the results of previous studies identified in online databases, and subsequently compared the overlapping of 95% confidence intervals (cis) between locations of diagnosis. the heterogeneity of the results of the included studies was also demonstrated. results: nine studies with level iv evidence were considered to be eligible for the meta-analysis, and a comparative analysis was only possible between patients diagnosed in wuhan and outside of wuhan in china. fever (84.8%; 95% ci, 78.5% to 90.1%) was identified as the most common clinical manifestation in all covid-19 patients, and signs of respiratory infection were also frequently present in these patients. when comparing the clinical features according to the location of diagnosis, fever and dyspnea were less frequent in patients diagnosed outside of wuhan (fever: 78.1%; 95% ci, 73.2% to 82.7%; dyspnea: 3.80%; 95% ci, 0.13% to 12.22%) than in patients diagnosed in wuhan (fever: 91.7%; 95% ci, 88.0% to 94.8%; dyspnea: 21.1%; 95% ci, 13.2% to 30.3%). the chest ct findings exhibited no significant differences between the groups. conclusion: fever was found to be the most common symptom in covid-19, and respiratory infection signs were also commonly present. fever and dyspnea were less frequently observed in the patients diagnosed outside of wuhan, which should be considered in covid-19 screening programs. these results may be attributable to the earlier diagnosis of the disease and the younger age of patients outside of wuhan although further analysis is needed. the role of chest ct in covid-19 diagnosis is inconclusive based on this study. during the short period of approximately 3 months since coronavirus disease 2019 (covid19) was first reported in the city of wuhan, hubei province, china at the end of december 2019, this disease became a pandemic, with large-scale outbreaks in china, south korea, iran, and europe [1] [2] [3] [4] . although the world health organization declared covid-19 to be a public health emergency of international concern on january 30, 2020 [5] , the number of patients diagnosed with covid-19 in europe, the united states, and south america exploded in march 2020 [6, 7] . the reproductive number of covid-19 estimated from previously reported studies, representing the average number of new patients infected by a patient in a naïve population, is over 3, which is considerably higher than those of severe acute respiratory syndrome and middle east respiratory syndrome (mers) [8, 9] . covid-19 is mainly diagnosed by using real-time reverse transcription-polymerase chain reaction (rrt-pcr) to detect severe acute respiratory syndrome coronavirus 2 (sars-cov-2) rna in samples obtained through nasopharyngeal or oropharyngeal swabs [10] [11] [12] [13] . although rrt-pcr for covid-19 was initially developed within 2 weeks after the emergence of the disease, this test cannot be performed on all suspected patients because covid-19 has rapidly spread beyond the capacity for testing [14] . thus, proper screening for the disease and isolation of suspected patients performed by the physicians and healthcare providers who first come into contact with them is the most important step in controlling this highly infectious disease, meaning that awareness and knowledge of the clinical features of co-vid-19 are necessary for physicians and health-care providers [15] . the most common symptom in patients diagnosed with covid-19 is known to be fever, which is frequently accompanied by coughing or difficulty in breathing [16, 17] . however, some covid-19 patients demonstrate no symptoms or complain of only gastrointestinal (gi) symptoms; furthermore, the clinical features of covid-19 patients diagnosed outside of wuhan, china differed from those of patients diagnosed in wuhan [18] . therefore, additional diagnostic clues for covid-19 have been investigated; promisingly, chest computed tomography (ct) has recently been reported to detect lung changes caused by covid-19 before the occurrence of symptoms [19, 20] . within only 2 months since the first report of covid-19, hundreds of reports related to covid-19 have been published in reputable scientific journals. at this point, it is impossible to conduct a randomized clinical trial or a well-designed prospec-tive study on the diagnosis and treatment of covid-19, as only a short time has passed since this new disease emerged. proportion meta-analysis is a statistical technique that provides integrated information in the absence of studies with a high level of evidence [21] [22] [23] [24] . it should be kept in mind that this technique provides a relatively low level of evidence compared to other types of meta-analysis, as it generates results from studies with low levels of evidence, such as case series or observational studies [23] . however, this technique is expected to provide more integrated information about covid-19 for health-care providers than is provided by extant studies in isolation. since the first report in wuhan, the medical environment surrounding covid-19 has undergone many changes, including increased awareness of the disease and the dissemination of diagnostic kits. thus, it is expected that there will be changes in the clinical features of patients diagnosed with covid-19, and identifying such differences will help health-care providers better understand and diagnose this disease. the objectives of this study were to identify the clinical features and chest ct findings of covid-19 patients and to compare the characteristics of patients diagnosed in wuhan and in other areas by integrating the findings reported in previous studies. this study was conducted under the recommendations of reporting items for systematic reviews and meta-analyses. this study was performed by two teams for rapid review, one team was in charge of the survey and collection of included studies, and the other team was in charge of quality assessment of the included studies. each team consisted of two main reviewers and a supervisor who adjusted the disagreements of the review results. for rapid review considering the urgency of a target disease for analysis, all types of the article what identified in the online databases were considered as candidates for inclusion in the study. on march 17, 2020, two reviewers (ysl and wj) searched the online databases of the u.s. national library of medicine (medline) and excerpta medica (embase) for identifying reports published in english that used the terms: covid-19; sars-cov-2; and novel coronavirus 2019. the titles, abstracts, and authors' information were saved into excel files, and later screened by two reviewers. all type of reports in the english language that contained the descriptions of clinical features and ct findings except for the review articles were included in a data-set for detailed review, and two reviewers included only studies with data on four or more patients (case-series, cohort, or observational study) into the data-set to provide a higher level of evidence fever was found to be the most common clinical manifestation in all coronavirus disease 2019 (covid-19) patients. fever and dyspnea were less frequent in patients diagnosed outside of wuhan than in those diagnosed in wuhan, which may be attributable to the earlier diagnosis of the disease and the younger age of patients outside of wuhan. since there were no significant differences in pathologic patterns and their distribution on chest computed tomography (ct) between the patients diagnosed in wuhan and outside of wuhan, the role of chest ct in the diagnosis of covid-19 is inconclusive based on this study. [25] . published editorials and letters to editors were also considered as candidates for the study to a maximum extent possible. in the review process (the assessments of study eligibility), to minimize the risk of duplicating data in this analysis [26] , only the largest study was included if the duration of patient inclusion overlapped among reports from the same hospital. if data were reported from the same hospital without information about the date of patient inclusion, this study was also eventually excluded. all data were collected using identical forms to minimize the variability of reviewers, and disagreements of in the review results were adjusted by the third reviewer (jl). the extraction of data from included studies was independently conducted by two reviewers. name of the first author, the origin of reports including hospital and province, the initial date of patient inclusion, and the number of patients included were recorded in the microsoft excel database. demographic data, symptoms of patients, and chest ct findings were extracted. the results were categorized into the regions where covid-19 patients were diagnosed as follows: wuhan, outside of wuhan in china, and other country groups. quality assessments of included studies were independently performed by two reviewers (professors of college of medicine, cgc and swp), who did not participate in the data review process, using a quality assessment tool for case-series study from the national institutes of health, which consisted of nine questions (supplementary table 1 ) [27] . the disagreements in the quality assessment were also discussed by a third reviewer (jl). the results of the quality assessment were represented in a fair, good, and poor grouping to assist in the understanding of this study. proportion meta-analysis was conducted to determine the clinical features and chest ct findings of covid-19 patients; subsequently, clinical and chest ct characteristics of patients were compared after the areas diagnosed with covid-19 were classified as wuhan, outside of wuhan in china, and other countries. we used a random-effect model provided by medcalc statistical software due to the presence of uncontrolled variables of included studies. all results were represented as a forest plot with the horizontal bar corresponding to the 95% confidence interval (ci) of the effect estimates, and overlap of 95% ci was defined as the absence of difference among the groups in the comparative analysis [28] . i 2 test and cochran q were used for evaluating heterogeneities of the results belonging to analysis. i 2 lied between 0% to 100% and additional descriptions were made if they complied with the criteria described as follows: low (<40%), moderate (30%-60%), and considerable (75%-100%), retrospectively [29] . this parameter stated the percentage of variability in effect estimates calculated from heterogeneity. cochran q test is the parameter computed by summing squared deviations of the estimate of each study, and the parameter of <0.10 determined the heterogeneity [30] . although we described these two parameters for measuring heterogeneity, i 2 which is not affected by the number of included studies for meta-analysis was considered as a more appropriate parameter for the evaluation of heterogeneity in this study [30] . the publication bias among included studies was determined when the p-value was <0.05 on egger's regression test [31] . forest plot calculated by medcalc was redrawn using microsoft excel program (microsoft, redmond, wa, usa) for easy interpretation of figure [32] . chi-square test was used to compare the compositions of gender among groups. in total, 783 abstracts and titles were identified and screened, and 102 abstracts were excluded in this step as they were not written in english. additionally, abstracts presenting clinical features and chest ct findings from four or fewer patients were excluded. eighty-seven reports were completely reviewed, and studies that were likely to present duplicate patient data were also excluded. finally, nine studies (four studies reporting findings from wuhan and five studies reporting findings from outside of wuhan in china) with level iv evidence (case series, observational studies, or cohort studies) were eligible for the meta-analysis ( fig. 1 ) [33] [34] [35] [36] [37] [38] [39] [40] [41] . as only one study each from south korea and europe described the clinical features and chest ct findings of patients from outside china, a comparative analysis was only possible between patients diagnosed in wuhan and outside of wuhan in china. information about 627 patients (male, 345; female, 282) diagnosed with covid-19 was obtained from nine studies (table 1) . however, it was not possible to consistently present the mean or median age of the included patients because five studies reported age as a median value and four studies reported age as a mean value. there was no significant difference in the sex ratio between the two groups (p =0.157) upon chisquare analysis. among the clinical features described in the included studies, fever, cough, sputum, dyspnea, myalgia, fatigue, and gi symptoms were available for meta-analysis and comparisons ( table 2) . comparisons of chest ct findings were possible for pathologic findings (ground-glass opacity [ggo] and consolidation) and the distribution of abnormal findings (single lobe, multiple lobes, and both lungs) ( table 3) . laboratory findings (leukocytosis, leukopenia, and decreased lymphocyte count) could also be analyzed, as demonstrated in supplementary table 2 . clinical features covid-19 was diagnosed despite the absence of symptoms in 4.1% of the patients (9/242) from outside of wuhan (table 2) . fever (84.8%; 95% ci, 78.5% to 90.1%; i 2 =73.6%) was the most common symptom of covid-19, followed by cough (52.0%; 95% ci, 34.1% to 69.7%; i 2 =95.0%) ( fig. 2a and b) . sputum and dyspnea were only present in 21.3% (95% ci, 17.2% to 25.7%; i 2 =0%) and 10.4% (95% ci, 2.0% to 24.5%; i 2 =88.87%) of patients, respectively (fig. 2c ). myalgia and fatigue were present in 27.3% (95% ci, 16.6% to 39.4%; i 2 =87.6%) and 16.7% (95% ci, 10.4% to 24.2%; i 2 =72.5%) of patients, respectively. gi symptoms were reported by 11.6% (95% ci, 7.7% to 16.1%; i 2 =54.6%) of patients (fig. 2d) . in a comparison of symptoms between the patients diagnosed in wuhan and outside of wuhan, fever was more frequently observed in the patients diagnosed in wuhan (91.7%; 95% ci, 88.0% to 94.8%; i 2 =17.94%) than in those diagnosed outside of wuhan (78.1%; 95% ci, 73.2% to 82.7%; i 2 =0%) (fig. 3a) . (fig. 3b) . however, no significant difference was observed in the frequency of sputum between the wuhan group (23.33%; 95% ci, 18.1% to 29.1%; i 2 =0%) and the non-wuhan group (17.7%; 95% ci, 11.5% to 24.9%; i 2 =0%). the chest ct findings of the included studies are presented in within only 3 months after it was first reported in china, the covid-19 pandemic has spread to south korea, iran, italy, and the united states, and the number of patients worldwide has rapidly increased [6, 7] . since covid-19 is estimated to be more infectious than mers and more fatal than influenza, physicians and health-care providers should actively work to diagnose co-vid-19 and to keep covid-19 patients in isolation to minimize the spread of the disease and prevent deterioration of the current situation. although covid-19 is diagnosed using rrt-pcr tests, proper screening conducted by health-care providers is the most important prerequisite for controlling the spread of cov-id-19, as diagnostic capacity and accessibility of medical care differ from country to country [15, 42] . patients' symptoms are important clues for the diagnosis of a disease, and the same is true for the screening of diseases [15] . essentially, all the relevant guidelines recommend that symptoms and epidemiological risk (history of contact with covid-19 patients and history of visits to pandemic-affected areas) should be considered as part of covid-19 screening [7, 12, 43, 44] . according to the centers for disease control and prevention, screening for covid-19 should be based on the presence of symptoms of fever, cough, and shortness of breath [12] . the most common symptom in patients diagnosed with covid-19 was fever (84.8%; 95% ci, 78.5% to 90.1%; i 2 =73.6%), which was frequently accompanied by cough (52.0%; 95% ci, 34.1% to 69.7%; i 2 = 95.0%). in addition, 21.3% and 10.4% of patients complained of sputum and dyspnea (other signs of respiratory infection). moreover, myalgia (27.3%) and fatigue (16.7%), which are symptoms of inflammation due to sars-cov-2, were also less common than fever and cough. although all of symptoms mentioned above, except sputum, exhibited significant heterogeneity, fever accompanied by the signs of a respiratory infection can be considered as a reasonable parameter for suspecting covid-19, especially in patients with epidemiological risk, as has been recommended by many guidelines [7, 12, 43, 44] . interestingly, over 10% of patients in the present study complained of gi symptoms. gi symptoms are thought to be a characteristic of sars-cov-2 infection, especially in light of the previous finding that over 30% of mers patients complained of gi symptoms [45] . recently, olfactory and gustatory dysfunction as determined by a questionnaire evaluation has been observed in 85% of mildto-moderate covid-19 patients in europe; the reported frequency of this symptom is therefore similar to that of fever and higher than that of cough in the present study [46] . thus, physicians, especially otorhinolaryngologists, should be aware of these symptoms, in addition to fever accompanied by the signs of respiratory infection, as a possible clinical presentation of covid-19. olfactory and gustatory complaints were the initial symptoms in approximately 15% of covid-19 patients, and 11.8% of patients complained of only olfactory changes without other nasal symptoms [46] . however, we could not find any information on these symptoms in the studies included in this meta-analysis. the patients included in this study were mainly diagnosed with covid-19 in january 2020, not long after the emergence of covid-19. since these diagnoses were made in the early phase of covid-19 transmission, a lack of awareness of olfactory/gustatory dysfunction, as well as differences in disease severity in patients depending on the time of covid-19 diagnosis, may explain why information on these symptoms was missing in the included studies. although the results of this study did not address olfactory or gustatory dysfunctions observed in covid-19 patients, based on current knowledge, otorhinolaryngologists must consider the possibility of covid-19 if patients with epidemiological risk of this disease complain of olfactory or gustatory dysfunction. fever is known to occur in a relatively early phase of covid-19, whereas dyspnea is a symptom that generally occurs in the rapid progression phase, which takes place 3 to 7 days after the onset of symptoms [44] . the present meta-analysis revealed that fever and dyspnea were less frequent in the patients diagnosed outside of wuhan than in those diagnosed in wuhan. in addition, asymptomatic covid-19 patients were only reported in the non-wuhan group. in a report from south korea, among a total of 28 patients, three patients without symptoms (10.71%) were diagnosed with covid-19, and only 32.14% of patients (9/28) complained of fever [47] . this trend was also observed in a study reporting the clinical features of 38 covid-19 patients in europe; 5.26% of patients (2/38) were asymptomatic and fever was observed in only 52.63% (20/38) [48] . most studies of both groups (the wuhan group and the non-wuhan group) in this meta-analysis included patients diagnosed in a similar period. since the initial outbreak of covid-19 is assumed to have occurred in wuhan, the interval between infection and covid-19 diagnosis is thought to have been shorter in the non-wuhan group than in the wuhan group. thus, the lower frequency of fever and the higher number of asymptomatic patients observed outside of wuhan is thought to be due to the early diagnosis of covid-19 as a consequence of physicians' increased awareness of the disease and epidemiological assessments of high-risk individuals. although it was not practicable to conduct a meta-regression analysis of the effect of age on clinical manifestations because of variation in how age was reported in the included studies, the patients from outside of wuhan seemed to be younger than the patients diagnosed in wuhan. since the clinical manifestations and disease severity of covid-19 vary depending on age [38] , these results should be interpreted with caution, in light of the possibility that the age difference between the groups may have affected the differences in clinical manifestations found in this study. regarding disease screening, we still should be aware that fever and dyspnea were less frequent in patients diagnosed outside of wuhan in china. it is apparent that only using symptoms as screening criteria for covid-19 results in an increased chance of failure of early diagnosis of covid-19 in actual patients. therefore, the assessment of epidemiological risk is of prime importance in patients complaining of fever accompanied by signs of respiratory infection. if it is not possible to conduct rrt-pcr for covid-19 in high-risk individuals, proper isolation of these patients for 2 weeks to minimize their contact with other people around them-even if they do not have symptoms or their symptoms are minor-is necessary considering the incubation period of covid-19 [43] . in addition, it would be preferable to have a monitoring system for identifying patients' history of visits to pandemic-affected areas and for keeping track of high-risk individuals through government interventions with the purpose of controlling this infectious disease. numerous studies have reported the radiologic findings of covid-19 patients. while simple chest radiography plays a limited role in covid-19 screening, chest ct is known to detect lung abnormalities, single or focal ggo patterns, the presence of a nodule in the central lobule, and patchy consolidation even before the onset of symptoms because of its high resolution [34, 40, 44] . ggo is an initial pathologic finding that can be observed in the lungs even before symptom onset, whereas the consolidation pattern is a relatively late finding in the progression of covid-19 [44] . these pathologic findings gradually involve bilateral and multiple lobes during the course of disease progression. although we assumed that covid-19 was diagnosed earlier in the non-wuhan group, no significant betweengroup differences were found in the distribution of patterns involving a single lobe, multiple lobes, and the bilateral lungs. the results regarding ggo and consolidation are similar to results reported from south korea (ggo, 8/9; consolidation, 2/9) [49] . since all five parameters reflecting chest ct findings exhibited considerable heterogeneity in the results extracted from the included studies, the present study does not provide support for any conclusions regarding the role of chest ct in covid-19 screening. this study has several limitations and the results should be interpreted with caution. first, the results of this study can only serve as the basis for weak recommendations because of the low level of evidence of the included studies, the small number of patients, and methodological limitations [24] . second, there was considerable heterogeneity in the results of the included studies. it is hypothesized that these outcomes could reflect differences between the groups. third, it is possible that this study did not include exhaustive information about covid-19, as case reports and studies with insufficient information were excluded from the present analysis to increase the level of evidence. in conclusion, fever accompanied by signs of respiratory infection is considered to be the most reliable manifestation of cov-id-19. fever and dyspnea were observed less frequently in patients diagnosed outside of wuhan in china, which should be considered in covid-19 screening. regional differences in the proportion of symptoms may be attributable to the earlier diagnosis of the disease and the younger age of the patients outside of wuhan although further analysis is needed. finally, the results of this study do not support any specific conclusions regarding the 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(covid-19): analysis of nine patients treated in korea no potential conflict of interest relevant to this article was reported. supplementary materials can be found via https://doi.org/10. 21053/ceo.2020.00570. key: cord-328859-qx7kvn0u authors: zhu, hongjun; li, yan; jin, xuelian; huang, jiangping; liu, xin; qian, ying; tan, jindong title: transmission dynamics and control methodology of covid-19: a modeling study date: 2020-09-21 journal: appl math model doi: 10.1016/j.apm.2020.08.056 sha: doc_id: 328859 cord_uid: qx7kvn0u the coronavirus disease 2019 (covid-19) has grown up to be a pandemic within a short span of time. to investigate transmission dynamics and then determine control methodology, we took epidemic in wuhan as a study case. unfortunately, to our best knowledge, the existing models are based on the common assumption that the total population follows a homogeneous spatial distribution, which is not the case for the prevalence occurred both in the community and in hospital due to the difference in the contact rate. to solve this problem, we propose a novel epidemic model called seir-hc, which is a model with two different social circles (i.e., individuals in hospital and community). using the model alongside the exclusive optimization algorithm, the spread process of covid-19 epidemic in wuhan city is reproduced and then the propagation characteristics and unknown data are estimated. the basic reproduction number of covid-19 is estimated to be 7.9, which is far higher than that of the severe acute respiratory syndrome (sars). furthermore, the control measures implemented in wuhan are assessed and the control methodology of covid-19 is discussed to provide guidance for limiting the epidemic spread. a total of 113,702 confirmed cases have been reported worldwide as of 10:00 cet on mar. 10 . the statistical data shows that the covid-19 outbreak constitutes an enormous threat to human in the world. many factors, including human connectivity, urbanization, as well as international travel, pose difficulties for prevention and control of covid-19 [1] . fortunately, mathematical models offer valuable tools for understanding epidemiological patterns and then for decision-making in global health. however, modeling the transmission dynamics of epidemic is still a challenging task, since the usefulness of a mathematical model depends on the existence of its solution [2] . a prime difficulty is to obtain the reliable data due to the fact that the available data is often patchy, delayed, and even wrong [3] [4] [5] [6] . the second cause is that the classical epidemic models describe epidemic transmission in the absence of interventions, which scarcely occurs in the real world. daily activities and travel, which are tightly linked to the spread of infection, tend to make the case more complex. the last but not least reason is that there are too many incidences, which cannot be ignored anyhow, happened in hospital where the contact rate is entirely different from that in the community. in this case, the general epidemic models do not work. additional problem encountered here is related to the estimation of the parameters of the epidemic model [2] . in order to probe propagation characteristics and transmission mechanism, several attempts have been done on modeling the transmission dynamics of covid-19, using observations of the index case in wuhan [7] [8] [9] [10] . unfortunately, the models fail to consider the difference of contact rate between in communities and in hospitals. this may limit the accuracy of the proposed models and hence the reliability of results. and hence, the results are very different from one another and even contradictory. most of them indicate that the basic reproduction number of covid-19 is lower than that of sars. on the contrary, the number of the individuals infected by covid-19 to date has been far higher than that infected by sars (8, 422) in 2003 [11] . moreover, there is no comparison of model output with real-world observations, though such a comparison is necessary to establish the performance of the models. to resolve this problem, this paper presents a novel epidemic model, which based on the standard assumption: the population is divided into susceptible (s), exposed (e), infectious (i), and recovered (r) groups [12] . the model proposed here, referred to as seir-hc for simplicity, extends the susceptible-exposed-infectious-removed (seir) model to handle epidemic transmission in two different but coupled social circles. furthermore, a two-step optimization is built for the parameter estimation. with the limited data, transmission process of covid-19 in wuhan city reproduced by the proposed model. then, the propagation characteristics and unreported data are estimated, and the end time of covid-19 is also predicted. in the end, the control measures implemented in wuhan are assessed and the control methodology of covid-19 is discussed to provide guidance to cease the covid-19 outbreak. the remainder of the paper is structured as follows: section 2 introduces the previous work; section 3 defines the related terminology; section 4 explains the seir-hc model in detail; section 5 describes the two-step optimization for parameter estimation; section 6 shows the analysis results, and finally, section 7 states the conclusions. transmission dynamics of an epidemic disease have long been a topic of active research. in 1866, farr [13] mathematically described the cattle-plague epidemic by means of curve fitting method. in 1889, p. d. en'ko presented a discrete-time model in which the population consists of infectious individuals and susceptible individuals [14] . in 1906, hamer [15] proposed that the incidence depends on the product of the densities of susceptibles and infectives. the susceptibleinfectious-removed (sir) model was formulated by martini in 1921 [16, 17] . in 1927, kermack and mckendrick [18] investigated the sir model in a homogeneous population by using differential equations and discovered that the epidemic course would inevitably be terminated once the density of population becomes smaller than a critical threshold. stone et al. [19] analyzed the rationale of the pulse vaccination strategy with the sir model. the sir model is ideally suited to describe the process of virus spread. however, it is not always congruent with epidemic course. some infections do not confer the lasting immunity. in this case, one should resort to the sis model, in which the infectious becomes susceptible again, rather than recovered. the sis model has many potential applications such as modeling the spread behavior of computer viruses [20] . on the other hand, if the epidemic lasts for a very long time, births and deaths heavily affect the population size. so, hethcote [21] introduced births and deaths into the deterministic models of sis and sir. on account of the fact that the sis and sir model only hold for the case without a latent period, which is not the case for many kinds of infectious diseases. to alleviate this problem, cooke [22] proposed an epidemic model for the case that after a fixed time the infected susceptibles can get infectious. in this model, the population is divided into four classes of individuals: susceptibles, exposed individuals, infectives and recovered individuals. such an epidemic model is known as the seir model. later, longini [23] presented a general formulation of the discrete-time epidemic model with permanent immunity. lipsitch et al. [24] estimated the infectiousness of sars and likelihood of an outbreak with modified seir model. krylova and earn [17] found that the dynamical structures of seir models have a less effect on the stage duration distribution, relative to that of the sir models. indeed, a family of seir models is being used to support epidemic control, elimination, and eradication efforts. see [14] and [25] for an extensive review of classic epidemic models. during the disease spread, a high degree of chance enters into the conditions under which fresh infections take place. therefore, statistical fluctuations should be taken into account for a more precise analysis [26] . for this reason, bailey [27] introduced probability distribution into the sis epidemic model. in the standard models, the incubation and infectious periods are typically assumed to be exponential distribution, which makes the model sensitive to stochastic fluctuations [12, 28] . however, because of more robustness, weibull distribution is used to investigate sars by marc lipsitch et al [24] . for the stochastic case, even the simplest representations present difficulties in obtaining algebraic solutions [2] . to address this issue, saunders [29] constructed an approximate maximum likelihood estimator for the chain seir model by using the poisson approximation to the binomial distribution. recently, wu et al. [10] provided an estimate of the size of the covid-19 epidemic based on the seir model. using an assumption of poisson-distributed daily time increments, read et al. [9] fitted a deterministic seir model to the daily number of confirmed cases in chinese cities and cases reported in other countries/regions. zhao et al. [5] estimated the number of unreported cases in mainland china based on the assumption that the initial growth phase followed an exponential growth pattern. to sum up, a number of models have been proposed to formulate the transmission process of epidemic disease, which lay a good foundation for our work. unfortunately, none of these studies have been done on the epidemic transmission under two different but coupled conditions. such a mathematical model is desired to explore, understand, predict and anticipate covid-19, including changes caused by intervention. in many cases, canonical representation will be the starting point for obtaining a clear or concise expression. for this reason, let us introduce the notation used throughout the paper before describing our work. fig. 1 presents a pictorial display of disease natural history in order to make these terms easy to be understood. (1) latent period: time from exposure to onset of infectiousness, during which the infectious agent develops in the vector, and at the end of which the vector can infect a susceptible individuals [22] ; (2) incubation period: time from exposure to first appearance of clinical symptoms of infection [25] ; (3) infectious period: period during which an infected person can transmit a pathogen to a susceptible [10] ; (4) length of stay: time from the day of admission in the hospital to the day of discharge, i.e., the number of days a patient stayed in a hospital for treatment [30] ; (5) serial interval: time from the onset of symptoms in an index case to the onset of symptoms in a subsequent case infected by the index patient [24] ; (6) susceptibles: individuals who have possibility of contacting with infectious individuals but still stay uninfected [18] ; (7) exposed individuals: individuals in the latent period, who are infected but not yet infectious [25] ; (8) infectives: individuals who are infectious in the sense that they are capable of transmitting the infection [25] ; (9) removed individuals: individuals who are removed by recovery and death, among them recovers obtain permanent infection-acquired immunity [18, 25] ; (10) quarantined individuals: suspected or exposed individuals who are separated and controlled to see if they become sick [24] ; (11) isolated individuals: infectives who are separated and controlled to avoid disease transmission [24] ; (12) basic reproduction number: expected number of secondary infectious cases generated by an average infectious case in an entirely susceptible population [24] ; (13) contact rate: average number of individuals with which one infective have an adequate contact in unit time, where an adequate contact is an interaction which results in infection [25, 31] ; (14) incidence rate: rate of new infections [32] , or, more precisely, total number of exposed individuals who move into infective class in unit time; (15) death rate: the death probability of a person per day on average [18] . based on the basic principle that if the model is tightly close to the real world, then the optimization algorithm will converge to the most reasonable solution, we build a new seir model with intervention mechanism which takes two different social circles into consideration. to estimate the parameters, the model of a complex physical situation tends to involve a certain amount of simplification for real world applications. however, it is not straightforward to obtain a balance between simplicity and practicality. to resolve this dilemma, generality of epidemic and particularity of covid-19 are considered simultaneously in our work and then a set of assumptions are determined carefully as follows. (1) the population is homogeneous and uniformly mixed [22, 31, 33] . (2) recovered individuals are permanently immune and newborn infants have temporary passive immunity to the infection [25] . (3) infectiousness remains constant during an infectious period [25] . (4) the natural disease-independent death rate is constant throughout the population [28] . (5) the disease-caused death rate is a time-independent constant. (6) latent period and infectious period follow weibull distribution [24] , which is a versatile distribution that has the ability to take on the characteristics of other types of distribution. (7) contact rate is constant over the entire infectious period [23] . (8) the first index case is infected on dec 1, 2019 [10] . (9) travel behavior was not affected by disease before lockdown on jan 23,2020 [10] . consider a time interval ( , + ℎ], where h represents the length between the time points at which measurements are taken, here h = 1 day. for convenience, a variable x at a time interval ( , + 1] is represented as ( ) . then, the variables and parameters are denoted as follows: ( ) : size of population at time t, that is, total number of susceptibles, exposed individuals, infectives and removed individuals at time t; ( ) : number of inbound travellers every day in wuhan at time t; ( ) : number of outbound travellers every day in wuhan at time t; : contact rate in the community; ℎ : contact rate in hospitals; ( ) : incidence rate of the exposed individuals who are infected days ago, which follows the weibull distribution; : shape parameter of the weibull probability density function (pdf) of incidence rate ; : scale parameter of the weibull pdf of the incidence rate ; ( ) : removal rate of infectives by disease-caused death or recovery who have been infectious for days, which follows the weibull distribution; : shape parameter of the weibull pdf of the removal rate ; : scale parameter of the weibull pdf of the removal rate ; : proportion of hospitalized infectives to total number of infectives; : proportion of quarantined susceptibles to total number of susceptibles; : maximum of latent period; : maximum of infectious period; : disease-independent death rate. for notational convenience, index c is used to denote community and h hospital in the following expressions. the variables without the indices c and h mean they are applicable in both cases. from classical seir model, the population is roughly classified as four classes: susceptible, exposed, infectious, and recovered individuals. among them, exposed and infectious individuals fall into a series of groups according to disease progression in our work so that the weibull distribution, which armed with high generalization capability [34] , can match accurately number of individuals and duration time. in order to accommodate the quarantine and isolation measures, and take the infectivity difference between hospital and community into consideration, the standard seir structure should be modified as shown in fig. 2 . note that the size of population is varied with control measures and is also affected by the inbound and outbound travellers. for the individuals respectively in hospital and community, disease transmissions are different in infection pattern but share the common nature of the virus. for this reason, two populations are considered simultaneously and analyzed separately for the sake of accuracy. with the reservations mentioned in section 4.1, we used the seir-hc model to simulate the epidemic process in wuhan. from the rules of node dissemination, the dynamic transfer equations of the seir-hc model are stated as follows. for the individuals in the community, given contact rate , ( ) / ( ) is the average number of susceptibles with which per infective contacts in unit time, and thus ( ) ( ) / ( ) is the total number of susceptibles with which ( ) infectives contacts in unit time (i.e., the total number of new infections in unit time). notice that the population of wuhan city was suddenly reduced from 14 million to 9 million before lockdown on the morning of jan 23, 2020. on the day, the preventive and control measures of category a infectious diseases were implemented to fight against covid-19. therefore, we assume that ( ) , ( ) , ( ) , ( ) , ( ) decrease proportionately by 5/14 and then the number of susceptibles became 5 ( ) /14 for restrictions on outdoor activities on the same day. we further assume that the disease-independent death rate is 1.50959 × 10 −5 , which is the same as that reported by the wuhan government in december 2019 [35] . according to the data presented by wu et al [10] , , are set to 490,856, 505,646 before jan 10, 814,046, 720,859 from jan 11 to jan 22, and 0, 0 after jan 22, respectively. for the individuals in hospital, where depending on the data provided by li et al (in fig. 3) , there are no more than 5 new cases every day from dec 8 to dec 28. at the same time, the basic reproduction number of the covid-19 in wuhan must be more than 1 or else the outbreak is impossible [24, 36] . in addition, a susceptible can be infected within 15 seconds of standing next to an infective. for these reasons, it is highly probable that the parameter z, which reflects the force of infection of the huanan seafood market, is small and hence let z=1. as defined in equation (6), the number of susceptibles in hospital is equal to the number of infectives stayed in hospital. in fact, ( ) + ℎ( ) in (6) is substituted by the number of the hospitalized patients in wuhan city, which is reported by wuhan municipal health commission (wmhc) [37] and health commission of hubei province(hchp) [38] . in addition, the execution of (12) and (13) is a time-consuming process. so, they are reformulated by it is readily seen from equation (10) that the exposed individuals can be classified as belonging to one of + 1 groups. and, the sizes of these groups are changed every day. the update formula is in this section, we propose a solution based on constraint optimization to estimate the parameters of the seir-hc model mentioned in section 4. the epidemic model is devised to estimate the unobserved variables and to predict the transmission process. the output data of the model is desired to be close to the real. unfortunately, it is difficult for the lack of the credible observations. to alleviate this problem, reasonable data is considered as an alternative. the data collection is completed by integrating multiple data sources: (1) number of new cases every day from dec 1, 2019, to jan 8, 2020, provided by li et al (in fig. 3 (2) number of new cases every day from feb 20 to mar 10, 2020, reported by wmhc [37] and hchp [38] , (3) number of the infectives among the nationals who returned to america [39] , japan [40] , south korea [41] and singapore [42] from jan 29 to jan 31, 2020 (as tabulated in table i (5) numbers of discharged and dead patients reported by wmhc [37] and hchp [38] , sum of which is theoretically equal to the number of the individuals removed by both recovery and death. note that, among them, several numbers were corrected for the contradiction between accumulated cases and new cases. based on the above data, the objective function consists of the five error sums of squares as follows: where (1) = ∑( (0, ) + ℎ(0, ) −̂( 0, ) ) note that the sign (^) denotes recorded value. here, ̂( 73) +̂( 73) indicates the total of the infectious hospital staff members by feb 11, 2020. statistically, the nationals in wuhan city can be regarded as the samples of population in the community. the ratio of the cases confirmed during the time from jan 29 to jan 31 among nationals is approximately equal to that on jan 30. in this sense, the number of infectives is likely to be about 36880 in wuhan city on jan 30. hence, ̂( 61) is set to 36880. the parameter estimation is, in general, a complex task partly due to so many unknown parameters: , , , ℎ , , , , . correct convergence is hard to reach unless a reliable initial guess is provided. therefore, an optimum initial estimation based on knowledge is crucial in this case. for this reason, all the parameters are dichotomized into two classes. the parameters , , , ℎ belong to class one and the others class two. among the first-class parameters, , are determined by intervention, , ℎ reflect the combined effect of virus and control. the second-class parameters are related to the characteristic of the virus. to estimate the parameters of the first class, we first investigated the implementation of control measures in wuhan city. from the report of hchp [38] , we found that an absolute increment of the number of confirmed infectives was more than 10 thousand on feb 12, 2020 compared to about one thousand the day before that day. this implies that many patients are likely to fail to be hospitalized before feb 12. taking into account the strict restriction on outdoor activities imposed before, and are set at 0.8 and 0.2. the permanent resident population of wuhan city is about 14 million[35]. moreover，wuhan is well known for being the transport hub of china. the contact rate was set 3 for the infectiousness in the community. on the other side, ideally, infections hardly spread in hospital. but, this is not the case for the inadequacy of medical supplies. and, according to the report of hchp, a lot of medical supplies had been distributed after feb 12. from these points under consideration, the initial contact rate ℎ is set equal to 0.05. at the same time, the contact rate ℎ is assumed to decrease by 99% after feb 12. with regard to class two, the parameters are relevant to the weibull pdf of the latent period and the infectious period. according to the medical records of 138 patients at zhongnan hospital of wuhan university, the median hospital stay is 10 days [44] . li et al [4] declared that the mean incubation period is 5.2 days. assuming that the latent period and the infectious period is approximately equal to the incubation period and the length of stay, the mean values of the latent period and the infectious period are preliminarily estimated to be 5 and 10 days, respectively. the profiles of the weibull pdf with various shape parameters are shown in fig. 4 . as a result, the initial guesses of the parameters , , , are 2.4, 5.64, 2.4 and 11.28, respectively. similarly, we determined the low bound and upper bound of the parameters. it is worth noting that to cut down the domain may not be a good strategy for global optimization since that may block the way to the global optimal point. global solutions are usually difficult to locate, whereas the situation may be improved when constraints are add [45] . consequently, an inequality constraint is defined to allow algorithms to make good choices for search directions. based on the knowledge that solation and quarantine are a useful control measures [36] , the numbers of exposed and infectious individuals in the presence of control efforts are consequentially no more than those in the absence of interventions. in theory, if only the mean values of the latent period and the infectious period are unchanged, the result is almost invariable in number. in this sense, for a given mean value, the second-class parameters only affect the shape of the seir-hc model. as a result, we explored a two-step optimization by adopting the sequential quadratic programming (sqp) method. in the first step, the first-class parameters are estimated by the sqp method. here, the results are taken as the initial guesses of the first class in the second step. in the second step, the second-class parameters are determined by the same way. the above process is iterated many times. the flow chart is presented in fig. 5 . in brief, the complete process of the two-step parameter optimization can be divided into four steps: (1) guess all the parameters and their low bound and upper bound as described in section 5.2. (2) estimate the first-class parameters using the sqp method with the objective function presented in section 5.1 and inequality constraints stated in this section. (3) estimate the second-class parameters in the same manner with the first-class parameters updated in step (2) . (4) repeat the computing process from (2) to (3) until the bias is small than a given threshold value or cycle index reaches 5. (a) (b) fig. 4 . weibull pdf with various shape parameters while (a) mean value is 5, and (b) mean value is 10. after the two-step iterative optimization, all the parameters of the seir-hc model are determined for covid-19 in wuhan. the low bound, the upper bound, the initial value and the estimated results are summarized in table ii . all results fall within the range between the upper and lower limits. some are very close to the initial value, but some far from the guess. fig. 5 . flow chart of the complete two-step iterative optimization. with the parameters estimated, it is easy to derive that the mean and variance of the latent period are 4.19 and 1.53, and those of the infectious period are 12.53 and 11.40. the weibull pdfs of the latent period and the infectious period are shown in fig.6 . it can be observed that a large proportion of exposed individuals become infectious in a short time and most cases are mild. the cumulative probability of the latent period for 10 days is up to 99.99%, by which the 14-day period of active monitoring is well supported. the difference between the latent period and the incubation period is equal to 1.01 days and the difference between the infectious period and the length of stay is 2.53 days. it is worth noting that 1 − (= 20.1%) infectives, which is equivalent to, on the average, 2.52 days per infective, still stayed in the community before feb 12. assuming that the infectiousness is constant during the entire infectious period, the basic reproduction number is up to 7.90 where everyone is susceptible. the basic reproduction number estimated here is compared with others in table iii . furthermore, even though an infective is hospitalized at the beginning of clinical symptoms, he still can make 3.48 individuals infected. as a result, the outbreak is inevitable in the absence of interventions for the difference between the latent period and the incubation period. of course, this is not necessary true for districts other than wuhan city, because basic reproduction number varies from population density and social enthusiasm besides characteristics of pathogenic bacteria [46] . with the seir-hc model proposed here, the transmission process of covid-19 epidemic in wuhan city is reproduced as shown in fig.7 . in our baseline scenario, we estimate that the outbreak would be over before apr 15, 2020 , and the total of infectives no longer increases by mar 15, 2020. at the same time, the total number of removed individuals would reach 111383 finally (as shown in fig. 7(a) ). among them, the number of hospital staff members would be up to 2950, which is likely to be slightly more than the reported cases due to asymptomatic infection. the number of the infected individuals in wuhan on jan 25, 2020, is estimated to be 46029, which is less than the count 75815 estimated by wu et al [10] . the number of infectives on jan 30 is 35962 (2.52% difference to 36880), which is much higher than 20767 (the number of the infected individuals estimated by nishiura et al [3] ). number of infectious hospital staff members on feb 11 is equal to 1241 (11.87% difference to 1022). it is readily seen from fig. 7(b) , (c) and (d) that there is a sudden decrease of the number of the exposed individuals on jan 23 and on feb 12, which implies control measures launched have a conspicuous effect on the infection rate. though mathematical models of epidemic transmission often scarce contrast model output with real-world observations [1] , the comparison is necessary to demonstrate the performance of the models and the validity of the results. for this reason, fig.8 provides a pictorial display of comparison of the estimated data and the reported ones. the two curves show the same trend after feb 12. but, before that day, the number of infectious individuals estimated here is far more than that reported by wmhc and hchp. a probable reason for this is the underreporting of incidences before feb 12 [3] [4] [5] [6] , which is the main reason for the underestimation of basic reproduction number. from fig. 8(a) , it seems that there is a delay of the estimated number of the removed individuals relative to the reported. the underlying cause of the delay may be the fact that the discharge time is later than the end time of infectious period for functional recovery. in this sense, it appears to be appropriate that the outbreak in wuhan terminates later than the expected time. however, the warmer weather is helpful in preventing the virus from reproducing. given these points, the outbreak is likely to be ended as we expected before if the control measures are kept on as usual. additionally, it also can be observed from fig. 8(a) that, in the worst case, up to 33620 infectives failed to be hospitalized on jan 30. to assess the control measure, a series of experiments are carried out using the seir-hc model. the control measures are simulated by the first-class parameters and the effect is captured by the number of infectives. since the proportion of quarantined susceptibles to the total number of susceptibles 1 − implies control level, the function of quarantine is tested by adopting . from the seir-hc model, we can see that impacts primarily on the community infection. so, only ic-t and (ic+rc)-t graphs are shown here for space limitations. fig. 9 (a) shows varing when increases from 0.032 to 0.932 and fig. 9 (b) shows + . fig. 9 (c) and (d) display the results with a delay of 0~9 days. it was clear that the number of infectives dramatically increases with the proportion and delay time. as a result, control measures played a key role in prevention of the spread. it also can be found from fig. 9 that the resulting divergence begins after jan 28. therefore, jan 23, on which the measures imposed, is the right time to stop the outbreak. given the proportion of hospitalized infectives to total number of infectives , 1 − is equivalent to the proportion of the average time during which infectives stay in the community to the average infectious period, which reflects how quickly the infectives are allowed to hospitalize. in this section, the effect of the time of hospital admission is test by changing parameter . fig. 10(a) shows that the number of infectives in the community varies with and fig. 10(b) is the corresponding accumulative value. fig. 10(c) and (d) depict the case in hospital. the delay of hospital admission makes an increase in the number of infectives both in the community and in hospital. however, the increase of the number of infectives slows down when is small enough due to the depletion of susceptibles in the population. it can be observed from fig. 10(b) that, as a result of a large number of inbound travellers every day, the accumulative total of the infectives can be even more than permanent resident population. in fact, this is almost impossible because the implicit assumption that travel behavior was not affected by epidemic is not valid. contact rate is primarily determined by the nature of pathogen. in fact, it can also be changed in some degree by intervention strategies [24] . assuming that c is varied from 3. number of infectives in the community varying with c is demonstrated in fig. 11 . a clear result is that the number of infectives in the community increases exponentially with c . note that, following the same idea mentioned in section 6.4.1, only the number of infectives in the community is shown here. the contact rate h partly reflects the prevention level in hospital. from fig.12 , the number of infectives in hospital increase sharply with ℎ . according to the experimental results, it is easy to find out about the control methodology. the basic principle is taking measures as early as possible to lower , c , h and to enhance . the control measures of covid-19 list as follows. (1) keeping in home quarantine and reducing travel to lower ; (2) tracing, testing and quarantining the suspected case, immediately isolating symptomatic individuals and speeding hospital admission to enhance ; (3) strengthening personal protection to lessen c and h . this work provides the seir-hc model, a novel seir model with two different social circles. if let = 0, the seir-hc model is easy to degrade into the standard seir model. for exploring the transmission dynamics of covid-19, a two-step optimization method exclusively designed for parameter estimation of seir-hc model. with the model, the spread process of covid-19 is reproduced clearly even without enough observation data. the latent period, infectious period and basic reproduction number of covid-19 are estimated to be 4.19, 12.53 and 7.90, respectively. obviously, covid-19 is highly transmissible. furthermore, the outbreak in wuhan is anticipated to be over before apr 15, 2020 . the total number of removed individuals would reach 111383 finally. among them, the number of hospital staff members would be up to 2950. according to the seir-hc model, the principle of prevention and control of covid-19 is taking measures as early as possible to lower , c , h and to enhance . a set of measures such as quarantine have significant impacts on lessening the spread. by the way, an international effort is required to prevent virus transmission since covid-19 has spread all over the world. as a whole, the conclusions are well interpretable and reasonable. as evidenced by the success in estimation and prediction, the seir-hc model is useful. although the results are based on the data from wuhan and hence they are not necessary to be reliable for other cities, the seir-hc model is valid everywhere, which allows us to capitalize on new data streams and lead to an ever-greater ability to generate robust insight and collectively shape successful local and global public health policy. modeling infectious disease 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caused by novel coronavirus quarantine of evacuees at march air reserve base ends two new cases of asymptomatic infection in japan were the third group of people evacuated from wuhan to japan details: a seventh case of novel coronavirus infection has been confirmed in the republic of korea past updates on covid-19 local situation three departments: a number of measures to care for anti-epidemic frontline medical staff clinical characteristics of 138 hospitalized patients with 2019 novel coronavirusinfected pneumonia in wuhan numerical optimization complexity of the basic reproduction number. emerging infectious diseases key: cord-323882-127c5bve authors: yu, wen-bin; tang, guang-da; zhang, li; corlett, richard t. title: decoding the evolution and transmissions of the novel pneumonia coronavirus (sars-cov-2 / hcov-19) using whole genomic data date: 2020-05-17 journal: zool res doi: 10.24272/j.issn.2095-8137.2020.022 sha: doc_id: 323882 cord_uid: 127c5bve the outbreak of covid-19 started in mid-december 2019 in wuhan, china. up to 29 february 2020, sars-cov-2 (hcov-19 / 2019-ncov) had infected more than 85 000 people in the world. in this study, we used 93 complete genomes of sars-cov-2 from the gisaid epiflu(tm) database to investigate the evolution and human-to-human transmissions of sars-cov-2 in the first two months of the outbreak. we constructed haplotypes of the sars-cov-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. the date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. a total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the sars-cov-2 genomes. forty non-synonymous substitutions are potentially associated with virus adaptation. no combinations were detected. the 58 haplotypes (31 found in samples from china and 31 from outside china) were identified in 93 viral genomes under study and could be classified into five groups. by applying the reported bat coronavirus genome (bat-ratg13-cov) as the outgroup, we found that haplotypes h13 and h38 might be considered as ancestral haplotypes, and later h1 was derived from the intermediate haplotype h3. the population size of the sars-cov-2 was estimated to have undergone a recent expansion on 06 january 2020, and an early expansion on 08 december 2019. furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases. betacoronaviruses are characterized by enveloped, positivesense, single-stranded rna, and hosted in animals, particularly mammals (cui et al., 2019) . before december 2019, four species/strains of betacoronavirus, hku1, mers-cov, oc43, and sars-cov, had been reported to cause severe human diseases (cui et al., 2019) . the fifth species/strain, a novel betacoronavirus sars-cov-2 / hcov-19 / 2019-ncov (gorbalenya et al., 2020; jiang et al., 2020) causing human pneumonia (i.e., , was first reported in wuhan, hubei, central china (wu et al., 2020a; zhou et al., 2020; zhu et al., 2020) . up to 29 february 2020, sars-cov-2 had infected more than 85 000 people in all provinces/regions of china, and another 59 countries/regions across africa, asia, europe, north america, oceania, and south america (wikipedia, 2020) . because sars-cov-2 can transmit from human to human , the massive exodus of people before the chinese spring festival boosted the infection frequencies, as predicted . daily confirmed infection cases were more than 2 000 between 30 january and 16 february, 2020, and the highest was more than 15 100 (wikipedia, 2020), almost twice the total number for sars-cov (chan-yeung & xu, 2003) . as a member of subgenus sarbecovirus, sars-cov-2 has been suggested to be of bat origin (lu et al., 2020b; , and may have been transmitted to humans through non-bat intermediate mammals (e.g., pangolins (cyranoski, 2020; lam et al., 2020; wong et al., 2020; xiao et al., 2020; zhang et al., 2020b) ). medical information for the first 41 infected patients in wuhan showed that 27 patients were linked to the huanan seafood wholesale market (abbreviated as huanan market in the text below) , which sold living wild mammals. this suggests a high possibility that sars-cov-2 originated in the market, then the infected people transmitted it to other people outside of the market. however, this conclusion has been challenged because the first identified infected person and 12 others had no link to the huanan market. some researchers have therefore argued that the huanan market was not the original and/or only source of sars-cov-2 transmission to humans (cohen, 2020) . the market was closed on 01 january 2020, making it very difficult to identify the intermediate animal vectors of sars-cov-2. in the absence of information on potential intermediary reservoirs, the origin and transmission pattern of sars-cov-2 are still unresolved (wong et al., 2020) . since the outbreak of covid-19 was first identified in wuhan in mid-december 2019, the first infected individuals identified in other provinces and regions of china, and other countries, during january 2020, have been assumed to have been infected in wuhan or through contact with people from wuhan (chan et al., 2020; holshue et al., 2020; phan et al., 2020; rothe et al., 2020) . in this study, we used 93 genomes of sars-cov-2 from the gisaid epiflu tm database (shu & mccauley, 2017 ) (access date 12 february 2020) to decode the evolution and transmissions of sars-cov-2 in the first two months of its spread. our aims were to: (1) characterize genomic variations of sars-cov-2; (2) infer the evolutionary relationships of the worldwide samples; and (3) deduce the transmission history of sars-cov-2 within wuhan and out of wuhan to the world. to decode the evolutionary history of sars-cov-2, we retrieved 96 complete genomes from gisaid (supplementary table s1 , access by 12 february 2020) (shu & mccauley, 2017) . the genome epi_isl_402131 (bat-ratg13-cov, hereafter) from gisaid was also included as the outgroup, because it is the closest sister betacoronavirus available to sars-cov-2 . the 97 genome sequences were aligned using mafft (katoh & standley, 2013) , then the alignment was manually checked using geneious (biomatters, new zealand). in the alignment, we found that epi_isl_404253 contains six ambiguous sites at variable positions and epi_isl_407079 and epi_isl_408978 have 175 "n" and 1476 "n" bases, respectively, so these three genomes were excluded in this study. in addition, four genomes (epi_isl_407071, epi_isl_407894, epi_isl_ 407896, and epi_isl_409067) have their own private ambiguous sites, which were conservatively replaced by the common nucleotide at that position in the alignment; notably, epi_isl_406592 (h15) and epi_isl_406595 (h17) had excessive amounts of private variable sites, which were possibly affected by sequencing errors. in the alignment, the 5' untranslated region (utr) and 3' utr regions contain missing and ambiguous sites, so these regions were excluded in the following analyses. the alignment was then imported into dnasp (rozas et al., 2017) for haplotype analyses. population size changes were estimated based on a constant population size hypothesis using dnasp, in combination with neutrality tests (tajima's d and fu's f s ). we also used arlequin (excoffier & lischer, 2010) to test the sudden population expansion hypothesis and to calculate the expansion parameter tau (τ), since the sudden population expansion was not rejected. we used the formula t=τ/2u (rogers & harpending, 1992) to estimate the time since expansion (in days). in the formula, u is the cumulative substitution rate per year for the genome sequence, so we used the formula u=μk to calculate it, where μ is the substitution rate per site per year, and k is the genome sequence length (29 358 bp for the coding sequence (cds) matrix). the substitution rate was set as 0.92×10 −3 (95% ci, 0.33×10 −3 -1.46×10 −3 ) substitution/site/year based on the most recent estimation for sars-cov-2 (rambaut, 2020) . to adjust the time, we used a mean value of the expansion time calculated from the three substitution rates, i.e., 0.33×10 −3 , 0.92×10 −3 , and 1.46×10 −3 substitution/site/year. in addition, the expansion date was estimated based on the sampling date from hospitalized patients. the estimated date should be later than the "real" date of massive human-to-human transmission events. phylogenetic networks of the haplotype coding region matrix and 120 substitution sites of sars-cov-2 (supplementary datasets) were inferred using splitstree (huson & bryant, 2006) . a median-joining network of haplotypes was generated by the network program (bandelt et al., 1999 (bandelt et al., , 2020 with the reported bat coronavirus (bat-ratg13-cov, ) as the outgroup. transversions were arbitrarily weighted three times as high as transitions. hypervariable sites (if number of mutations ≥5) were weighted as 1, and the other sites were weighted as 10. genetically, sars-cov-2 and bat-ratg13-cov, as well as sars-cov, have been proposed as the same species (gorbalenya et al., 2020) , and genome sequence identity between bat-ratg13-cov and sars-cov-2 was 96.2%. we carefully used three datasets (i.e., four core substitution sites, 120 substitution sites, and 1 235 substitution sites, supplementary datasets) to evaluate the relationship between bat-ratg13-cov and four associated/central haplotypes of sars-cov-2 (h1, h3, h13, and h38). phylogenomic analyses of haplotypes were performed using iq-tree (minh et al., 2020) . we conducted likelihood mapping and sh-like approximate likelihood ratio tests to assess the phylogenetic information and branch supports, respectively. genome size of sars-cov-2 varied from 29 782 bp to 29 903 bp. the aligned matrix was 29 910 bp in length, including 140 variable sites. the cds regions contained 120 substitution sites (supplementary figure s1 ), which were classified as 58 haplotypes (supplementary table s2 ). nucleotide diversity (p i ) was 0.15×10 −3 ±0.02×10 −3 (standard deviation, sd, hereafter). haplotype diversity (h d ) was 0.953±0.016 (sd) and variance of h d was 0.26×10 −3 . there were 120 substitution sites found in eight coding sequence (cds) regions of sars-cov-2 ( figure 1 , supplementary table s2), including 79 transitions (65.83%) and 41 transversions (34.17%). a chi-squared test showed that the distribution of substitution sites across cds regions in the genome was even (χ 2 =1.958, d f =9, p=0.99). substitution sites occurring at the 1st to 3rd frame positions were 27 (25.55%), 44 (40.0%), and 49 (44.55%), respectively. the 120 substitution sites were associated with 119 codons, including 79 non-synonymous (65.83%) and 40 synonymous (33.61%) substitutions. forty non-synonymous substitutions (50.63%) changed the biochemical properties of the amino acid (aa), and are therefore potentially associated with virus adaptation. the current samplings showed that the h1 haplotype has been found in 19 patients, but most haplotypes were just sequenced once, suggesting that the haplotype h1 was rapidly circulated at an early stage of human-to-human transmissions ( figure 2 , supplementary table s1). in comparisons with published genomes of sars-cov (luk et al., 2019) and mers-cov (cotten et al., 2013) , genomic variations of sars-cov-2 are still low, without evident table s1 ). although the incubation period can be over 24 days, there was only one case of this out of 1 099 observations . estimation of the substitution rates using 90 genomes of sars-cov-2 (rambaut, 2020) showed that the rate for sars-cov-2 was close to or lower than the rates for mers-cov (cotten et al., 2014; dudas et al., 2018) and sars-cov (zhao et al., 2004) . due to the mild symptoms and low mortality zhang et al., 2020a) , the immune systems of the infected humans may provide a suitable environment for propagation of sars-cov-2 (andersen et al., 2020) . sars-cov-2 is highly infectious and is able to infect humans not only through the mucous membranes of the nose and mouth, but also use the mucous membranes in the eyes (lu et al., 2020a) , which may boost regional circulation and large-scale spread. some large mutations may have occurred in wuhan or other regions, but the strict quarantine policy over china since 23 january 2020 may have reduced the circulation and spreading of some mutants. of the 93 genomes of sars-cov-2, 39 (41.93%) were from infected patients in 11 countries outside china and encoded 31 haplotypes (h d =0.987±0.009 (sd), p i =0.16×10 -3 ± 0.01×10 -3 ), with 27 nationally/regionally private haplotypes. the 54 genomes (58.07%) from china also encoded 31 haplotypes (h d =0.906±0.001 (sd), p i =0.14×10 -3 ±0.03×10 -3 ). a proportion z-test showed significant differences in haplotype diversity of samples between china and other countries (χ 2 =4.024, d f =1, p<0.05). the high haplotype diversity found in samples from other countries may be because the sampling dates were mostly after 22 january 2020, while those in china were before this date (supplementary table s1 and figure s2 ). in addition, the low level of radiation exposure on longdistance international flights (bottollier-depois et al., 2000) may have accelerated mutation rates of sars-cov-2 (shibai et al., 2017) . we used a variety of parameters to estimate the population dynamics of sars-cov-2. constant population size of sars-cov-2 was rejected (ramos-onsins and rozas's r 2 =0.025, p<0.001; raggedness r=0.011, p<0.05) using dnasp (rozas et al., 2017) (also see supplementary figure s3 ), while both fu's test (f s =-67.681.964, p<0.001) and tajima's d test (d=-2.701, p<0.001) indicated that the population size of sars-cov-2 was rapidly increasing. mismatch distribution analysis using arlequin (excoffier & lischer, 2010) strongly supported that the population of sars-cov-2 underwent sudden expansion (τ=2.887, sum of squared deviation, the confirmed samples from the huanan seafood wholesale market are indicated using red circles, and a confirmed sample with no link to the market is indicated using a blue circle. ssd=0.541×10 -3 , p=0.88, harpending's raggedness index, r=0.010, p=0.88). the calculated expansion was 28.72 days (95% confident interval: 12.29-54.36 days) ago. of the 93 genomes, the latest one was sampled on 03 february 2020, so the estimated expansion date was on 06 january 2020 (95% ci: 11 december 2019-22 january 2020), which may be related to the new year holiday. before 06 january 2020, 129 patients were identified as sars-cov-2 infected through field investigations . of 22 genomes (17.05% of 129 patients) sequenced before 06 january 2020 in wuhan, china, 13 haplotypes (22.41% of 58 haplotypes) were recovered, which were h1 and its derived descendant haplotypes, and h3 (figures 2 and 3a) . coincidentally, the china cdc (chinese center for disease control and prevention) started to activate a level-2 emergency response on 06 january 2020 . the china cdc's emergency response greatly reduced public activities and travel, and might have reduced the local circulation and largescale spread in the following weeks of january. furthermore, mismatch distribution analysis of the 22 genomes before 06 january 2020 also showed a sudden population expansion of sars-cov-2 at an earlier stage of transmission ( . this suggests that sars-cov-2 might have already circulated widely among humans in wuhan before december 2019, probably beginning in mid to late november (rambaut, 2020) . phylogenetic networks showed that the 58 haplotypes were clustered into two main clades (figure 4) . clade i included 19 haplotypes and clade ii included 39 haplotypes. the outgroup bat-ratg13-cov was connected to clade i, supposed to be an ancestral clade for clade ii. the long branches of h15 and h17 correspond to an excessive amount of mutations, which are possibly affected by sequencing errors, but this is still to be determined. three different datasets were used to infer evolutionary networks, which consistently supported h13 and h38 as the potentially ancestral haplotypes, i.e., the outgroup bat-ratg13-cov could connect to both h13 and h38, or h38 alone, or through a medium vector mv1 (an intermediate host or the first infected humans) connected to both h13 and h38 by single mutations at positions 18067 (s, synonymous substitution) and/or 29102 (s), referring to the numbering of the alignment length 29 910 bp ( figure 5 ). five main groups can be recognized in the network using the dataset of 120 substitution sites ( figure 3a ). the h1, h3, and h13 were three core haplotypes, so that groups a-c were recognized using them as the central (i.e., ancestral super-spreader) haplotypes. groups d and e were recognized based on two new super-spreader haplotypes, h56 and a medium vector mv2, which was a hypothesized (often ancestral) haplotype not sampled in the current samples. these two groups can be also treated as subgroups of group c. moreover, the sh-like approximate likelihood ratio test further enhanced the phylogenetic relationship retrieved from 58 haplotypes, that either h13 or h38 (with h45) appeared in the basal lineages (supplementary figure s4) , although it was difficult to distinguish which one, h13 or h38, originated earlier (supplementary figure s5) . in the network, four satellite haplotypes and h35 connected to h13 (group a), and nine satellite haplotypes and h38+h45 and h50 connected to h3 (group b). the connections between the h3 and h1 are two mutations at positions 8789 (s) and 28151 (ns, non-synonymous substitution) (figure 5 ), the latter mutation changed both residues and the biochemical properties of the aa. this biochemical change may be associated with the infectivity of sars-cov-2. the h1 haplotype, the most abundant, included 19 samples, while 26 satellite haplotypes and h40+(h43 and h47) haplotypes are directly derived from h1 (group c). moreover, five haplotypes of group d and four haplotypes of group e were also derived from h1. phylogenetic networks showed that bat-ratg13-cov was nested with group b in clade i, and clade ii tends to be derived from clade i, i.e., h1 and its descendant haplotypes were new mutants from an ancestral haplotype in clade i. the rooted network suggested two potential evolutionary paths of available haplotypes that can be from h13 through h3 to h1 and h38, or from h38 through h3 to h1 and h13 ( figure 3c ). both scenarios suggested that h3 might be the ancestral haplotype of h1. h13 was only recovered from five shenzhen (guangdong province) samples, including patient 2 of the familial cluster (chan et al., 2020) . two derived haplotypes were also only found in shenzhen of guangdong province (h14 from the grandson of patient 2), and the other three haplotypes were found in three samples from japan and one sample from arizona in the united states (figure 3 ). according to an epidemiological study, the shenzhen family could have been infected during their visit to wuhan (chan et al., 2020) . this suggests that h13 might have originated from wuhan. genetically, haplotypes of group a have links to only wuhan haplotype h3 (only epi_isl_406801). it is possible that h13 was newly derived from h3 ( figure 3c ) and did not spread in wuhan, or that three repatriated japanese might be infected by an unknown source of h13 in wuhan, china or somewhere else (the asahi shimbun, 2020), or that no samples have been sequenced yet. h38 has three genomes from the same patient (supplementary table s1 ), who was the first identified infected patient in the united states (holshue et al., 2020) . this patient might have been infected while visiting his family in wuhan, china, or was infected in some other place. the original source of h38 can be explained as that of h13, which can be also derived from h3 ( figure 3c ), and the derived h45 was from a chongqing patient who was reported as working in wuhan and had no link to the huanan market. the h3 haplotype has only one sample from wuhan, which was not linked to the huanan market (lu et al., 2020b) , and the other samples in this group were from outside of wuhan ( figure 3a) . noteworthily, all the samples from the market belonged to h1 or its derived haplotypes (h2, h8-h12, see figure 2 and supplementary table s1), indicating that there were circulated infections within the market in the short term. other researchers have argued that the source of the coronavirus in the market should be imported from elsewhere, or at least it should be not the single source of sars-cov-2 the dataset of four core substitution sites is the four variable sites shared among bat-ratg13-cov and the four central node haplotypes. the dataset of 120 substitution sites refers to all variable sites of coding regions in sars-cov-2 haplotypes. the dataset of 1235 substitution sites refers to all variable sites of coding regions among bat-ratg13-cov and sars-cov-2 haplotypes. (cohen, 2020) . in this study, evolutionary relationships indicated that h1 and its descendant haplotypes from the market should be derived from h3 (figures 3, 4) . h3 mutated to the h1 by two substitutions, and none of the currently available market samples encoded h3, suggesting that h3 might have originated and spread outside of the market before an early stage of population expansion. the non-synonymous mutation from h3 to h1 might have enhanced the infectiousness of sars-cov-2, and a functional characterization should be performed to confirm this speculation. it is possible that sars-cov-2 in the market had been transmitted from other places ( figure 3d ), or at least, that the market did not host the original source of sars-cov-2 (cohen, 2020) . as the first identified infected patients had no link to the market , it is possible that infected humans transmitted the h1 haplotype of sars-cov-2 to workers or sellers in the market, after which it rapidly circulated there due to its special surroundings. the crowded market boosted sars-cov-2 transmissions to buyers and spread it to the whole city in early december 2019, corresponding to the estimated population expansion time. due to insufficient sampling from wuhan in the currently available samples, it is not clear whether h3 never appeared in the market, or h1 was quickly derived from h3 to adapt in the market. of the 54 genomes from patients in china, chongqing (3 samples), guangdong (18), hubei (22), taiwan (2), and zhejiang (4) have more than two samples, and the other five provinces have one sample. hubei (wuhan) samples dated from 24 december 2019 to 05 january 2020 encoded 13 haplotypes, belonging to groups c (h1 and 11 satellite haplotypes) and b (only h3). these relationships indicated a rapid transmission and circulation of sars-cov-2 in wuhan at an early stage of human-to-human transmissions. h1 (no satellite haplotypes) and h3 are the ancestors of haplotypes outside of wuhan/hubei because most of early confirmed patients might have history in wuhan or hubei. eighteen guangdong samples, collected from 10-23 january 2020, encoded 15 haplotypes, belonging to groups a, c, and e, showing that there were multiple sources imported into guangdong. three haplotypes (h14, h15, and h17) may have evolved locally, indicating that human-to-human transmissions happened when sars-cov-2 initially spread to shenzhen in guangdong province (chan et al., 2020) . two samples from taiwan province, china, encoded h3 and h24 in groups b and d, respectively, and three samples from chongqing encoded h1, h40, and h45 in groups b and c, respectively. there were two sources imported into these two provinces. four zhejiang samples encoded h1 and h24 in group c, which might be only imported from the source of the h1 haplotype. the samples outside china encoded 31 haplotypes belonging to groups a-e. of these, 27 haplotypes are private by regional samplings, only two samples from thailand were the h1 haplotype, one each from australia and belgium were the h3 haplotype, one from the united states was the h19 haplotype, and one from singapore was the h40 haplotype. twelve samples, encoding 10 haplotypes, were from patients in five countries in asia. six haplotypes linked to h1, and two each linked to h3 and h1, respectively, indicating the 12 patients were infected by different sources. human-to-human transmissions may have happened from patients with h53 to h52 haplotypes in tokyo, japan. five australian samples, encoding six haplotypes in groups b, c, and d, were from patients of three states. patients with h3, h25 and h26, and with h55 were in groups b and c, respectively, and humanto-human transmission might have happened from the patients with h25 to h26, who were in a same tour group in queensland (aap reporters, 2020). the connection between the patients with h56 and h27 is not clear. one possibility is that there was an intermediary spreader with h56, who also transmitted sars-cov-2 to other patients in france, the united states, and taiwan province of china. eight european samples, encoding seven haplotypes, were from patients in four countries. the patients in england were reported as a household transmission from h28 to h29 (lillie et al., 2020) . the patients in france may have been infected by three different sources, i.e., h44 was linked to h1, h43 might link to h40 (in chongqing, singapore or somewhere else), and h30 might link to an intermediary spreader with h56. of the 13 genomes from the united states, three were from the same patient in washington encoding the same haplotype h38, while the other ten samples encoded eight haplotypes, covering all five groups ( figure 3a, b) , so the sources of infections are complicated. there is no evidence of human-tohuman transmission in the united states from these 11 cases. to clarify the exact origins of these haplotypes outside china, we need more epidemiological investigative efforts and more sars-cov-2 genomic data from patients at the early stage of transmissions. epidemiological study of sars-cov-2 using traditional approaches is very difficult, because it was not identified as a new coronavirus until 29 december, and some infected people with mild symptoms or without symptoms (heymann & shindo, 2020; rothe et al., 2020; wu & mcgoogan, 2020) may have been overlooked in late november and early december. evolutionary analyses suggested that the source of the h1 haplotype in the huanan market was imported from elsewhere, as has been suggested by other researchers (cohen, 2020) . the rooted network suggested that h13 and h38 should be ancestral haplotypes that connected to the outgroup bat-ratg13-cov through a hypothesized intermediate haplotype ( figure 5 ). the most common ancestral haplotype was missed because the currently available samples do not include the first identified infected patient and other patients from early december, and because of the relatively high mutation rate of the viral genome. if there are any frozen samples from those patients, it would be worth doing genomic sequencing for phyloepidemiologic study to help to locate the birthplace of sars-cov-2. meanwhile, we expect that the h13 and h38 haplotypes might be found in some samples from infected patients in wuhan or in other places across the world if more samples are sequenced in future. this will be very helpful in the search for the original sources of sars-cov-2, because both h13 and h38 tend to be ancestral haplotypes. the evolutionary network of haplotypes can be used to recover the directions of human-to-human transmissions at the local scale and spread at the larger scale. the central haplotype can be considered as the super-spreader haplotype, and the tip haplotype is the most recent descendant, similar to the definition and use of mtdna haplogroups in tracing human demographic history (yao et al., 2002) . the transmission direction can be identified using the connection information of tips and branches. for example, the confirmed patients from the huanan market shared the common ancestral haplotype h1, indicating they might be infected from a common source, who may have been a superspreader in the market. this approach has recovered potentially specific directions of human-to-human transmission in the shenzhen family (h13 → h14), the queensland tour group (h25 → h26), the england family (h28 → h29), and the japanese (h53 → h52). it is possible that some infections could link to wuhan or hubei directly or indirectly, because the patients claimed connections to wuhan or hubei, but for some of them it is not clear exactly where they were infected. we suspect that there were super-spreaders mediating the spread of sars-cov-2 at the early stage of transmissions. our findings showed that sars-cov-2 has not had legitimate recombination. thus, the haplotype-based phyloepidemiologic analyses provide a powerful way to understand the evolution of sars-cov-2 at the very early stage of transmission when reverse mutations and illegitimate recombination are rare. in our analysis, recombination is rejected but the outgroup bat-ratg13-cov is relatively highly diverged from sars-cov-2 haplotypes, which may affect the phyloepidemiologic analyses. based on the estimated mutation rate of current sars-cov-2 viruses, the reverse mutations should be 6×10 −3 (0.92×10 −3 ×0.92×10 −3 per site per year×29 358 sites×2/12 year), with a neglectable influence on our result. but our observations leave one important question: why are ancestral haplotypes, like h13 and h38, less frequent than h1? it is highly possible that h1 acquired adaptive mutations, such as ns of site 28151, from h3 or h13 (and/or h38), evolved in an independent circulation after they jumped into intermediate hosts or directly transmitted to humans, which should be investigated in future studies if more early genome datasets are available. the exact original sources of h13 and h38 will stay as unsolved mysteries if the early stage samples were not preserved. an early version of our manuscript was posted at chinaxiv (doi: 10.12074/202002.00033) on 19 february 2020. since then, there have been many news stories stemming from our manuscript with a biased interpretation of the results. this is beyond our expectation. during the review of this manuscript, there were some reports of analyses of sars-cov-2 genomic variations based on a larger sample size (e.g., forster et al., 2020; tang et al., 2020) , which showed a similar phylogenetic pattern as we present here. we expect more data-mining of the increasing number of sars-cov-2 genomes will provide updated insights into the origin and transmission of this virus. supplementary data to this article can be found online. coronavirus outbreak: second case confirmed in queensland the proximal origin of sars-cov-2 median-joining networks for inferring intraspecific phylogenies assessing exposure to cosmic radiation during long-haul flights a 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of 72 314 cases from the chinese center for disease control and prevention isolation and characterization of 2019-ncov-like coronavirus from malayan pangolins. biorxiv epidemiological and clinical features of the 2019 novel coronavirus outbreak in china. medrxiv phylogeographic differentiation of mitochondrial dna in han chinese transmission and epidemiological characteristics of novel coronavirus (2019-ncov) pneumonia (ncp): preliminary evidence obtained in comparison with pangolin homology associated with 2019-ncov moderate mutation rate in the sars coronavirus genome and its implications a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus from patients with pneumonia in china we are grateful to scientists and researchers for depositing whole genomic sequences of novel pneumonia coronavirus (sars-cov-2 / hcov-19 / 2019-ncov) at the global initiative on sharing all influenza data (gisaid) epiflu™; to gisaid database for allowing us to access the sequences for noncommercial scientific research; and to two reviewers for their valuable comments and suggestions. this study was supported by grants from ten thousand talents program of yunnan for top-notch young talents, and the open research project of "cross-cooperative team" of the germplasm bank of wild species, kunming institute of botany, chinese academy of sciences. the authors declare that they have no competing interests. w.b.y. conceived the research, analyzed the data, interpreted the results, and wrote the draft manuscript; w.b.y. and g.d.t. collected data. all authors read and approved the final version of the manuscript. key: cord-342012-1w3x0g42 authors: wu, joseph t.; leung, kathy; bushman, mary; kishore, nishant; niehus, rene; de salazar, pablo m.; cowling, benjamin j.; lipsitch, marc; leung, gabriel m. title: estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china date: 2020-03-19 journal: nat med doi: 10.1038/s41591-020-0822-7 sha: doc_id: 342012 cord_uid: 1w3x0g42 as of 29 february 2020 there were 79,394 confirmed cases and 2,838 deaths from covid-19 in mainland china. of these, 48,557 cases and 2,169 deaths occurred in the epicenter, wuhan. a key public health priority during the emergence of a novel pathogen is estimating clinical severity, which requires properly adjusting for the case ascertainment rate and the delay between symptoms onset and death. using public and published information, we estimate that the overall symptomatic case fatality risk (the probability of dying after developing symptoms) of covid-19 in wuhan was 1.4% (0.9–2.1%), which is substantially lower than both the corresponding crude or naïve confirmed case fatality risk (2,169/48,557 = 4.5%) and the approximator(1) of deaths/deaths + recoveries (2,169/2,169 + 17,572 = 11%) as of 29 february 2020. compared to those aged 30–59 years, those aged below 30 and above 59 years were 0.6 (0.3–1.1) and 5.1 (4.2–6.1) times more likely to die after developing symptoms. the risk of symptomatic infection increased with age (for example, at ~4% per year among adults aged 30–60 years). of case fatality risk warrants these interventions, which seriously disrupt social and economic stability. for a completely novel pathogen, especially one with a high (say, >2) basic reproductive number (the expected number of secondary cases generated by a primary case in a completely susceptible population) relative to other recently emergent and seasonal directly transmissible respiratory pathogens 4 , assuming homogeneous mixing and mass action dynamics, the majority of the population will be infected eventually unless drastic public health interventions are applied over prolonged periods and/or vaccines become available sufficiently quickly. even under more realistic assumptions about mixing informed by observed clustering of infections within households and the increasingly apparent role of superspreading events (for example, the diamond princess cruise ship, chinese prisons and the church in daegu, south korea) 5, 6 , at least one-quarter to onehalf of the population will very likely become infected, absent drastic control measures or a vaccine. therefore, the number of severe outcomes or deaths in the population is most strongly dependent on how ill an infected person is likely to become, and this question should be the focus of attention. we therefore extended our previously published transmission dynamics model 4 , updated with real-time input data and enriched with additional new data sources, to infer a preliminary set of clinical severity estimates that could guide clinical and public health decision-making as the epidemic continues to spread globally. estimation of true case numbers-necessary to determine the severity per case-is challenging in the setting of an overwhelmed healthcare system that cannot ascertain cases effectively. therefore, as in our prior work 4 , our approach has been to use a range of publicly available and recently published data sources (numbered 1 to 8 below) to build a picture of the full number of cases and deaths by age group. briefly, because the healthcare structure has been overwhelmed in wuhan and milder cases were unlikely to have been tested, we used the prevalence of infection in travelers (both on commercial flights before 19 january and on charter flights from 29 january to 4 february) to estimate the true prevalence of infection in wuhan; we also used the wuhan case numbers from only the first 425 cases to estimate the growth rate of the epidemic (assuming that the ascertainment proportion was constant between 10 december 2019 and 3 january 2020) (fig. 1) . specifically, we inferred the epidemiologic parameters listed in extended data fig. 1 by fitting an age-structured transmission model to the following data: 1. the epidemic curve of confirmed cases of covid-19 in wuhan with no epidemiologic links to huanan seafood wholesale market (which was postulated to be the index zoonotic source of the covid-19 epidemic) between 10 december 2019 and 3 january 2020 ( fig. 1 table 6 ). 7. the time between onset and death or the time between admission and death for 41 death cases of covid-19 in wuhan [10] [11] [12] (supplementary table 7 ). 8. the time between the onset dates (that is, serial intervals) of 43 infector-infectee pairs (supplementary table 8 ). the clinical severity of infectious diseases is typically measured in terms of infection fatality risk (ifr), symptomatic case fatality risk (scfr) and hospitalization fatality risk (hfr). the case definitions underlying these severity measures are as follows: 1. ifr defines a case as a person who would, if tested, be counted as infected and rendered (at least temporarily) immune, as usually demonstrated by seroconversion or other immune response 13 . such cases may or may not be symptomatic. 2. scfr defines a case as someone who is infected and shows certain symptoms. 3. hfr defines a case as someone who is infected and hospitalized. it is typically assumed in such estimates that the hospitalization is for treatment rather than isolation purposes. figure 2 summarizes our estimates of age-specific scfrs and susceptibility to symptomatic infection. both parameters increase substantially with age. if the probability of developing symptoms after infection, p sym , is 0.5, the scfr values are 0.3% (0.1-0.7%), 0.5% (0.3-0.8%) and 2.6% (1.7-3.9%) for those aged <30 years, 30-59 years and >59 years, respectively. the overall scfr is 1.4% (0.9-2.1%). compared to those aged 30-59 years, those aged <30 years and >59 years are 0.16 (0.15-0.17) and 2.0 (1.95-2.08) times more susceptible to symptomatic infection. our estimates of scfrs would be lower if p sym were higher than the baseline value of 0.5; for example, the overall scfr is 1.3% (0.8-2.3%) and 1.2% (0.7-1.9%) if p sym is 0.75 and 0.95, respectively. our estimates of age-specific susceptibility are not sensitive to p sym . figure 3 summarizes our estimates of the key epidemiologic parameters of covid-19 in wuhan. in the baseline scenario i.e., cases due to human-to-human (h2h) transmission) between 1 december 2019 and 3 january 2020 (blue), the daily number of cases exported from wuhan to cities outside mainland china via air travel between 25 december 2019 and 19 january 2020 (orange) and the proportion of expatriates on charter flights between 29 january and 4 february 2020 who were laboratory-confirmed to be infected (green). the numbers of passengers and confirmed cases who returned to their countries from wuhan on chartered flights are provided in supplementary table 3 . bars indicate the 95% confidence intervals (cis) of the proportion. b, the daily number of deaths in wuhan reported between 1 december 2019 and 28 february 2020. (p sym = 0.5), the basic reproductive number is 1.94 (1.83-2.06). the mean serial interval is 7.0 (5.8-8.1) days, with a standard deviation of 4.5 (3.5-5.5) days. the mean time from onset to death is 20 (17) (18) (19) (20) (21) (22) (23) (24) days, with a standard deviation of 10 (7-14) days. the epidemic doubling time (the time it takes for daily incidence to double) was 5.2 (4.6-6.1) days before wuhan was quarantined and public health interventions implemented within wuhan reduced transmissibility by 48% (24-71%). we estimate that only 1.8% (0.9-3.3%) of symptomatic cases that occurred between 10 december 2019 and 3 january 2020 were ascertained. figure 3 suggests that our estimates of the basic reproductive number, mean generation time and intervention effectiveness would be slightly lower if p sym were higher than the baseline value of 0.5, whereas our estimates of the other parameters are largely insensitive to p sym . there is a clear and considerable age dependency in symptomatic infection (susceptibility) and outcome (fatality) risks, by multiple folds in each case. given that we have parameterized the model using death rates inferred from projected case numbers (from traveler data) and observed death numbers in wuhan, the precise fatality risk estimates may not be generalizable to those outside the original epicenter, especially during subsequent phases of the epidemic. the experience gained from managing those initial patients and the increasing availability of newer, and potentially better, treatment modalities to more patients would presumably lead to fewer deaths, all else being equal. public health control measures widely imposed in china since the wuhan alert have also kept case numbers down elsewhere, so that their health systems are not nearly as overwhelmed beyond surge capacity, thus again perhaps leading to better outcomes 6, 8 . indeed, so far, the death-to-case ratio in wuhan has been consistently much higher than that among all the other mainland chinese cities (extended data fig. 2 ). given the intensive efforts of case finding and the sharp drop in community transmission of covid-19 in chinese cities outside hubei over the past few weeks, the ascertainment rates in these cities were probably very high. as such, we postulate that confirmed case fatality risk in these cities should be in some ways comparable to our scfr estimates for wuhan, which attempt to account for under-ascertainment of cases in wuhan. nonetheless, crude case fatality risks estimated from cities outside wuhan should be, and are, lower than our scfr estimates for wuhan, because the former do not account for the delay between onset and death (thus being artefactually lower) and because healthcare outside hubei is less overwhelmed (thus allowing a truly lower cfr). indeed, as of 29 february 2020, the crude case fatality risk in areas outside hubei was 0.85%, which is ~23-41% lower than our scfr estimates of 1.2-1.4% for wuhan 9 . considering the risk estimates in context, extended data fig. 3 compares infection, case and hospitalization fatality risks for pandemic influenza in 1918 and 2009, sars and mers. sars causes moderate to severe disease requiring hospitalization, so the infection fatality risk and case fatality risk are essentially the same as the hospitalization fatality risk. the hospitalization fatality risk for mers is well documented, although the shape and depth of the clinical iceberg remains less well defined. in contrast, because (1) the majority of covid-19 infections do not cause severe disease 8 and (2) hospitals in wuhan have been overwhelmed, presumably having led to prioritized admission of more serious cases, the scfr will be substantially lower than the hfr. however, despite a lower scfr, covid-19 is likely to infect many more (given emerging evidence of presymptomatic transmission 14, 15 and growing evidence of extensive community spread in numerous countries 16 ), thus ultimately causing many more deaths than sars and mers. compared with the 1918 and 2009 influenza pandemics, our estimates are intermediate but substantially higher than 2009, which was generally regarded as a low-severity pandemic. we find that scfr is highest in the oldest age group. unlike any previously reported pandemic or seasonal influenza, we find that risk of symptomatic infection also increases with age, although this may be in part due to preferential ascertainment of older and thus more severe cases. one largely unknown factor at present is the number of asymptomatic, undiagnosed infections. these do not enter our estimates of scfr, but if such asymptomatic or clinically very mild cases existed and were not detected, the infection fatality risk would be lower than scfr. further clarifying this requires new data sources that are not yet available, specifically including agestratified serologic studies. our inferences were based on a variety of sources, and have a number of caveats that are highlighted below, but considering the totality of the findings they nevertheless indicate that covid-19 transmission is difficult to control. with a basic reproductive number of around two, we might expect at least half of the population to be infected, even with aggressive use of community mitigation measures. perhaps the most important target of mitigation measures would be to 'flatten out' the epidemic curve, reducing the peak demand on healthcare services and buying time for better treatment pathways to be developed. in due course, but almost certainly after the first global wave of infections, vaccines may also be available to protect against infection or severe disease. although our estimates of scfr are concerning, these could be reduced if effective antivirals were identified and widely adopted for the treatment of severe cases. timely data from clinical trials of remdesivir, lopinavir/ritonavir and other potential chemotherapies, as well as supportive care modalities, would be extremely informative. several important caveats are worth mentioning, as follows. first, and most importantly, our modeled estimates have necessarily relied on numerous strong assumptions, given the paucity of definitive data elements such as serosurveys, serial viral shedding studies, robust ascertainment of sufficient transmission chains and incomplete testing of travelers and returnees from wuhan, all of which need to be underpinned by systematic unbiased sampling of the underlying population and by important age and other sub-groups. our estimates of scfr are inevitably affected by under-ascertainment of cases and deaths of covid-19. on the one hand, overstretched and overwhelmed healthcare surge capacity in wuhan could result in scfrs that are higher than they would be in a less stressed healthcare setting, as presumably the sicker patients would have been prioritized for admission while leaving the milder cases untested and thus unconfirmed. our prevalence estimates relying on travelers are based on those well enough to travel, so may slightly underestimate prevalence in wuhan by not including those who are already in a serious condition and perhaps hospitalized. we have accounted for the possibility that travelers may underestimate the prevalence of infection in wuhan 17 by using our best estimate, from a separate analysis, of the probability of detection for international travelers (38% (22-64%)) 17 . on the other hand, the numerator of the number of deaths could also have been undercounted, although much less likely compared to enumerating the denominator, for the same surge capacity reason or due to imperfect test sensitivity, especially during the first month of the outbreak 18 . if deaths in wuhan were under-ascertained, this would bias our severity estimates downward. another caveat concerns one of our key inputs-the infection prevalence among returnees airlifted out of wuhan on charter flights. their point prevalence might well be lower than that among local residents, because of a generally more advantaged socioeconomic background, and the sensitivity for detecting infected individuals among them might not be 100%, as assumed. as such, this would be a lower bound of the cross-sectional disease prevalence. if this were the case, then we would have overestimated the reduction in transmissibility conferred by public health interventions in wuhan and overestimated the severity. based on only publicly available data, there is necessarily substantial uncertainty in our estimates of the effectiveness of intra-wuhan public health interventions in reducing transmissibility. calculating the instantaneous reproductive number from a set of line lists that are updated daily would be the most reliable method for detecting changes in transmissibility associated with interventions. there has been refinement of case definitions at both national and provincial levels, such as excluding rt-pcr-test-positive asymptomatics (perhaps, in fact, very mildly symptomatics) from being labeled an officially 'confirmed' case 19 or including test-naïve clinically diagnosed cases with clear epidemiologic links as 'confirmed' 20 . although these should not affect our estimation given our data sources from the earlier phase of the epidemic, such changes in the reporting criteria may influence the interpretation of future data. finally, given that wuhan is no longer the only (albeit the first) location with sustained local spread, it would be important to assess and take into account the experience from elsewhere, both domestically in mainland china and overseas. these secondary epicenters, having learned from the early phase of the wuhan epidemic, might have had a systematically different epidemiology and response that could impact the parameters estimated here 21-31 . any methods, additional references, nature research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and estimates of basic reproductive number, mean serial interval, initial doubling time, intervention effectiveness, ascertainment rate and the mean time from onset to death, assuming p sym is 0.50 (red), 0.75 (green) and 0.95 (blue). the markers show the posterior means and the bars show 95% cris. we made the following assumptions in the model: 1. the population of wuhan is stratified into m = 9 age groups: 0-9, 10-19, 20-29, 30-39, 40-49, 50-59, 60-69, 70-79 and >79. the relative susceptibility to infection of age group i is α i with respect to those aged 30-39 years (that is, α 4 = 1). the scfr of age group i is scfr i . 2. the probability density function (pdf) of the incubation period, f incubation , is gamma, with a mean of 6.5 days and standard deviation of 2.6 days 32 . 3. the pdf of the time between onset and death, f onset-to-death , is gamma. we inferred the values of the mean and standard deviation of f onset-to-death (extended data fig. 1 ). 4. the pdf of the generation time, f gt , is gamma and the same as that of the serial interval. we inferred the values of the mean and standard deviation of f gt (extended data fig. 1 ). 5. the infection-symptomatic probability (p sym ; the proportion of infections that progress to develop symptoms) is the same for all age groups. we assume p sym = 0.50 in the baseline scenario and 0.75 and 0.95 in alternate scenarios. 6. the sensitivity of detecting symptomatic cases exported from mainland china is p det = 38% (22%-64%) for cities that reported case importation between 25 december 2019 and 19 january 2020 (supplementary table 2 . as such, we assume that the epidemic in wuhan was seeded by a single zoonotic event that generated z 0 infections on 15 november 2019. we inferred the value of z 0 (extended data fig. 1 ). 10. public health interventions in wuhan reduced local transmissibility by φ 0 . we inferred the value of φ 0 (extended data fig. 1 ). 11. given that the epidemic curve in wuhan was weeks ahead of that in other mainland chinese cities, we ignored the effect of case importation at wuhan. these assumptions were reflected in the following susceptible-infectedrecovered (sir) model for simulating the covid-19 epidemic in wuhan, where s i (t), and r i (t) are the number of susceptible and recovered individuals in age group i at time t, and i(t, τ) is the number of infected individuals in age group i at time t who were infected at time t − τ: the next-generation matrix for this sir model is where t g is the mean generation time. the basic reproductive number r 0 is the largest eigenvalue of this matrix, which is βtg n p m i¼1 α i n i i . the incidence rates of infection, onset and death for age group i at time t are calculated as follows: the number of new cases (onset) and the cumulative number of cases in age group i on day d are be the summation of the number of new cases, the cumulative number of cases and the cumulative number of deaths across all age groups up to time t, respectively. similarly, is the total number of infected individuals at time t. we inferred the parameters listed in extended data fig. 1 assuming that the remaining parameters are fixed at the values shown in extended data fig. 4 . we use θ to denote the set of parameters that are subject to inference (extended data fig. 1 ). the likelihood function is a product of several components associated with the data in supplementary tables 1-8: the formulation of each component was as follows: 1. the number of observed international case exportations on each day is assumed to be an imperfect poisson observation of the number of infected travelers leaving wuhan on that day who had or would develop symptoms. let x d be the observed number of such international case exportations on day d between 25 december 2019 (d s , 1 ) and 19 january 2020 (d e , 1 ) based on the data in supplementary table 2 . we assume that travel behavior is not affected by disease and hence such case exportation occurs according to a non-homogeneous process with rate λ t ð þ ¼ p sym lw;i t ð þ n t ð þ iðtþ: i let p det be the probability that an infected traveler who has or will develop symptoms is detected in the destination country. the expected number of detected case exportations on day d is and hence x d ≈ poisson(λ d ). as such, the likelihood function associated with the data in supplementary table 2 is where g is the posterior distribution of p det from a separate study that had a mean of 38% and a 95% credible interval of 22-64% 17 . 2. let y d be the observed number of confirmed cases of covid-19 in wuhan with no epidemiologic links to huanan seafood wholesale market (which is presumed to be the index zoonotic source of the covid-19 epidemic) on day d between 10 december 2019 (d s , 2 ) and 3 january 2020 (d e,2 ) based on the data in supplementary table 1 7 . these cases are assumed to be a poisson observation of the true number of newly symptomatic cases on that day, with ascertainment rate ε, which remained fixed over this time period. as such, assuming y d ≈ poisson(εω d ), the likelihood function for the data in supplementary table 1 is table 3 . the prevalence of infection and symptoms among travelers are assumed to reflect a representative binomial sample of the same quantities in the wuhan population on their day of departure. the likelihood function associated with the data in supplementary table 3 is is the proportion of individuals who were infected on day d. 4 . we assume that all deaths from covid-19 infection in wuhan were confirmed. let g be the cumulative number of death cases in wuhan as of 25 february 2020 (time t). we assume g ≈ poisson(d(t)) and hence the likelihood function associated with this data is l 4 θ ð þ ¼ e �dðtþ dðtþ g g! 5. we assume that the age distribution of confirmed cases is a multinomial sampling process from the age distribution of true cases. let c i be the observed number of confirmed cases in age group i in wuhan based on the data in supplementary table 4 . the likelihood function for the data in supplementary table 4 is 6. we assume that the age distribution of confirmed deaths is a multinomial sampling process from the age distribution of true deaths. given that most covid-19 deaths were wuhan-related, we assume that the age distribution of confirmed deaths for wuhan is the same as that for mainland china 8 . let b i be the observed number of death cases in age group i in wuhan based on the data in supplementary table 5 . the likelihood function for the data in supplementary table 5 is with regard to the data in supplementary table 7 , let a be the set of death cases whose onset dates are known, and b the set comprising the remaining cases. let v j be the observed time delay between onset and death for the jth case in a and let v l j i be the observed time between hospital admission and death (which serves as a lower bound for the delay between onset and death) for the jth case in b. the likelihood function for the data in supplementary table 7 is where f onset-death and f onset-death are the pdf and cumulative density function (cdf) of the time between onset and death (assumed to be gamma-distributed with mean μ d and standard deviation σ d ). 8. with regard to the data in supplementary table 8 , let a be the set of infectorinfectee pairs for whom the serial interval (time elapsed between their onset dates) is known and b the set comprising the remaining pairs for whom only the ranges of their serial intervals are known. let s j be the observed value of the serial interval for the jth pair in a, and s l j ; s u j i be the observed range of the serial interval for the jth pair in b. for some infector-infectee pairs, the travel history and onset dates of the infector impose a lower bound on the serial interval (supplementary table 8 ). let s * j be such a lower bound for the jth pair. the likelihood function for the data in supplementary table 8 is where f si and f si are the pdf and cdf of the serial interval. we assume that the serial interval and the generation time have the same pdf. we estimated the model parameters θ using markov chain monte carlo methods with gibbs sampling and non-informative flat priors. point estimates and statistical uncertainty are presented using posterior means and 95% cris, respectively. reporting summary. further information on research design is available in the nature research reporting summary linked to this article. we collated epidemiological data from publicly available data sources (news articles, press releases and published reports from public health agencies). all the epidemiological information that we used is documented in the main text, the extended data and supplementary tables. the codes are available upon request to the corresponding author. last updated by author(s): mar 5, 2020 reporting summary nature research wishes to improve the 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associated raw data -a description of any restrictions on data availability all raw data have been provided in supplementary tables. please select the one below that is the best fit for your research. if you are not sure, read the appropriate sections before making your selection. behavioural & social sciences ecological, evolutionary & environmental sciences methods for estimating the case fatality ratio for a novel, emerging infectious disease case fatality risk of influenza a (h1n1pdm09): a systematic review human infection with avian influenza a h7n9 virus: an assessment of clinical severity nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study secondary attack rate and superspreading events for sars-cov-2 report of the who-china joint mission on coronavirus disease 2019 (covid-19) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19)-china chinese center for disease control and prevention. dashboard of reported 2019-ncov cases data platform of shanghai observer. line list of 2019-ncov confirmed fatal cases (from publicly available information wuhan municipal health commission. wuhan municipal health commission's briefing on the current pneumonia epidemic in the city hubei municipal health commission's briefing on the current pneumonia epidemic in the province infection fatality risk of the pandemic a(h1n1)2009 virus in hong kong sars-cov-2 viral load in upper respiratory specimens of infected patients viral load of sars-cov-2 in clinical samples time to use the p-word? coronavirus enters dangerous new phase quantifying bias of covid-19 prevalence and severity estimates in wuhan, china that depend on reported cases in international travelers the state council of the people's republic of china national health commission of people's republic of china. notice of the general office of the national health commission on the distribution of the plan of prevention and control of the pneumonia caused by the novel coronavirus situation of the epidemic of pneumonia caused by the novel coronavirus in hubei case fatality of sars in mainland china and associated risk factors epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in hong kong the epidemiology of severe acute respiratory syndrome in the 2003 hong kong epidemic: an analysis of all 1755 patients a comparative epidemiologic analysis of sars in hong kong, beijing and taiwan influenza: the mother of all pandemics age and sex incidence of influenza in the epidemic of 1943-44, with comparative data for preceding outbreaks: based on surveys in baltimore and other communities in the eastern states epidemiologic characterization of the 1918 influenza pandemic summer wave in copenhagen: implications for pandemic control strategies mortality from pandemic a/h1n1 2009 influenza in england: public health surveillance study middle east respiratory syndrome: what we learned from the 2015 outbreak in the republic of korea hospitalization fatality risk of influenza a (h1n1)pdm09: a systematic review and meta-analysis middle east respiratory syndrome coronavirus (mers-cov) neutralising antibodies in a high-risk human population incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china extended data fig. 3 | a summary of severity estimates among pandemic influenza strains and coronaviruses with pandemic potential in the past the study is a mathematical modeling study. we have provided the full information of data in figures data exclusions not applicable. the study is a mathematical modeling study. we have provided the full information of data in figures replication all the data have been provided in figures, extended data and supplementary tables randomization not applicable. the study is a mathematical modeling study. we have provided the full information of data in figures blinding not applicable.not applicable. the study is a mathematical modeling study. we have provided the full information of data in figures reporting for specific materials, systems and methods we require information from authors about some types of materials, experimental systems and methods used in many studies. here, indicate whether each material, system or method listed is relevant to your study the authors declare no competing interests. extended data is available for this paper at https://doi.org/10.1038/s41591-020-0822-7.supplementary information is available for this paper at https://doi.org/10.1038/ s41591-020-0822-7.correspondence and requests for materials should be addressed to j.t.w.peer review information joao monteiro was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. key: cord-317465-ucwuptgg authors: fang, h.; wang, l.; yang, y. title: human mobility restrictions and the spread of the novel coronavirus (2019-ncov) in china date: 2020-03-26 journal: nan doi: 10.1101/2020.03.24.20042424 sha: doc_id: 317465 cord_uid: ucwuptgg we quantify the causal impact of human mobility restrictions, particularly the lockdown of the city of wuhan on january 23, 2020, on the containment and delay of the spread of the novel coronavirus (2019-ncov). we employ a set of difference-in-differences (did) estimations to disentangle the lockdown effect on human mobility reductions from other confounding effects including panic effect, virus effect, and the spring festival effect. we find that the lockdown of wuhan reduced inflow into wuhan by 76.64%, outflows from wuhan by 56.35%, and within-wuhan movements by 54.15%. we also estimate the dynamic effects of up to 22 lagged population inflows from wuhan and other hubei cities, the epicenter of the 2019-ncov outbreak, on the destination cities' new infection cases. we find, using simulations with these estimates, that the lockdown of the city of wuhan on january 23, 2020 contributed significantly to reducing the total infection cases outside of wuhan, even with the social distancing measures later imposed by other cities. we find that the covid-19 cases would be 64.81% higher in the 347 chinese cities outside hubei province, and 52.64% higher in the 16 non-wuhan cities inside hubei, in the counterfactual world in which the city of wuhan were not locked down from january 23, 2020. we also find that there were substantial undocumented infection cases in the early days of the 2019-ncov outbreak in wuhan and other cities of hubei province, but over time, the gap between the officially reported cases and our estimated "actual" cases narrows significantly. we also find evidence that enhanced social distancing policies in the 63 chinese cities outside hubei province are effective in reducing the impact of population inflows from the epicenter cities in hubei province on the spread of 2019-ncov virus in the destination cities elsewhere. human mobility contributes to the transmission of infectious diseases that pose serious threats to global health. indeed, in response to pandemic threats many countries consider and impose measures that restrict human mobility flows as one of their response plans (bajardi et al., 2011; wang and taylor, 2016; charu et al., 2017) . however, restrictions on human mobility are controversial not only because of their negative economic impacts, but also because of the uncertainty about their effectiveness in controlling the epidemic. even if restricting human movement could lead to improvements in disease control and reductions in health risks, it is empirically challenging to quantify the impact of human mobility on the spread of infectious diseases, and to understand the detailed spatial patterns of how the infectious disease spreads. both granular disease occurrence data and human mobility data (charu et al., 2017 ) are hard to obtain; moreover, it is difficult to disentangle the impact of human mobility from other potential contributing factors in the spread of epidemics hollingsworth et al., 2006) . in this paper, we exploit the exogenous variations in human mobility created by lockdowns of chinese cities during the outbreak of the novel coronavirus (2019-ncov), and utilize a variety of high-quality data sets, to study the effectiveness of an unprecedented cordon sanitaire of the epicenter of covid-19, and provide a comprehensive analysis on the role of human mobility restrictions in the delaying and the halting of the spread of the covid-19 pandemic. 1 the fast-moving 2019-ncov that infected 266,073 people and claimed 11,184 lives as of march 21, 2020 is deteriorating into one of the worst global pandemics. 2 the virus emerged in the city of wuhan in the hubei province of china in early december of 2019, spread mainly through person-to-person contact (chan et al., 2020) , and rapidly reached more than 183 countries as of march 21, 2020. 3 currently, there are no licensed vaccines or specific therapeutics to combat covid-19. the lockdown of 11 million people in wuhan from january 23, 2020 represents by then the largest quarantine in public health history, and offers us an opportunity to rigorously examine the effects of the city lockdown and understand the relationship between human mobility and virus transmission. specifically, this paper studies five research questions. first, how does the lockdown of the city of wuhan amid the novel coronavirus outbreak affect population movement? second, how do population flows among chinese cities, particularly outflows from wuhan and other cities in hubei province, affect virus infection in the destination cities? third, is there evidence of, and if so, what is the magnitude of, undocumented cases of covid-19 cases in wuhan and other cities in hubei province during the early stages of the epidemic? and how does the extent of undocumented infection cases evolve over time? fourth, how many covid-19 cases elsewhere in china were prevented by the unprecedented wuhan lockdown? fifth, are social distancing policies in destination cities effective in reducing the spread of the infections? we utilize reliable datasets on population migration among pairs of chinese cities and the within-city population movements of each city at the daily level from baidu migration, and the city-level daily numbers of confirmed covid-19 cases, recovered patients, and death tolls from the chinese center for disease control and prevention (ccdc) during a sample period of january 1-february 29, 2020, covering 22 days before and 38 days after the city lockdown on january 23, 2020, as well as the matched data from the same lunar calendar period in 2019. we first employ various difference-in-differences (did) estimation strategies to disentangle the effect of wuhan lockdown on human mobility reductions from other confounding effects including panic effect, virus effect, and the spring festival effect-the spring festival of the chinese new year is on january 25, 2020 (table 2) . we find that the lockdown of wuhan reduced inflow into wuhan by 76.64%, outflows from wuhan by 56.35%, and within-wuhan movements by 54.15%. we also estimate the dynamic effects of up to 22 lagged population inflows from wuhan and other hubei cities, the epicenter of the 2019-ncov outbreak, on the destination cities' new infection cases ( figure 4 ). we discover that the estimated effects of the different lags of inflows from wuhan and hubei both show a clear inverted u -shape with respect to the lags, with the largest impact on the newly confirm cases today comes from the inflow population from wuhan or other cities in hubei about 12 to 14 days earlier. we find, using simulations with these estimates, that the lockdown of the city of wuhan on january 23, 2020 contributed significantly to reducing the total infection cases outside of wuhan, even with the social distancing measures later imposed by other cities. we find that the covid-19 cases would be 64.81% higher in the 347 chinese cities outside hubei province, and 52.64% higher in 16 non-wuhan cities inside hubei, in the counterfactual world in which the city of wuhan were not locked down from january 23, 2020. we also find that there were substantial undocumented infection cases in the early days of the 2019-ncov outbreak in wuhan and other cities of hubei province, but over time, the gap between the officially reported cases and our estimated "actual" cases narrows significantly. we also find evidence that imposing enhanced social distancing policies in the 63 chinese cities outside hubei province is effective in reducing the impact of population inflows from the epicenter cities in hubei province on the spread of 2019-ncov virus in the destination cities elsewhere. by providing a rigorous estimation of the impact of within and cross-city migration on the spread of the 2019-ncov virus in china, our study contributes to fast-growing literature on 2019-ncov infection, mostly in the medical and public health fields. huang et al. (2020) describe high rates of respiratory distress, intensive care admission, and abnormal findings on chest computed tomography (ct) in the first 41 patients hospitalized from december 16 to january 2 in wuhan, as well as a 15% death rate. chan et al. (2020) investigate a family cluster and confirm the human-to-human transmission of this novel coronavirus within hospitals and families. the basic reproduction number (r0) for covid-19 in 12 studies has a mean of 3.28 and a median of 2.79 (liu et al., 2020 ) (compared to 3 for sars (wto, 2003) ). this study is also related to disaster-induced migration, which has often occurred during flooding (gray and mueller, 2012) , drought (munshi, 2003) , earthquake (lu et al., 2012) , and other destructive climatic phenomena. given that the 2019-ncov has rapidly spread worldwide due to human travel and caused severe illness and significant mortality, it is therefore essential to understand the impact of various control measures on human mobility and the virus transmission. qiu et al. (2020) apply machine learning tools and use exogenous temperature, wind speed, and precipitation in the preceding third and fourth weeks as the instruments to show that the massive lockdown and other control measures significantly reduced the virus transmission. their results highlight that the population outflow from the outbreak source city poses higher risks to the destination cities than other social and economic factors, such as geographic proximity and similarity in economic conditions. our results are also in line with the results of the latest modeling exercises, which mostly rely on model calibrations of various parameters, such as generation time, incubation period, detection rates, and changes in travel flow. using the global epidemic and mobility model, chinazzi et al. (2020) project the impact of travel limitation on the national and international spread of the 2019-ncov. the study finds that only 24.4% of infected cases were reported as of february 1, and the wuhan lockdown reduced the cases by 10% in cities outside wuhan by january 31. the study most closely related to ours is li et al. (2020) , which shows that contagious but undocumented covid-19 cases facilitated the geographic spread of the epidemic in china. using a networked dynamic meta-population model and bayesian inference, li et al. (2020) find that 86% of all infections were undocumented before the wuhan lockdown and reported infections would have been reduce by 78.7% in china, without transmission from undocumented cases between january 10 and january 23. lai et al. (2020) build a travel network-based susceptibleexposed-infectious-removed (seir) model to simulate the outbreak across cities in mainland china. they use epidemiological parameters estimated from the early stage of outbreak in wuhan to parameterize the transmission before the non-pharmaceutical interventions (npi) were implemented. the npis they consider include travel bans and restrictions, contact reductions and social distancing, early case identification and isolation. through their sim-ulations, they find that the npis deployed in china appear to be effectively containing the covid-19 outbreak, but the efficacy of the different interventions varied, with the early case detection and contact reduction being the most effective. moreover, deploying the npis early is also important to prevent further spread. relative to our study, it is important to point out that in their simulations, they assumed that the pattern of population movements was the same in years when there were no outbreaks and interventions. to the best of our knowledge, this paper is the first to provide a causal interpretation of the impact of city lockdown on human mobility and the spread of 2019-ncov, and to clearly disentangle the lockdown effects from other potential contributing factors such as panic and virus effect, as well as the seasonal spring festival effect (see section 3). the remainder of the paper is structured as follows. in section 2, we describe the data sets used in our analysis. in section 3, we present different difference-in-difference estimation strategies to separate the lockdown effect, panic effect, virus (deterrence) effect, and the spring festival effect on population movements in china. in section 4, we estimate the distributed lag effects of inflows from the epicenter cities of the 2019-ncov outbreak on destination cities' daily infection cases. in section 5, we study how the enhanced social distancing policies, or "lockdown" policies, in the destination cities' impact the effects of the population inflows from the epicenter cities. in section 6, we conclude. population migration data. we obtain inter-city population migration data from baidu migration, a travel map offered by the largest chinese search engine, baidu. 4 . the baidu migration data set covers 120,142 pairs of cities per day for 364 chinese cities between january 12 and march 12 in 2019, and between january 1 and february 29 in 2020. note that, by the lunar calendar, the data covers the same period of 24 days before and 36 days after the spring festivals, respectively for year 2019 and year 2020. the daily inter-city migration data consist of 2,977,899 city-pair observations each year. in addition, baidu provides the daily within-city mobility data for each city in the sample period, which is a panel consisting of 21,655 city-day level observations each year. the baidu migration data is based on real-time location records for every smart phone using the company's mapping app, and thus can precisely reflect the population movements between cities. 5 for each of the 364 cities, baidu migration provides the following information: (1). the top 100 origination cities (oc) for the population moving into the city and the corresponding percentages of inflow population that originated from each of the top 100 oc; (2). the top 100 destination cities (dc) for the population moving out of the city, and the corresponding percentages of the outflow population that go into each of the top dc. in the data, the cumulative percentages of the inflow population from the top 100 origination city, and the cumulative percentages of the outflow population into the top 100 destination cities, reach 97% per city on average. this ensures that the baidu migration data capture near complete inflows and outflows for each of the 364 cities in the data. in addition, the baidu migration data provides three migration intensity indicators: the daily in-migration index (imi) of a city, the daily out-migration index (omi) of a city, and the daily within-city migration index (wcmi). the intensity indicators are consistent across cities and across time. to convert the index to the number of people, we use the actual number of inflow population into shanghai by airplanes, trains and buses/cars, and the number of within-shanghai trips using subways, buses and expressways, collected by the national earth system science data center for the period of february 6 to february 22, 2020. using this data, we estimate that one index unit in the imi and omi corresponds to 90,848 person movements, and one index unit in wcmi corresponds to 2,182,264 person movements. we are thus able to calculate the number of daily inflow and outflow migrants in each city-pair, as well as the number of within-city population movements. 6 table 1 presents the summary statistics of the population flows at the city-pair-day level and city-day level. it shows drastic declines in the average inflows, average outflows, and average within-city migration in 2020, compared to a sample period in 2019 (matched by the lunar calendar date). the plummeting of the migration statistics due to the wuhan lockdown is also depicted in figure 2 . the three figures on the top show the inflows into wuhan, outflows from wuhan and within-wuhan flows, for year 2020 (solid line) and year 2019 (dashed line), matched by the lunar calendar; and the bottom shows the corresponding figures for the national city averages. the first vertical line indicates the date of january 20, 2020 when experts confirmed that 2019-ncov could transmit from human to human; and the second vertical line indicates the date of january 23, 2020 when wuhan was locked down. it is clear that while the flows in 2020 tracked that of 2019 well until january 20, the 2020 level dropped to a fraction of their corresponding 2019 levels, particularly after the lockdown of wuhan. [ table 1 about here] [ figure 2 about here] 6 it is important to emphasize here that the mobility data is about the movement of people from one city to another based on geo-location services of the smartphones; as such a person flowing out of city a to city b is not necessarily a resident of city a, but he/she must have been to city a before moving to city b. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . outbreak data. covid-19 daily case counts are collected from china cdc, which provides daily updates on confirmed, dead, and recovered covid-19 cases in each city. 7 from january 11 to february 29, 2020, the data covers 77,105 laboratory-confirmed covid-19 cases, 2,778 death cases, and 39,392 recovered cases in 296 cities in china. panel b of table 1 presents the summary statistics of covid-19 data, and figure 3 plots the trends of daily statistics of covid-19separately for the epicenter city of wuhan, for other cities in hubei province, and for cities outside of hubei. 8 there are many possible reasons for us to treat the officially reported numbers of confirmed cases in wuhan and other cities of hubei with more caution, and to treat them differently from the data of cities outside of hubei. as the epicenter of covid-19, the health care systems in wuhan and other cities in hubei were overwhelmed by the sheer number of patients who needed laboratory testing, especially in the early phases of the virus outbreak. as such, the over-extended medical system in wuhan and other cities in hubei might have caused delays in the testing of the patients who contracted covid-19; and because of the delay, some patients who contracted covid-19 might have self-recovered, or might have died, before being officially tested; and some who were infected with the virus might be asymptomatic. there is also a possibility that government officials in the epicenter cities had incentives to downplay the severity of the outbreak, at least initially. these considerations impact how we use the outbreak data in section 4. the incubation period of 2019-ncov is long in comparison with sars; moreover, the virus can transmit while the person is still asymptomatic, which increases the probability a person with the novel coronavirus will travel and unknowingly spread the virus to others. 9 to suppress the spread of 2019-ncov, the central government of china imposed an unprecedented lockdown in wuhan starting from 10 am of january 23, 2020, and in other hubei cities several days later. as of february 29, 2020, 80 cities in 22 provinces issued different 7 source: http://2019ncov.chinacdc.cn/2019-ncov/ 8 the spike of confirmed cases observed on february 12 in hubei province is. for the most part, the result of a change in diagnosis classification for which 13,332 clinically (rather than laboratory) confirmed cases were all reported as new cases on february 12, 2020, even though they might have been clinically diagnosed in the preceding weeks. also on february 12, 2020, a new communist party secretary of hubei province was appointed who started his position on the next day. 9 the range of the incubation period for 2019-ncov is estimated to be 2-14 days, or even as long as 24 days. the median incubation period is about 5 days, see lauer et al. (2020) . in contrast, the incubation period for sars is 2-7 days. in addition, sars transmits only after showing symptoms. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . levels of lockdown policies. 10 table a1 in the appendix provides the detailed information about the various forms of population mobility control in different cities. we also plot the geographic distributions of sample cities and cases in figure 1 . [ figure 1 about here] there are several confounding factors in our attempt to causally quantify the impact of lockdown on human mobility, and on the spread of infectious viruses. first, the virus outbreak happens right before the spring festival of the chinese lunar new year, which causes the largest annual human migration every year. 11 second, the virus itself, even in the absence of a mandatory lockdown, may lead to curtailed human movement as people attempt to avoid exposure to the virus in the journeys and public spaces. we refer to this deterrence effect as the virus effect. third, for the city of wuhan and other cities in hubei that are close to wuhan, there is also the possibility of a panic effect, in reaction to the virus. the panic effect can lead to an increase in the population outflow from the epicenter of the virus outbreak, and a decrease of the population inflow to the epicenter, particularly the city of wuhan. the panic effect is likely to peak when the government officially confirmed on january 20, 2020 that the novel coronavirus can transmit from person-to-person. in our analysis below, we create a specific pre-lockdown period before 2,t , which includes the threeday period between january 20 and january 22, 202, to capture the panic effects. 12 note that while the virus effect applies to movement into and out of all cities, the panic effect is more specific to the cities in the epicenter, especially wuhan, and can have a positive effect on outflows, and a negative effect on inflows. 10 within hours of the wuhan lockdown, travel restrictions were imposed on the nearby cities of huanggang and ezhou, and were eventually imposed on all 14 other cities in hubei, affecting a total of about 57 million people. on february 2, the city of wenzhou implemented a partial lockdown in which only one person per household was allowed to exit once every two days, and most of the highway exits were closed. following wenzhou, another six cities, hangzhou, zhumadian, ningbo, haerbin, fuzhou, and zhengzhou also launched similar partial lockdowns on february 4. in another 56 cities, surveillance and tighter controls applied to each neighborhood. in the provinces of liaoning and jiangxi, as well as major cities such as shenzhen, guangzhou, nanjing, ningbo, chengdu and suzhou, checkpoints have been set up to control the inflow population. 11 the migration across china, which officially begins from about two weeks before, and ends about three weeks after, the lunar new year is often referred to as chunyun (meaning spring movement). in 2019, approximately 3 billions trips were made during chunyun, see https://www.cnn.com/travel/article/ lunar-new-year-travel-rush-2019/index.html. 12 the large outflow from wuhan is possible because many people in wuhan are migrant workers and college students with hometowns elsewhere. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . we first examine the impact of city lockdown on inter-city population mobility, including inflow and outflow, between a city pair (i, j). to disentangle the contributions of these confounding factors on human mobility, we exploit many unique sources of variations in the data, and employ several did estimation strategies by comparing different treatment and control groups. the did specification can be described as follows: where i, j, and t respectively index the destination city, origination city, and date; the dependent variable, ln(flow i,j,t ), is the logarithmic population flows received by city i from city j at date t. the definition of treat varies by specific did designs, and we will be explicit about its definition below. the city-pair fixed effect âµ i,j is included to absorb the city-specific and the city-pair specific heterogeneities that may contaminate the estimation of our interested coefficient î² 3 . we also control for the date-fixed effect î¸ t to eliminate the time-specific impact, including the spring festival travel effect. the standard errors are clustered at the daily level. in equation (1), we include two pre-lockdown period indicators: before 1,t is a dummy that takes value 1 for the period from january 11 to january 19, 2020 (4 to 11 days before the wuhan lockdown), which can be used to examine the parallel trend assumption in the did analysis; before 2,t is a dummy that takes value 1 for the period from january 20 to january 22, 2020, three days before the unprecedented wuhan lockdown, but after the official announcement that the novel coronavirus can spread from person to person. 13 before 2,t allows us to capture the panic effect. finally, after t is a dummy that takes value 1 for the sample period after the wuhan lockdown, between january 23 and february 29, 2020. the omitted benchmark period is from january 1 to january 10, 2020. 13 on january 20, 2020, an expert at china cdc confirmed that the novel coronavirus can spread from human to human. the confirmation highlighted the increasing risk of an epidemic. prior to the january 20 announcement, the experts' assessment of the virus was that it was "preventable and controllable," and "at this time, there is no evidence of person to person transmission." 8 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . we also estimate the effect of lockdown on the within-city population movement utilizing the city-level data and a variety of did specifications: where i and t index the city and date. ln(withincityflow i,t ) is the logarithmic within-city population mobility measure for city i at date t. similar to equation (1), treat will be defined according to the did design. before 1,t , before 2,t and after t are defined in the same way as in equation (1). we include the city fixed effects âµ i and date fixed effects î¸ t . the standard errors are clustered at the daily level. [ table 2 about here] in table 2 , we report the results from three sets of regressions specified according to equation (1) for inter-city inflows (panel a) and outflows (panel b), and according to equation (2) for within-city movement (panel c). we implement three models that differ in the estimation sample, and the definition of the variable treat. model 1: wuhan 2020 vs. 284 unlocked cities in 2020. the estimation sample used in the regressions reported in column (1) is the 2020 data for wuhan and 284 cities that were never locked down during the coronavirus outbreak. 14 in panel a when we examine the inflow population, treat takes value 1 if the destination city i is wuhan; in panel b when we examine the outflow population, treat takes value 1 if the origination city j is wuhan. the control group consists of 284 cities that are not subject to any mobility restrictions. in panel c when we examine the within-city mobility, treat takes value 1 if city i is wuhan. we interpret the coefficient estimate of treat * before 2,t as measuring the panic effect of wuhan relative to the unlocked cities; and the coefficient estimate of treat * after t as measuring the lockdown effect. 15 the coefficient estimate of treat * before 1,t allows us to examine whether the parallel trend assumption for did is 14 recall that baidu migration data covers 364 chinese cities, 80 cities implemented some level of mobility restrictions (see table a1 ). 15 if the virus effect is stronger in wuhan than in the unlocked control cities, then the coefficient estimate of treat * after t also includes the excess virus effect on the population in wuhan over the average virus effect experienced by the population in the control cities. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . satisfied. it is important to note that the possibly time-varying spring festival effects and the virus effects are both absorbed in the day fixed effects. based on the coefficient estimate of the term treat * after t , we find that wuhan's lockdown reduces the inflow population to wuhan by 88.06% (= 1 â�� exp(â��2.215)), the outflow population from wuhan by 74.44% (= 1 â�� exp(â��1.364)), and within-city population movements in wuhan by 73.79%(= 1 â�� exp(â��1.339)), relative to all other unlocked cities in the post-lockdown period in 2020. in panel c, we also find that the coefficient of treat * before 2,t is significantly negative at -0.323, suggesting that the official confirmation of the person-toperson transmission reduces the within-city movement in wuhan by 27.6% from jan 20 to jan 22 in 2020. this points to a panic effect for the within-city population flow in wuhan, but we do not observe a significant panic effect for inter-city flows in and out of wuhan in model 1. model 2: wuhan 2020 vs. wuhan 2019. model 1 could be criticized on the ground that wuhan may not be comparable to the 284 unlocked cities -after all, these 284 cities that never imposed any mobility restrictions in the covid-19 outbreak could be very different from wuhan. in model 2, we compare the population movements of wuhan in 2020 to itself in the same matched lunar calendar period in 2019, during which wuhan is free of lockdown and coronavirus outbreak. thus, the estimation sample in model 2 is the daily inflows into and outflows out of wuhan, as well as the daily within-city movements in wuhan for years 2019 and 2020. under model 2, in panel a when we examine the inflow population, treat takes value 1 if the destination city i is wuhan and year is 2020; in panel b when we examine the outflow population, treat takes value 1 if the origination city j is wuhan and the year is 2020. the control group is wuhan 2019. in panel c when we examine the within-city mobility, treat takes value 1 if the year is 2020. under model 2, the coefficient estimate of treat * before 2,t measures the panic effect related to the virus outbreak in wuhan; and the estimate of treat * after t measures the sum of the lockdown effect and the virus effect. the coefficient estimate of treat * before 1,t still allows us to examine whether the parallel trend assumption for did is satisfied. the day fixed effects absorb the possibly time-varying spring festival effects. notice that the interpretation of the coefficient estimate of the term treat * after t differs from that in model 1 because of the differences in the treatment and control groups. under model 2, the estimated coefficients on treat * after t , which, as we explained above, capture both the lockdown and the virus effects, remain negative, and economically and statistically significant in all panels. the estimates suggest that the lockdown of wuhan, together with the deterrence effect of the virus (the virus effect), on average reduces the 10 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . inflow population into, outflow population from, and within-city movements in wuhan by 91.97% (= 1 â�� exp(â��2.522)), 72.39% (= 1 â�� exp(â��1.287)), and 69.49% (= 1 â�� exp(â��1.871)), respectively, relative to the same lunar calendar days in 2019. we also find that the coefficient on treat * before 2,t is significantly positive in panel b and significantly negative in panel c, suggesting that the official confirmation of person-to-person spread of covid-19 creates a panic effect, causing an increase of outflow from wuhan of 107.09% (= exp(0.728) â�� 1), and a decrease of within-city movements in wuhan of 24.19% (= 1 â�� exp(â��0.277)), during the three days after the announcement but before the city lockdown. however, we do not observe a statistically significant panic effect for the population inflow into wuhan, suggesting that people in other cities were not yet sufficiently concerned about the virus outbreak in wuhan and did not avoid traveling to wuhan, even after the official confirmation of the personto-person transmission. finally, we should also point out that the coefficient estimates for treat * before 1,t are all statistically insignificant, which suggests that the parallel trend assumption for the dids are plausible. model 3: wuhan 2020 vs. seven other lockdown cities 2020. in model 2, the coefficient estimates of treat * after t provide us with an estimate of the sum of the lockdown and the virus effects. in order to isolate the lockdown effect from the virus effect, we consider model 3, where the estimation sample consists of data of the city of wuhan and seven other cities that went into partial lockdown on february 2 and february 4, 2020, 12 to 14 days after the lockdown of wuhan, in an effort to curtail the spread of the virus. 16 as we show in table a2 in the appendix, these seven cities are more comparable to wuhan than other unlocked cities in terms of the epidemic situation and other economic indicators, and thus provide a reasonable control group to partial out the virus effect. in particular, it is much more plausible than in model 1 (where the control cities are cities that were never locked down) to assume that the deterrence effect of the virus on human mobility in the seven cities is similar to that in wuhan. the estimation sample for model 3 consists of data from wuhan and the seven cities for the period between january 1 and february 2, 2020. note that during this period, none of the seven control cities were locked down yet, even though they were soon eventually locked down. the definition for treat variables are as follows. in panel a, treat takes value 1 if the destination city i is wuhan; in panel b, treat takes value 1 if the origination city j is wuhan; in panel c, treat takes value 1 if city i is wuhan. the control group consists of the 16 these seven cities are: wenzhou, which was partially lockdown from february 2, 2020; and ningbo, zhumadian, hangzhou, zhengzhou, haerbin, and fuzhou, which were partially locked down on february 4, 2020. as summarized in table a1 in the appendix, partial lockdown includes "closed-off management" on highways, railways and public transport systems; and sets up checkpoints to control the inflow population, and implements surveillance and tighter controls in each neighborhood. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . seven cities. under model 3, the coefficient estimate of treat * before 2,t measures the panic effect related to the virus outbreak in wuhan relative to the seven control cities; and the estimate of treat * after t measures the lockdown effect only. the coefficient estimate of treat * before 1,t still allows us to examine whether the parallel trend assumption for did is satisfied. the possibly time-varying spring festival effects and the virus effects are both absorbed in the day fixed effects. we find that the wuhan lockdown significantly reduces the inflow into, outflow from, and within-city movements in wuhan by 76.64% (= 1 â�� exp(â��1.454)), 56.35% (= 1 â�� exp(â��0.829)), and 54.16% (= 1 â�� exp(â��0.780)), respectively. we interpret these as the pure lockdown effect on population mobility related to wuhan. summary. based on our preferred estimation models, which are models 2 and 3, table 3 summarizes our estimates of the panic effect, the virus effect, and the lockdown effect on inflows into, outflows from wuhan, and within-city population movements in wuhan. [ table 3 about here] in table 3 , the lockdown effects are directly calculated from the corresponding coefficient estimates of treat * after from model 3 discussed above; the panic effects are from the coefficient estimates of treat * before 2 in model 2. for the virus effect, we recognize that the coefficient estimates of treat * after in model 2 incorporate both the lockdown and the virus effects. thus we calculate the virus effect on inflows into wuhan to be exp(â��2.522 â�� (â��1.454)) â�� 1 = â��65.63%, on the outflows from wuhan to be exp(â��1.287 â�� (â��0.829)) â�� 1 = â��36.75%, and on the within-city flow in wuhan to be exp(â��1.871â��(â��0.780))â��1 = â��54.15%. because our models assume that the different effects enter exponentially in explaining the flows -recall the natural log specifications in equations (1) and (2-when we would like to calculate the impact of two or more effects on the population flows, we should not simply add the individual effects. for example, the joint impact of the panic and virus effects on outflows out of wuhan is (1 + 107.09%) * (1 â�� 36.75%) â�� 1 = 30.98%, instead of the simple sum of 107.09% â�� 36.75% = 70.34%. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . we now examine the impact of human mobility on the transmission of 2019-ncov. considering that almost all the new covid-19 cases outside the city of wuhan were confirmed after the wuhan lockdown while almost all inter-city population flows occurred prior to the wuhan lockdown (see figures 2 and 3) , we investigate the imported infections by specifically looking at the impact of population inflows from cities in the epicenter of the novel coronavirus outbreak, namely, wuhan and other cities in hubei province, on the new cases in the destination cities. recognizing that 2019-ncov has a long incubation period, we estimate a dynamic distributed lag regression model taking into account that inflows from wuhan with different lags may have differential impacts on the current new cases in the destination cities. most of the medical literature states that the 2019-ncov virus has a median incubation period of five days, and some can have an incubation period of 14 days or more (see lauer et al. (2020) , e.g.). luckily, our data allows us to incorporate the possibility that contact with an infected person from wuhan or other cities in hubei can result in confirmed infections in the destination city for up to 22 days. the analysis focuses on the daily new confirmed covid-19 cases in the post-wuhan lockdown period from january 23 to february 29, 2020, for cities i that are outside of hubei province. specifically, we run the following regression: 17 where i indexes the cities outside of hubei, and t â�� {23, ..., 60} indicate the date. 18 îº â�� {1, ..., 22} indicates the time lapsed from the inflows from wuhan or other hubei cities till the current date t. ln(1+newcase i,t ) is the logarithm of the number of new confirmed cases in city i at date t. inflow i,wh,tâ��îº and j =i,j =wh,jâ��hb inflow i,j,tâ��îº are the inflows from wuhan, and the inflows from the 16 other cities in hubei to city i, respectively, îº days prior 17 our log-log specification is based on the classical susceptible-infectious-removed (sir) model in epidemiology. 18 date t = 23 indicates the date of january 23, 2020, and t = 60 the date of february 29, 2020. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . to the focal date t. we control for destination city fixed effects âµ i and date fixed effects î¸ t . note that, in this regression we include only cities outside of hubei province for two reasons. first, wuhan and other cities in hubei province are the epicenter of the novel coronavirus outbreak, and we are interested in how population outflows from these cities to other cities outside hubei affect the destination cities' covid-19 cases. second, the confirmed covid-19 cases in wuhan and other cities in hubei province are likely to be inaccurate for the following reasons. first, as widely reported, the health care systems in wuhan and other cities in hubei were totally overwhelmed by the sheer number of covid-19 patients. this made it impossible to conduct laboratory tests on all patients, which can lead to delayed confirmation of infected patients. second, during the delay some of the infected may have healed on their own, or have died before being confirmed. third, local government officials may face strong incentives to under-report the number of infected cases. in section 4.2, we will evaluate the possible downward biases of the officially reported cases in wuhan and other cities in hubei based on our estimates. in contrast, the confirmed cases in other cities are likely to be accurate, as their numbers are not large enough to overwhelm their local health care system; and the incentives to under-report are much weaker in cities outside of hubei. the estimated coefficients î² 1îº and î² 2îº in equation (3) respectively represent the impact of the inflows from wuhan and other cities in hubei îº â�� {1, ..., 22} days ago on the destination cities' new cases today. they are respectively plotted in the top and bottom panels of figure 4 . we also fit a spline smoothed curve of the estimated effects of the different lags of inflows from wuhan and hubei, which both show a clear inverted u -shape with respect to the lags. interestingly, both graphs show that the largest impact on the newly confirm cases today in chinese cities outside hubei comes from the inflow population from wuhan or other cities in hubei about 12 to 14 days ago. the pattern exhibited in figure 4 is consistent with the hypothesis that the incubation period of the 2019-ncov is up to 12 to 14 days, but also consistent with a shorter incubation period coupled with secondary infections. [ figure 4 about here] anecdotal evidence suggests the official statistics of covid-19 cases in wuhan may have been under-reported due to the shortages of testing equipment and other medical resources. with the estimated dynamic effects as shown in figure 4 , which is estimated under the plausible assumption that the reported cases outside hubei province are reliable, we can estimate the "actual"' number of infection cases in wuhan and other cities in hubei. 14 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . to estimate the "actual" number of infection cases in wuhan using the estimated equation (3), we technically need to impute a value for inflow wh,wh,tâ��îº , that is "inflows from wuhan to wuhan." we proxy these inflows by the daily within-wuhan population movement from january 1 to february 29, i.e., by withincityflow wh,tâ��îº . similarly, to estimate the "actual" number of infection cases in other cities in hubei, we need to replace the inflow from city j to itself by the corresponding daily within-city-j population movements. we need to make an additional assumption about the city fixed effects. recall that cities in hubei province were not included in the estimation sample for equation (3), as such there are no city fixed effects estimated for cities in hubei. luckily, it is plausible to assume that the city fixed effects in hubei is the average of the city fixed effects of all chinese cities outside hubei. according to world bank's (respectively, imf's) method of estimating per capita gdp, hubei's per capita gdp in 2018 was usd 10,067 (respectively, usd 10,054), and the average per capita gdp of mainland china was usd 9,769 (respectively, usd 9,750). hubei is not only geographically and demographically in the center of mainland china, it is also economically the average of china. thus we believe it is defensible to proxy the fixed effects of hubei cities by the average of the city fixed effects outside of hubei. [ figure 5 about here] in figure 5 , we plot the estimated daily new cases according to the above-described method using the estimated equation (3), as well as the corresponding cumulative cases for wuhan (panel a) and 16 other cities of hubei (panel b) for the period of january 23 to february 29, 2020. we also plotted the corresponding daily and cumulative officially reported (i.e., documented) cases. we find a persistent gap between the estimated and reported laboratory-confirmed cases in wuhan before february 11, 2020, just before the announcement of a new party secretary for hubei province on february 12, 2020. the estimated "actual" number of infection cases is 2.48 times the reported cases during the first 20 days after the wuhan lockdown, on average. in particularly, we estimate that on january 23, 2020, the day of the wuhan lockdown, 42.17% of our estimated infections in wuhan were undocumented in the sense that the number of officially reported cases on that day was only 57.83% of our estimated infection cases. this gap widened over time, possibly as a result of the overwhelmed health care system, and peaked at 80.03% on january 26. the proportion of undocumented infections started to decline gradually afterward, when more medical support and resources were mobilized across china to support wuhan. as of february 29, we estimate that there were 54,689 total covid-19 infections in wuhan, which is 11.33% higher than the official reported statistics for wuhan -a total of 49,122 cases. the 11.33% discrepancy can be plausibly be explained by the unaccounted for self-healing and death that might have occurred during the early periods of the outbreak between january 23 and early february. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . thus, we are led to conclude that the almost all infection cases in wuhan were able to be treated over time as the stress on the health system was relieved, and moreover, the official statistics were mostly accurate, as can be seen from the left figure on the daily new cases in panel a in figure 5 . it is useful to note that the general pattern of the undocumented covid-19 infections in wuhan before and after the lockdown based on our estimates is consistent with that reported in li et al. (2020) . they use a networked dynamic meta-population model and bayesian inference to estimate the proportion of undocumented infections in the epicenter of the outbreak, as well as the respective inflection rates for documented and undocumented cases. they estimate that 86% of all infection cases as of january 23, 2020 were undocumented. our interpretation of these undocumented cases is broader than the asymptomatic cases (i.e. covid-19 cases that do not show symptoms); we believe that some of the undocumented cases were due to the lack of ability to test the rapidly increasing infection cases in the early period of the outbreak. most of the undocumented cases become documented over time as the care capacity was strengthened in wuhan. in the bottom panel of figure 5 , we plot our estimated daily new confirmed cases and total infection case for 16 cities (other than wuhan) in hubei province, together with the officially reported series. we find that in the 16 cities, infections were more seriously underreported in the first week after the wuhan lockdown when our estimated infected cases are 1.87 times of the reported cases. our estimate reveals a very high rate of undocumented infections on the first day of wuhan lockdown: 79.8%. the gap narrowed gradually with more medical resources provided and more stringent control measures implemented in those cities. by the end of our study period on february 29, 2020, the estimated "actual" number of infections is 17,999 cases in 16 other cities in hubei, which is 17.4% higher than the officially reported cumulative cases (15, 330) . again, the discrepancy between the estimated and officially reported cumulative cases can at least be partially attributed to the unaccounted for self-healing and death that might have occurred during the early periods of the outbreak. locking down wuhan, a city of 11 million residents, was an unprecedented measure to contain the spread of the novel coronavirus. an important policy-relevant question is, then, how many covid-19 cases were actually prevented by the wuhan lockdown in china? to answer this question, we must estimate the counterfactual number of covid-19 cases that would have occurred in other cities in the absence of wuhan lockdown, which would, in turn, . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . require a counterfactual estimate of the outflows from wuhan to other chinese cities, had there been no lockdown of wuhan. in section 3, we provided the estimates of how panic effect and virus effect will separately affect the outflows from wuhan to other cities in china, separate from the lockdown effect. these effects are summarized in table 3 . it suggests that, in the absence of the wuhan lockdown, the virus effect and panic effects would have led to a 36.75% decrease and a 107.09% increase in the outflow population from wuhan, respectively. based on these effects, therefore, in the absence of wuhan lockdown, we would expect that the outflows from wuhan in days after january 23 -the date of wuhan lockdown -to be (1 â�� 0.3675) * (1 + 1.0709) = 1.31 (4) times higher than the normal outflows from wuhan to other cities. we use the daily level of outflows from wuhan to a city in 2019 on the same lunar calendar day as a measure of the normal outflow, and multiple the number by 1.31 to obtain the daily counterfactual inflows from wuhan to the city, had there been no lockdown of wuhan from january 23, 2020. using this estimation method, we find that on average, the estimated counterfactual outflows from wuhan to 16 other cities in hubei between january 23 and february 29, 2020 would be 16,568,984, a level that is 5.97 times the actually observed inflow population observed in the data in 2020 (with the lockdown), which is 2,774,793; similarly, the average inflows from wuhan to the 347 other cities outside hubei in china would be 2,274,455, 3.14 times the actual inflow population to those cities during the same period in 2020, which is 723,574. 19 we denote the counterfactual inflows from j = wuhan into city i at date s â�� {23, ..., 60} from the above calculation as inflow i,wh,s . we assume that the wuhan lockdown did not impact the population movements within other cities, and population flows among other cities. we also assume that all the control measures implemented by other cities after the wuhan lockdown remain in place. thus the parameter estimates of the dynamic lag effects of inflows from wuhan and other cities in hubei, estimated in equation (3), remain valid as an epidemiological diffusion equation that is not affected by human mobility restrictions that result from the wuhan lockdown; the lockdown only affected the human flows. with these considerations in mind, we simulate the counterfactual number of covid-19 cases, had there been no wuhan lockdown, on date t â�� {23, ..., 60} (i.e., from january 23 to 19 recall that outflows from wuhan are not just residents of wuhan; any travelers who entered wuhan for whatever reason and then leave wuhan would be included in the wuhan outflows measured by baidu migration data. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . february 29, 2020) in cities i outside hubei province by the following equation: inflow i,j,tâ��îº +î¼ i (5) whereî² 1îº andî² 2îº are coefficient estimates obtained from regressions specified in equation (3) and reported in figure 4 , and andî¼ i are the estimated city fixed effects from the same regression. note that in predicting the counterfactual covid-19 cases without wuhan lockdown, we use the counterfactual inflows from wuhan to city i for days after january 23 inflow i,wh,s discussed previously. we are also interested in predicting the counterfactual cases in other non-wuhan cities in hubei province using the same method as that described above, with two differences. first, since hubei cities are not included in the estimation of equation (3), we do not have the city fixed effects for the hubei cities. as we argued in section 4.2, it is plausible to assume that the fixed effects of hubei cities are the average of city fixed effects of the cities outside hubei. we maintain this assumption as well in this counterfactual exercise. second, following the same strategy of section 4.2, for a non-wuhan city j in hubei province, we use the within-city-j population movement at date t to proxy for the inflow to city j from city j when we implement equation (5) for non-wuhan hubei cities. in figure 6 , we present the counterfactual estimates of covid-19 cases had there been no wuhan lockdown (in solid curve), and the officially reported cases (in dashed curve) for cities outside hubei province (panel a) and non-wuhan cities of hubei (panel b). the left figure in each panel depicts the model's counterfactual prediction and the actual of daily infection cases, and the right figure depicts the evolution of cumulative cases from january 23 to february 29, 2020. the gap between the estimated counterfactual number of infection cases (the solid curve) and the officially reported cases (the dashed curve) on the right figure represent the number of covid-19 cases prevented by the wuhan lockdown. as of february 29, 2020, the officially reported number of covid-19 in the 347 cities outside hubei province was 12,626, but our counterfactual simulation suggests that there would have been 20,810 cases, had there been no wuhan lockdown. similarly, the officially reported number of covid-19 cases in the 16 non-wuhan cities in hubei was 15,330 by february 29, 2020, but our counterfactual simulation suggests that the number of infection cases would have been 23,400, had there been no wuhan lockdown. that is, the covid-19 cases would be 64.81% higher in 347 cities outside hubei, and 52.64% higher in 16 other cities in hubei as of february 29, in the counterfactual world in which the city of wuhan were not locked down from january 23, 2020. our findings thus suggest that the lockdown of the city of wuhan from january 18 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . 23, 2020 played a crucial role in reducing the imported infections in other chinese cities and halts the spread of 2019-ncov virus. our model also allows us to project when the new infection cases would have peaked in other cities in the absence of wuhan lockdown. as shown by the solid curves in the left figures of each panel, our model projects that in the absence of wuhan lockdown, the new daily infection cases in the 16 non-wuhan cities in hubei would have peaked on february 2, the 9th day after the lockdown of wuhan, at a level of 1,466 daily new cases; and elsewhere in china, it would have peaked on february 3, 2020, the 10th day after the lockdown of wuhan, at a level of 1,082 daily new cases. we also find that the estimated daily new cases in the counterfactual world gradually converge to the reported daily cases from february 22, suggesting that the social distancing measures implemented elsewhere in china would have worked eventually to contain the spread of 2019-ncov virus, even if the city of wuhan was not locked down on january 23 2020, but the initial onslaught on the medical system in all cities in china would have been much more severe, and the total number of infection cases elsewhere would have been significantly higher. [ figure 6 about here] as the 2019-ncov virus spread throughout the world, many countries are also implementing lockdown measures, and mandate social distancing as a policy response to contain the spread of the virus. up to now, our analysis has focused on the events of the lockdown of wuhan -the epicenter of the novel coronavirus outbreak, it would also be interesting to study the impact of lockdowns and/or the social distancing measures in the destination cities in reducing and containing the spread of virus. indeed, chinazzi et al. (2020) point out that travel restrictions to and from mainland china impact the global pandemic of the covid-19 only if transmission within the community is simultaneously reduced by 50% or more, which suggests that social distancing at the destination cities is crucial in preventing the possibly asymptomatic transmission from the source city. moreover, quantifying the effect of social distancing on virus transmission is especially relevant to the stage of pre-epidemic community spread when a person who is not known to have traveled to affected countries, or to have had contact with an infected person becomes infected. as shown in table a1 in the appendix, within the few weeks after the wuhan and hubei lockdowns, various human mobility restrictions were imposed on 63 other chinese cities outside hubei. as described in table a1 , the "lockdowns" in destination cities varied in their 19 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . degree of strictness, from building entrances checkpoints to establishing quarantine zones, and from public transit shutdowns to strict limits on the inflows into the city, outflows out of the city, as well as within-city population movements. we interpret the human mobility restrictions in the destination cities as an enhanced social distancing policy, because the "lockdown" rules in the destination cities are not as strict as those implemented in wuhan. in this section, we use the variations in the destination cities' "lockdown" policies to study how the effects of inflows from wuhan and other cities in hubei province on the spread of covid-19 cases in the destination cities are impacted by the changes in the destination cities' lockdown policies, which would drastically impact the within-city population movements in the destination cities. 20 specifically, we estimate the following specification that is a modified version of the regression specification described by equation (3): where the new variable lockdown i,t is a dummy that takes value 1 if time t is a date after destination city i's "lockdown" date, if at all; and 0 otherwise, where the lockdown dates of the 63 cities outside hubei are listed in table a1 . if city i never implemented any formal lockdown policy, the dummy is always 0. therefore, the coefficients, î² 1îº and î² 2îº , respectively, measure the impact of the lagged inflows from wuhan and hubei îº days earlier on the destination cities' current new cases before the city's imposition of its "lockdown," while î³ 1îº and î³ 2îº represent the effect on destination cities' of wuhan and hubei inflows after the imposition of the city's lockdown. if enhanced social distancing that comes from the "lockdown policies" imposed at the 63 chinese cities outside hubei is effective in reducing the spread of the virus from population flows from the epicenter of the virus, then we expect that î³ 1îº and î³ 2îº to be smaller than î² 1îº and î² 2îº , respectively. 20 see panel c of table 2 for the evidence from wuhan lockdown on within-wuhan population movement. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . in figures 7 (respectively, figure 8 ), we plot the estimated coefficients, î² 1îº and î³ 1îº (respectively, î² 2îº and î³ 2îº ) in panel (a), and their differences in panel (b) for the lagged effects of inflows from wuhan (respectively, 16 non-wuhan cities in hubei) on the daily new cases in destination cities outside hubei province. we find that the estimated lagged effects of inflows from wuhan and other cities in hubei before the destination city's lockdown, if any, show little change compared to the coefficients in figure 4 however, the coefficient estimates of lagged inflows after the destination city's lockdown policies appear to be insignificant and indifferent from zero on almost all lags. in panel (b) of figures 7-8 , we plot the differences between the estimated effects pre and post the destination cities' lockdown policies. we find that the differences between the estimated coefficients pre and post destination city lockdowns are positive and statistically significantly at at-least 10% level for 7 (respectively, 5) of the first ten lagged population inflows from wuhan (respectively, 16 other cities of hubei), and the other differences in lagged estimates are statistically insignificant. these results suggest that the enhanced social distancing policies in the destination cities are effective in reducing the impact of population inflows from the source cities of wuhan and other cities in hubei on the spread of 2019-ncov virus in the destination cities. this in turn implies that population inflows from the epicenter contribute to the spread of infection in the destination cities only before the social distancing measures are applied; it appears that after implementing their various control measures, cities adopting an extended lockdown can flatten the upward trajectory of the virus. in this paper, we quantify the causal impact of human mobility restrictions, particularly the lockdown of the city of wuhan on january 23, 2020, on the containment and delay of the spread of the novel coronavirus, and estimate the dynamic effects of up to 22 lagged population inflows from wuhan and other hubei cities, the epicenter of the 2019-ncov outbreak, on the destination cities' new infection cases. we find that the lockdown of wuhan reduced inflow into wuhan by 76.64%, outflows from wuhan by 56.35%, and within-wuhan movements by 54.15%. using counterfactual simulations with these estimates, we find that the lockdown of the city of wuhan on january 23, 2020 contributed significantly to reducing the total infection cases outside of wuhan, even with the social distancing measures later imposed by other cities. we find that the covid-19 cases would be 64.81% higher in the 347 chinese cities outside hubei province, and 52.64% higher in 16 non-wuhan cities inside hubei, in the counterfactual world in which the city of wuhan were not locked down from january 23, 2020. we also find that there were substantial undocumented infection cases in the early days of the 2019-ncov outbreak in wuhan and other cities of hubei province, 21 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . but over time, the gap between the officially reported cases and our estimated "actual" cases narrows significantly. we also find evidence that imposing enhanced social distancing policies in the 63 chinese cities outside hubei province is effective in reducing the impact of population inflows from the epicenter cities in hubei province on the spread of 2019-ncov virus in the destination cities elsewhere. the results from our analysis provide valuable causal evidence on the role of human mobility restrictions on the containment and delay of the spread of contagious viruses, including the 2019-ncov virus that is now ravaging the world. enhanced social distancing in the destination cities, and, if an epicenter can be identified as was the case for the city of wuhan in china, a lockdown, can play crucial roles in "flattening" the daily infection cases curve, giving the stressed medical system a chance to regroup and deal with the onslaught of new infection cases. although our study focuses exclusively on the effect of human mobility restrictions on the spread of 2019-ncov virus in china, our estimated results can have general implications to other countries in their fight against the novel coronavirus. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 /2020 . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . (1) and (2). the control and treatment groups for models 1-3 are described in the text. fixed effects of city-pair and daily are included in all columns in panels a and b, and fixed effects of city and daily are included in all columns in panel c. standard errors are clustered at the daily level. *** significant at the 1 percent level. ** significant at the 5 percent level. * significant at the 10 percent level. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . (2) and (3) of table 2 . *** significant at the 1 percent level. ** significant at the 5 percent level. * significant at the 10 percent level. . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.24.20042424 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10. 1101 /2020 notes: this figure plots the dynamic effects of lagged inflows from wuhan (left) and 16 other cities in hubei (right) from estimating equation (3). we add spline smoothing fit curves (in red) using the rcspline function and plot the 95% confidence intervals (the vertical green whiskers). . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/10.1101/2020.03.24.20042424 doi: medrxiv preprint . cc-by-nc-nd 4.0 international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint . it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint (6). we add spline smoothing fit curves using the rcspline function and plot the 95% confidence intervals (the vertical green whiskers). . it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint (6). we add spline smoothing fit curves using the rcspline function and plot the 95% confidence intervals (the vertical green whiskers). . it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint notes: this table provides summary statistics on the count of total confirmed cases as of february 2, 2020, and on daily average population inflow, outflow, and within-city flow between january 12 and march 12 in 2019, and on permanent population gdp as of december 2019, for cities with different level of controls. . it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the the copyright holder for this preprint human mobility networks, travel restrictions, and the global spread of 2009 h1n1 pandemic a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster human mobility and the spatial transmission of influenza in the united states the effect of travel restrictions on the spread of the 2019 novel coronavirus strategies for mitigating an influenza pandemic natural disasters and population mobility in bangladesh will travel restrictions control the international spread of pandemic influenza clinical features of patients infected with 2019 novel coronavirus in wuhan, china effect of non-pharmaceutical interventions for containing the covid-19 outbreak in china the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) the reproductive number of covid-19 is higher compared to sars coronavirus predictability of population displacement after the 2010 haiti earthquake networks in the modern economy: mexican migrants in the us labor market impacts of social and economic factors on the transmission of coronavirus disease (covid-19) in china patterns and limitations of urban human mobility resilience under the influence of multiple types of natural disaster consensus document on the epidemiology of severe acute respiratory syndrome (sars) which means all public transport and private vehicles are banned in the city, all residential buildings are locked down, and residents are not allowed to leave the city. cities in panel b are under partial lockdown, majority of the public transportation has been temporarily shut down, checkpoints has been set up to control the inflow population, and surveillance and tighter controls in each neighborhood. cities in panel c set up checkpoints and quarantine zones, and public transport maintains normal operation. key: cord-262104-oig3qrr7 authors: brüssow, harald title: covid‐19: test, trace and isolate‐new epidemiological data date: 2020-06-08 journal: environ microbiol doi: 10.1111/1462-2920.15118 sha: doc_id: 262104 cord_uid: oig3qrr7 in the absence of an efficient drug treatment or a vaccine, the control of the covid‐19 pandemic relies on classic infection control measures. since these means are socially disruptive and come with substantial economic loss for societies, a better knowledge of the epidemiology of the new coronavirus epidemic is crucial to achieve control at a sustainable cost, and within tolerable restrictions of civil rights. this article is protected by copyright. all rights reserved. comprising 10'800 participants (gudbjartsson et al., 2020) . very similar information was reported in data describing household transmission in wuhan, where children showed a 4% infection rate compared with 17% in adults. . likewise, in a study from hunan children had a threefold lower infection risk than adults . in contrast, the infection risk in children from shenzhen, china was similar to that in adults (bi et al., 2020) . however, all studies concur that disease in children is generally mild, if not asymptomatic. asymptomatic cases raise problems for contact tracing and containment, but it is currently not clear to what extent infected children transmit the disease. three asymptomatic sars-cov-2-positive adolescents showed transmission to family members (liao et al., 2020) while data for transmission from children are still absent. one special problem should still be mentioned in this context: in italy, pediatric hospitalization decreased substantially during the covid-19 epidemic. when the general population avoids hospitals for fear of infection, it can have a negative health impact. an increased number of deaths occurred in italy due to delayed arrival of children in hospitals, while no child died from covid-19 in italy (lazzerini et al., 2020) . the fear of hospitals has also been responsible for a deficit in the treatment against stroke in adults in the us (kansagra et al., 2020) . the statistics for the covid-19 epidemic have shown that the older population has suffered the greatest loss of life, and that nursing homes have been hotspots for transmission. two detailed studies from the us document these given facts. at the end of february 2020, a cluster of 167 epidemiologically linked covid-19 cases were reported in several long-term care facilities in washington state. of those, 144 cases were residents (median age 83 y), 55% of them were hospitalized, and 33% died. in comparison only 16 cases had been visitors, 50% of whom were hospitalized, but none died. further 50 cases were among the health care personnel, of whom only 6% were hospitalized, but again none died. factors favoring the outbreak were: health care personnel who showed up to work with symptoms; some of the personnel worked at more than one facility; and some residents were transferred between facilities. in the early stages of the epidemic, contributing factors to this outbreak were: an unawareness of the risk; a lack of diagnostic tests; and inadequate personal protection equipment (mcmichael et al., 2020) . currently, 1.3 million us americans reside in nursing homes. one in ten of >1'300 accredited nursing facilities reported covid-19 cases. an epidemiological survey in such a facility demonstrated the extent of the problem: the first infection in this nursing home was introduced by a symptomatic nurse, and then a week later the first resident tested positive. a further 5 days later, half of the residents from this unit tested positive for viral rna. during the following 2 weeks, 30 to70% of the residents in other units of this home became infected, along with 19% of the staff. notably, more than half of the residents were asymptomatic when they tested positive for viral rna. four days later, 89% of them had developed symptoms. the rest remained asymptomatic. mortality was high at 26%. importantly, asymptomatic, pre-symptomatic, and symptomatic residents did not differ with respect to viral load and infectious virus release. all viruses showed identical genome sequences guangdong cases. in guangdong province of china, all return visitors from wuhan/hubei province, their contacts, and all of the local hospitalized patients were tested for viral rna. 1.6 million tests were used to identify 1'400 sars-cov-2-positive cases; 1000 patients had had exposure to infected people from hubei. half of the local transmissions occurred within households. by mid-february, the local spread was controlled, but in march new cases were imported from abroad. sputum samples showed the highest viral titers, followed by oropharynx, stool, and finally nasopharynx samples. critical and severe cases showed higher viral titers than moderate and mild cases, but the differences were small. viruses from 53 patients were sequenced and compared with 177 sars-cov-2 sequences deposited in the database. single nucleotide polymorphism (snps) were detected at 97 nucleotide positions scattered through the viral genome; 77 variant sites were only seen in a single virus isolate. on a phylogenetic tree, the guangdong sequences were interspersed between the viral sequences from wuhan and those isolated abroad, documenting a recent, single source outbreak of a virus showing a low mutation rate (lu et al., 2020a) . usa west-to-east spread. the first case of covid-19 in the us was reported on jan 19 at the northwest coast of washington state and was imported from china. from march 1 to 19 the number of cases in the us increased from 70 to 13'000. epidemiologists investigated the first nine covid-19 cases on the east coast (connecticut) that were observed in mid-march with genome sequencing. only one sequence exactly matched the viral sequences from china, but the patient had not traveled to china. the viral sequences from seven further patients, clustered with a large us clade known from washington state, documented a rapid west-to-east national spread of the novel coronavirus in the us. international air travel restrictions had no, or low, impact on the epidemic spread in the us. the viral genome was rooted in a single ancestor coronavirus in wuhan by fewer than 10 mutations, and it had accumulated about 2 nucleotide changes per month during its spread across the us, which is a low mutation rate for a 30'000 nucleotide long viral rna genome. with the portable oxford nanopore technologies minion platform, viral genomes were sequenced within 14 hours after having received the sample, theoretically allowing near real-time molecular epidemiology of the epidemic spread (fauver et al., 2020) . china. in wuhan, 105 index cases of patients suffering from moderate covid-19 symptoms (fever, cough, fatigue) were investigated for secondary transmission to 392 household contacts. the average household size was 4 persons. the index case persons remained at home for a documented number of days before seeking medical advice. in total, 64 contacts (16%) were infected, 9 without symptoms, and the rest experienced moderate disease. the time lapse between primary and secondary infections was 6 days. the transmission probability was age-dependent: it was 4% in children and 17% in adults. the highest transmission rate was seen in 50 to 60 year-olds, but not in >60 year-old household members. spouses experienced a 28% infection transmission rate. when the index case was quarantined directly after symptom onset, transmission rate was 0% . in shenzhen, 391 cases were recorded, 77% of which were detected through the surveillance of symptoms. most cases were mild (26%) or moderate (65%). only 9% of infections were associated with severe disease, which correlated with male sex and older age; 3 patients died. the researchers identified 1'281 close contacts for the index cases; 8% of these had become infected. an increase to 16% in the rate of infection was seen in those who lived or traveled with index case persons. interestingly, infection risk was comparable for all age groups ranging from 0 to 70 y old. however, half of the children showed no fever, and severe infections were rare in people under the age of 40. notably, 80% of secondary infections were traced to only 9% of the index case persons (bi et al., 2020) suggesting an important role of "super-spreaders" in infection transmission. it would be helpful for public health if characteristic traits of super-spreaders were known. adding viral-specific igg antibody tests to the toolbox of covid-19 have allowed the connection between three previously separated infections clusters in singapore. an infected traveler from wuhan attended a church meeting, thereby infecting a secondary person (case x), who transmitted the virus to another subject during a family gathering, who then transmitted the virus to a large number of people in a second church. case x tested negative for viral rna and represented the missing link between the events. case x showed a strong serological response to sars-cov-2, then connecting the links in the chain (yong et al., 2020) . iceland. from among 9000 high risk icelanders (persons who were symptomatic, or had contact with infected persons, or who traveled to a high risk country) 13 % tested positive for sars-cov-2 rna. children under 10 years from that high risk group showed a 7% rna detection rate compared with 14% in subjects older than 10 y. before mid-march, travel exposure to austria and italy was a common denominator in the positive subjects. after mid-march, travel to uk was the biggest risk factor. in mid-march, a representative sample of 11'000 subjects from the general population of iceland (360'000 inhabitants) was tested, and 0.8% tested positive for sars-cov-2 rna. in april, another sample of 2000 subjects from the general population showed a similar rate of viral excreters. in the general population, males were more frequently virus-positive than females. the highest prevalence was seen in 40 y-old subjects, while no children under 10 y were infected. five hundred viral genomes, isolated from infected icelanders, were sequenced. the genomes were clustered into 42 distinct clades. during the early epidemic phase in iceland, nearly all sars-cov-2 isolates belonged to the a2 clade which was also frequently found in central european populations. viral genome sequencing identified networks of up to 14 linked infections. transmission occurred in the early phase via international travel, but later via infection from family members (gudbjartsson et al., 2020) . airborne: cough, sneeze and speech. australian engineers evaluated the literature about the reach of pathogen transmission by coughing and sneezing. the 1 to 2 meter rule has been set since the 1940s by photography, physical calculations, and through simulations. distinct models (turbulent jets vs. puffs) have been used, but not all used appropriate parameters for humidity and temperature. it remains unclear which conditions apply to the human respiratory excretions when handling infected patients in a clinic (bahl et al., 2020) . newer high speed pictures of a coughing volunteer show a turbulent jet plume that extends over 0.5 meter (tang and settles, 2020) . high speed pictures of a sneezing volunteer revealed exhaled air, muco-salivary filaments and drops. the turbulent puff cloud disintegrated into droplets that settled within 1 to 2 m distance. some droplets evaporate and become suspended in the puff and travel a room within a few minutes to land 6 to 8 m away from the sneezing person (bourouiba, 2020) speech generated droplets in front of the mouth increased with the loudness of the voice. holding a cloth in front of the mouth suppressed the droplet detection (anfinrud et al., 2020) . a who communication led to a controversy saying that there is not enough evidence that sars-cov-2 transmission is airborne. who defines airborne transmission as being via aerosols as opposed to transmission by droplets. since most covid-19 transmission seems to occur through close contact, droplets have been considered to be the more likely vehicles. whatever the exact transmission route by air, avoiding crowds, standing next to a person for too long, and increasing the rate of ventilation in closed rooms without air recirculation are reasonable precautions (lewis, 2020) . physicians recommended face mask use, even when scientific evidence for its effectiveness is lacking, in comments to leading medical journals. recent reviews have concluded that: no randomized trials with masks have been conducted; that the benefit of masks over no masks (but not of respirator masks over paper masks) was shown in an influenza epidemic in australia; that some benefit of masks was seen when worn by symptomatic, but not by asymptomatic cases during an influenza epidemic; that no data exist which directly support the use of mask wearing by the public; that no significant effect was seen for household use of masks against influenza transmission. therefore, who initially recommended masks only for symptomatic cases. cdc first advised against mask use by the public but have now changed their policy by recommending even self-made cloth masks for wide use. harm (e.g. increase of co 2 level under the mask) is low if not used by small children or elderly people with disabilities (cheng et al., greenhalgh et al., 2020) . as assessed by viral rna detection, air and surfaces in a wuhan hospital were widely contaminated during the height of the epidemic in china. contamination levels were greater on the intensive care unit ward than on the general ward. the transmission of sars-cov-2 might reach up to 4 meters distance. however, no medical staff in that particular hospital was infected. the authors admit two limitations of the study which prevent firm conclusions from being made. first, viral rna detection does not mean infectious virus detection, and second, the minimum infectious dose of sars-cov-2 for humans is unknown . when reviewing the official recommendations, the consensus seems to be to use a respirator for high risk interventions which create aerosols in the icu, and to use surgical masks on the general ward with low risk activities (bahl et al., 2020) . singapore hospital. the environment of three covid-19 patients from a ventilated hospital infection ward in singapore was tested for viral rna presence by rt-pcr. after routine cleaning of high touch areas and of the floor, no viral rna was found in the air, on hospital room surfaces or on the personal protection equipment of the treating physician. before routine cleaning, however, 16 of 20 room sites (table, chair, floor, window, toilet) and the shoe protection of a physician tested positive. room air samples and hospital corridor floors were, however, negative for viral rna. for infection control, regular room cleaning and handwashing were judged to be essential (ong et al., 2020) . primit study. it is more problematic to establish a control when a family member with mild infection remains at home. there is only one behavioral intervention study that has proved to reduce respiratory viral transmission within households, the primit germ defense study. the key interventions are web-based instructions about handwashing given to 10'000 intervention subjects in uk, but not to 10'000 controls. infection transmission was reduced by 20% and infection severity was also reduced, albeit modestly (little et al., 2015) . the rationale behind the idea was to reduce the viral load by which contacts are particularly exposed, such as through hand-to-eye contact, since the conjunctiva supports sars-cov-2 replication (hui et al., 2020; little et al., 2020) . in italy, the epidemic started in lombardy and veneto. lombardy strengthened their hospital capacity and increased icu beds, while veneto opted for strict containment and mass testing in 4% of the population. lombardy experienced 47'000 more cases than veneto and also had a much higher crude case fatality rate (18% vs 6%). the higher death rate is probably explained by the delayed public health response (odone et al., 2020) as also seen in the us (anonymus, 2020) . the swedish government had recommended a number of trust based measures (social distancing from old people, handwashing, home office, travel reduction), but refrained from closing borders, schools, restaurants and bars, partly because the swedish law does not allow lockdowns. the case reduction of seasonal influenza and norwalk diarrhea provided documented effectivity of the measures taken (paterlini, 2020) . however, compared with neighboring finland and norway, sweden experienced a tenfold higher number of deaths for a 1.5 fold larger population, but the absolute numbers are still small (3700 vs. 300 for sweden and finland, respectively, may 18). in the us, the individual states and cdc have many legal options for quarantine (for the segregation of exposed people) and isolation (separation of infected people from the general population) in such cases as with sars. the establishment of broad sanitary cordons in which entire geographical areas are quarantined (as has happened in wuhan) will raise constitutional questions in the us. the us recommendations say that patients who show mild symptoms should stay home and notify their employer electronically. low-wage workers cannot afford to stay off work, but the us senate is in the process of establishing bills for paid sick leave and unemployment insurance (parmet and sinha, 2020) . kong. the control measures that stopped the epidemic locally have included: intense infection surveillance of incoming travelers; isolation of covid-19 cases in hospitals; contact tracing and quarantine in holiday camps; and school closure but no lock-down, thus preventing the crisis from having a negative economic impact. a total of 715 cases were confirmed, half imported, and the rest locally transmitted with a reproduction number that quickly decreased to values around 1; and 13% of virus-positive subjects were asymptomatic. the control measures also stopped an ongoing seasonal influenza epidemic. surveys showed that the population agreed to participate in the measures. they kept social distancing and made behavioral changes (99% wearing masks outside house, 93% increased hand hygiene, 83% staying at home as much as possible). the study could not differentiate the impact of each individual measure. unfortunately the full effect of school closure is still unknown because the susceptibility of children for covid-19 and their capacity to transmit the infection has not yet been established . china has contained the covid-19 epidemic through a combination of different measures including drastic ones. an international team of epidemiologists developed a computer model that described the dynamics of the epidemic and tested the impact of the different containment measures by using computer simulations. without any intervention, a 100-fold higher number of cases would have occurred in china, resulting in over 10 million cases. without travel restrictions, the epidemic would have expanded more widely over the western provinces. early detection and isolation of patients reduced the number of cases by 5fold, while social distancing and contact reduction led to a 2.6-fold reduction. however, without contact reduction, the epidemic would have, over time, increased exponentially across the regions. initiating the intervention one week earlier would have decreased the number of cases by 66% or, if done one week later the number of cases might have increased by 3-fold. a delay of 2 or 3 weeks would have increased cases by 7-and 18-fold, respectively. lifting travel restrictions will result in a new rise in case numbers, but even moderate levels of social distancing could keep this increase in check. partial maintenance of npi may prevent, or at least delay, the arrival of second wave infections (lai et al., 2020) . contact surveys were conducted in wuhan and shanghai during the height of the covid-19 epidemic in china. before the epidemic, people reported between 15-18 contacts (two-way conversations, physical contact) per day. this number was reduced to 2 during the containment period. contact reduction was most significant for school-age children who, before the intervention, reported the greatest numbers of contacts out of all of the age groups, followed by adults at the workplace. during containment, contacts were mainly within families (80-95%). the survey was consistent with data from inner city mobility. all contacts of patients in hunan province were placed under medical observation and tested for excretion of viral rna. from these contact data it was deduced that children (<14 y) had an infection rate that was only a third as high as adults (15-65y), while older individuals had a 50% higher infection rate than young adults. based on these data and on a mathematical infection model, the authors concluded that social distancing alone is sufficient to control covid-19 spread. proactive school closure alone cannot interrupt transmission but can reduce the peak incidence of the disease by half, and it can delay the epidemic ). these are model simulations based on assumptions on infection transmission by children for which only few data are currently available. the reopening of schools in several countries will hopefully settle some questions with observational data. psychologists argue that contact-seeking is a basic human response to danger. this inclination takes over when an invisible infection threat is perceived. this instinct is only opposed by disgust when infected persons show appalling clinical signs which is not the case for sars-cov-2 infected subjects in pre-symptomatic or asymptomatic state. it will be increasingly difficult for health authorities to impose social distancing, as proven by the street demonstrations against containment measures in the us and in european countries by differently motivated opposition groups. the authors argue that the increased use of the internet as a substitute for contact can become an important public health tool to achieve physical distancing without social distancing (dezecache et al., 2020) . by may 18, the johns hopkins university registered 4.7 mio cases worldwide. the lion's share is from the us with 1.4 mio cases, compared with 84'000 cases reported by china. one should interpret these data with caution. the definition for a confirmed case of covid-19 was changed five times in china, which accounts for the increase in knowledge about the epidemic. scientists from the who collaboration center in hong kong calculated that when the fifth version is applied, the total number of cases in china would increase from 55'000 to 230'000, but the transmission patterns in mainland china would not change . the case number also depends on the intensity of viral testing and the capacity of the public health system to report the number of cases. with nearly 90 '000 deaths, the us number greatly surpasses the 4'600 deaths reported in china. it is still difficult to assess the morbidity and mortality impact of the covid-19 pandemic on the population. even mortality rate is not a clear figure since it is reported differently in different countries. while death is a clear diagnosis, the cause of death isn't. it might not be evident whether somebody died with or from covid-19, particularly in nursing homes. some countries attribute death to covid-19 if the virus was present at death. others attribute each death in nursing homes to covid-19 during the height of the epidemic -as was done in belgium, which explains its high mortality data. many deaths occurred while people also had underlying health problems (comorbidities), therefore they were already at increased risk of death. an international consortium of demographers called for the publication of excess mortality data. by comparing mortality statistics for a given epidemic period with a corresponding time period during previous years without that epidemic, the absolute impact of an infection can be assessed. such data are still largely lacking in the literature. excess mortality rates should best be calculated for both sexes and for each 5-y age range separately (leon et al., 2020) . first data have just now been reported: in march/april the care sector of england and wales alone has seen 20'000 excess deaths over the figures of previous years. covid-19 deaths at care homes were three times as high as covid-19 deaths in hospitals (burki, 2020) . excess mortality calculations have been done globally for seasonal influenza, arriving at 300'000 to 600'000 influenza-associated deaths occurring annually (iuliano et al., 2018) . while the majority of influenza mortality applies to elderly people, the death rate is also substantial for children at an estimated 34'000 deaths in 2018 . in comparison, the global death toll of covid-19 is now 315'000 (status may 18). a direct comparison of these two figures is difficult for two reasons: death levels are affected by vaccination campaigns against seasonal influenza and by strict containment measures for covid-19. it seems plausible that without any containment measures covid-19 mortality would surpass greatly the number of deaths from seasonal influenza. the presumption that the covid-19 mortality is comparable to that of seasonal influenza deaths is fundamentally flawed because it compares numbers which are obtained by different methods. the death rate for covid-19, which has just crossed the 100'000 figure in the us, is an actual count of dead patients. in contrast, the 23'000 to 61'000 annual deaths from seasonal influenza quoted after influenza epidemics in the us are estimates by the cdc of influenza deaths based on calculations from models. the death counts actually reported to us health authorities ranged from 3'400 to 15'000 deaths per year during an influenza epidemic in the us. expressed as deaths per peak week, influenza claimed a maximum 1'616 deaths per week, while covid-19 took about 15'000 lives per week at its peak in the us (faust and del rio, 2020) . wuhan. an international consortium of epidemiologists has estimated that 66'000 people were infected in wuhan and that 2800 have died; 70% were infected through household contact, 25% through public contact, and 5% in hospitals. from a peak number of 2000 new infections, wuhan currently has 10 or fewer new infections per day. safe strategies are now needed for the exit from lockdown measures. when lifting the lockdown to a 100% pre-quarantine social contact level, a computer model showed that a 95% face mask wearing would be needed to ensure a complete elimination of infections. in contrast, with only 50 % face mask use and a lifting date of strict measures before april 25 to pre-quarantine level, the conditions in this model would lead to a major second wave of infection. maintaining a contact rate below pre-quarantine level combined with a high percentage of face mask wearing is essential while now the restrictions have been lifted in wuhan-at least until a vaccine becomes available. however, face mask provision for such large populations represents logistical challenges and must not cause a shortage of protective gear for health personnel (zhang et al., 2020a) . in mainland china, 13'400 confirmed cases and 120 deaths were reported by march 18. in beijing and shenzhen, most cases have been imported from wuhan and the reproduction number r remained below 1.0. in shanghai and wenzhou, local cases dominated but r rose to greater than 1 for only one january week. case fatality was 1% compared with 6% in hubei. relaxing the restrictions could lead to a second wave of exponential infection from imported cases in a nonimmune, susceptible population. maximizing economic productivity under the < 1 constraint can, according to this study, only be possible with a real time prevalence determination of new infections through extensive testing . other epidemiologists working on outbreak data from mainland china observed a sub-exponential increase of cases from the beginning, instead of an expected exponential growth for an unconstrained epidemic. model calculations showed that the containment measures (the quarantine of exposed, and the isolation of infected persons) which depleted the number of susceptible individuals for the virus, reproduced the actually observed case development. similar strategies are recommended in the event of a future outbreak (maier and brockmann, 2020) . harvard model. epidemiologists from harvard university derived projections from model calculations about the future dynamics of the covid-19 epidemic. when anticipating short term immunity (as observed for seasonal common cold coronaviruses), they predict annual winter epidemics for sars-cov-2. with intermediate levels of immunity persistence, epidemics would become biannual. long-term immunity (as in the case of sars-cov) would lead to the extinction of the virus, even in the absence of social distancing. they also calculated that it needed 20 weeks of social distancing to reduce the peak number of infected persons. if the reproduction of the virus is reduced by more than 60% through lockdowns, the infection peak is predicted to shift to the next winter season with high numbers because no herd immunity has been achieved (kissler et al., 2020) . a central concept of epidemiology is herd immunity; the percentage of persons with protective immunity needed in a population to stop the propagation of an infectious agent. when this threshold is crossed, the remaining susceptible persons are protected from infection. the threshold level depends on the "force" of the infectious agent which is expressed by the basic reproduction number r 0 ,which is defined as the number of secondary infections caused by an index case. in infection modeling, herd immunity threshold and r 0 are linked by a simple mathematical function. sars-cov-2 has a higher r 0 "infectious force" than influenza virus, but a much lower one than "flying infections" such as chickenpox or measles. it is anticipated that a population needs a herd immunity of 50 to 80 % protected people to stop the covid-19 epidemic. the initial strategy of the uk government was to let the epidemic roll over the country to achieve this herd immunity, in contrast to containment policies which prevent exposure, but which also prevent immunity development in the population. this strategy has theoretical advantages (fewer economic losses when a lockdown is avoided, and a protected population in the event that no vaccine becomes available). however, it comes at a cost. if you allow, let's say, 60% of the population to get infected, you can calculate the cost of this strategy with the help of the infection fatality rate (ifr). in contrast to the case fatality rate (cfr) which expresses the number of deaths per clinically ill patients (which varies from 1.4% to 15% for covid-19), ifr is the number of deaths per infected individual. the number is, of course, lower than crf. while we know, approximatively, the number of covid-19 deaths and covid-19 cases, we do not definitively know the number of infected persons, since this would require large and systematic seroprevalence studies, but which are lacking. current estimates suggest 0.6% as a realistic approximation for ifr. with that figure, one can calculate that achieving herd immunity through natural infection with sars-cov-2 would cost the lives of 150'000 uk citizen or more than 1'000'000 us citizens. this death toll was considered as too high by the uk government, which then changed strategy by declaring a late containment strategy (randolphe and barreiro, 2020) . delays in imposing containment measures were predicted to lead to 10-fold or higher number of cases and fatalities. this prediction might explain why the us and uk have such high case and death statistics in international comparison. mobile phone technology. epidemiologists from the uk and us have developed a real-time datacapture platform applicable for mobile phone use for the self-guided collection of population-level data (cope consortium). the app queries location, age, health risk factors and asks daily for new symptoms and diagnostic test results. a test run with 1.6 million users in uk showed that the most common symptoms were fatigue and cough. anosmia (loss of smell) appeared as a strong predictor of covid-19, while fever was not a diagnostic criterion unless combined with other symptoms. the reported symptoms predicted that there would be changes in the number of cases as indeed reported from health authorities 5 to 7 days later. the tool will be important for a controlled safe exit from confinement measures. also, long-term effects of the disease, and the impact of the covid-19 epidemic on social relations, mental health, and financial outcome can be evaluated with this tool. machine learning could also reveal new disease manifestations of the epidemic (drew et al., 2020) . anosmia is an interesting symptom. a preliminary evaluation of a covid-19 symptom tracker smartphone app from uk users showed that the loss of smell was reported by 59 % of people with respiratory infection who tested positive for sars-cov-2, compared with 18% of respiratory patients who tested negative. clinical criteria which allow a diagnosis of covid-19 without a viral rna test would be welcome for mass screening and telemedicine in an epidemic situation. french physicians have also reported that many covid-19 patients reported loss of smell and loss of taste, without nasal congestion. when these criteria were combined in a retrospective questionnaire this combination of signs had a sensitivity of 42% and a specificity of 95% for detecting covid-19 patients (bénézit et al., 2020) . these observations are not surprising since the highest expression level of the sars-cov-2 receptor ace-2 was shown in the respiratory tract, more specifically in the nasal epithelia. us physicians even suspected that sars-cov-2 might, in addition to the respiratory and alimentary tract, also infect cranial nerves (i.e. being neurotropic) which potentially explains the observation of neurological signs in 9 % of covid-19 patients (chu et al., 2020) . seroprevalence studies. antibody tests are an important tool in a staggered release of population groups out of lockdowns because such tests identify people who have been exposed to the infection and who are potentially immune to infection. so far, only preliminary data became available from 3'300 volunteers from santa barbara county in california. one out of 66 (1.5%) showed antibodies to sars-cov-2. this number is 50-fold higher than the number of the official case count was for this area in early april. in a preliminary survey in geneva, less than 5 % of a population sample showed viral-specific antibodies in preliminary surveys. in a town with 12'000 inhabitants in germany, 500 people were antibody tested following carnival parties and an infection rate of 15% was determined. these datasets cannot be extrapolated to the population at large. in addition, the antibody tests were only validated with a small set of positive and negative test samples, raising concerns about the reliability of the results (mallapaty, 2020; sood et al., 2020) . the next challenge will be the acquisition of reliable antibody data for representative samples from entire populations. the covid-19 epidemic continues to challenge our societies by its toll in deaths, by the disruption of social life; by its disastrous impact on the world economy; by increasing the debt of many nations; by endangering the survival of many industries; and by reversing the worldwide trend for poverty relief. for microbiologists, the covid-19 crisis has also revealed shortcomings in the public health sector, particularly in that of countries which were exemplary in this field during past decades. in the us, the covid-19 epidemic has taken more lives in one month than over 8 years during the vietnam war. with more than 1.7 million cases, and more than 100'000 deaths, the "america first" slogan has become sadly ironic in the context of covid-19. an article in the leading us medical journal, the new england journal of medicine, attributes this calamity to insufficient diagnostic testing caused by the delivery of faulty tests by cdc; non-approval through the fda of working tests by who resulting in a delayed start of viral detection activities; and then followed then by a shortage of test reagents. public health workers were therefore blind to the unfolding of the us epidemic and unable to design efficient containment measures, short of a lockdown. epidemiologists were left without population data for modelling the epidemic in the us at a moment when the country started reopening economic and public activity. in comparison with other countries the us has tragically "failed the test". in the words of this article "the us once a leader, seem oddly lost" (schneider, 2020) . an editorial in the leading british medical research journal, the lancet, comes to the same conclusion: the cdc, once a pillar and international reference for combating diseases worldwide, instrumental in eradicating smallpox and coping with aids or ebola, has lost its technical competence and public trust due to contradictory scientific messages and the undermining of trust in scientific evidence by the current us administration. according to the lancet editors, the "us administration is obsessed with magic bullets-vaccines, new drugs-while only basic public health principles, like test, trace, and isolate, will see the emergency brought to an end" (the lancet, 2020). the situation is not better in the uk, once also renowned for its excellent public health research, particularly in the field of respiratory infections (remember the common cold research unit). at the end of may, the uk directly follows the us in the international mortality ranking list with more than 38'000 covid-19 deaths. the late onset of large scale testing, the lack of personal protective equipment, and a delayed introduction of containment measures have certainly contributed to this high death toll. a correspondent to the lancet deplores that the situation in europe was no better with respect to the lack of a coordinated response to the pandemic. the european center for disease prevention and control (ecdc), which was established in 2004 to create a complement to the us cdc, failed to become a hub in europe of knowledge for covid-19 and a coordination center for europe-wide epidemic counter-strategies. ecdc is underfunded (cdc in 2020: 8 billion $, ecd 60 million $) and understaffed (cdc: 10'800, ecdc: 270 employees). an emergency structure for a pandemic was not set up, and ecdc played essentially no role in pandemic crisis management, which was done according to eu laws by national organizations without any european coordination (jordana and triviño-salazar, 2020) . even the city-state of singapore, where the early handling of the covid-19 was lauded as exemplary public health action, had "blind spots" on their screen in overlooking the miserable living conditions of migrant workers that became hotspots of covid-19 transmission. of special global health concern are refugee camps from bangladesh to europe. a refugee camp on lesvos/ greece has just one water tap per 1300 residents, making efficient handwashing an impossible mission (newland, 2020) . governments plan to spend billions on rescuing what they consider to be essential national industries. it will be important that they also find the money needed for covid-19 containment among migrant workers, refugees and populations at risk in developing countries . the beneficial epidemic effect of the lockdowns, obtained at enormous economic costs, would be canceled out if a second wave epidemic should start from these settings with relatively unrestrained viral transmission. at present it is not clear which institution, if not the united nations' suborganizations, will be able to implement such measures. when the leading nation of the western hemisphere leaves now the who, this is a disastrous signal for global public health at this crucial moment of the covid-19 pandemic. 2020) visualizing speech-generated oral fluid droplets with laser light scattering 100'000 and counting. the economist presymptomatic sars-cov-2 infections and transmission in a skilled nursing facility airborne or droplet precautions for health workers treating covid-19? utility of hyposmia and hypogeusia for the diagnosis of covid-19 epidemiology and transmission of covid-19 in 391 cases and 1286 of their close contacts in shenzhen, china: a retrospective cohort study investigation of a covid-19 outbreak in germany resulting from a single travel-associated primary case: a case series a sneeze england and wales see 20 000 excess deaths in care homes wearing face masks in the community during the covid-19 pandemic: altruism and solidarity comparative tropism, replication kinetics, and cell damage profiling of sars-cov-2 and sars-cov with implications for clinical manifestations, transmissibility, and laboratory studies of covid-19: an observational study impact assessment of non-pharmaceutical interventions against coronavirus disease 2019 and influenza in hong kong: an observational study 2020) pandemics and the great evolutionary mismatch rapid implementation of mobile technology for real-time epidemiology of covid-19 assessment of deaths from covid-19 and from seasonal influenza coast-to-coast spread of sars-cov-2 during the early epidemic in the united states asymptomatic transmission, the achilles' heel of current strategies to control covid-19 face masks for the public during the covid-19 crisis spread of sars-cov-2 in the icelandic population aerosol and surface distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards temporal dynamics in viral shedding and transmissibility of covid-19 estimates of global seasonal influenza-associated respiratory mortality: a modelling study where are the ecdc and the eu-wide responses in the covid-19 pandemic? collateral effect of covid-19 on stroke evaluation in the united states tropism, replication competence, and innate immune responses of the coronavirus sars-cov-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures projecting the transmission dynamics of sars-cov-2 through the postpandemic period effect of nonpharmaceutical interventions to contain covid-19 in china delayed access or provision of care in italy resulting from fear of covid-19 covid-19: a need for real-time monitoring of weekly excess deaths first-wave covid-19 transmissibility and severity in china outside hubei after control measures, and second-wave scenario planning: a modelling impact assessment is the coronavirus airborne? experts can't agree the characteristics of household transmission of covid-19 epidemiological and clinical characteristics of covid-19 in adolescents and young adults an internet-delivered handwashing intervention to modify influenza-like illness and respiratory infection transmission (primit): a primary care randomised trial reducing risks from coronavirus transmission in the home-the role of viral load genomic epidemiology of sars-cov-2 in guangdong province sars-cov-2 infection in children effective containment explains subexponential growth in recent confirmed covid-19 cases in china antibody tests suggest that coronavirus infections vastly exceed official counts epidemiology of covid-19 in a long-term care facility lost in transition covid-19 deaths in lombardy, italy: data in context air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2(sars-cov-2) from a symptomatic patient children with covid-19 in pediatric emergency departments in italy covid-19 -the law and limits of quarantine closing borders is ridiculous': the epidemiologist behind sweden's controversial coronavirus strategy herd immunity: understanding covid-19 failing the test -the tragic data gap undermining the u.s. pandemic response seroprevalence of sars-cov-2-specific antibodies among adults coughing and aerosols reviving the us cdc covid-19: pcr screening of asymptomatic healthcare workers at london hospital effect of changing case definitions for covid-19 on the epidemic curve and transmission parameters in mainland china: a modelling study global burden of respiratory infections associated with seasonal influenza in children under 5 years in 2018: a systematic review and modelling study virological assessment of hospitalized patients with covid-2019 connecting clusters of covid-19: an epidemiological and serological investigation detection of covid-19 in children in early changes in contact patterns shape the dynamics of the covid-19 outbreak in china what is required to prevent a second major outbreak of sars-cov-2 upon lifting the quarantine of wuhan city, china. preprint to the lancet acknowledgements i thank jacqueline steinhauser and sophie zuber for critical reading of the manuscript. the author consults nestlé, his former employer, on the scientific aspects of the covid-19 epidemic, but he does not consider this as a conflict of interest. key: cord-324559-p92y5er2 authors: lillie, patrick j.; samson, anda; li, ang; adams, kate; capstick, richard; barlow, gavin d.; easom, nicholas; hamilton, eve; moss, peter j.; evans, adam; ivan, monica; phe incident team; taha, yusri; duncan, christopher j.a.; schmid, matthias l.; the airborne hcid network title: novel coronavirus disease (covid-19): the first two patients in the uk with person to person transmission date: 2020-02-28 journal: j infect doi: 10.1016/j.jinf.2020.02.020 sha: doc_id: 324559 cord_uid: p92y5er2 nan in this journal, zhu et al. recently reported the results of their genomic analysis of multidrug-resistant klebsiella pneumoniae isolates from individual patients before and after colistin treatment highlighting the rapid emergence and multifaceted molecular mechanisms of colistin resistance in k. pneumoniae. 1 this work highlights the therapeutic and public-health challenges of colistinresistance (cr), which is increasingly used as a large resort antibiotic, despite its unattractive toxicity profile and narrow therapeutic window. 2 oral non-absorbed colistin has been proposed as a decontamination strategy in intensive care units and for patients carrying multidrug resistant enterobacterales (mdr-e). 3 , 4 the impact of decolonization strategies in terms of emergence of cr has rarely been monitored because no reliable selective medium existed and cr was not considered a public-health problem. recently, reliable universal culture media have been developed to screen for cr. 5 here, we studied the impact of non-absorbed oral colistin on the emergence of cr in the gut microbiota of patients from the rgnosis-wp3 randomized controlled trial. 6 thirty-nine subjects colonized with mdr-e were randomized to receive oral colistin sulfate 2 miu 4 times a day + neomycin sulfate 500 mg bid for 5 days followed by a fecal microbiota transplant (fmt) from healthy donors, or no intervention. stool samples were collected on visit v0 (screening sample), v2 (after 5 days of oral decontamination and before fmt for the intervention group), v3, v4 and v5, respectively 5-10 days, 30-40 days and 150-210 days later. 6 stool samples from donors and 15 subjects from the intervention group and 15 from the control group were available for this work and plated on drigalski plates (control) and superpolymyxin r plates. 5 colony forming units (cfu) counts of all gram-negative rods were determined. isolates growing on superpolymyxin r plates were identified by maldi-tof; cr was confirmed by the culture-based rapid polymyxin np test and mic determined by the microdilution method. the limit of detection was 10 2 cfu/g of stool. cr-e. coli were sequenced using the illumina hiseq technology. to determine whether cr isolates were present before the intervention, a specific mcr-1 pcr was performed on patients stool prior to intervention (v0) and on the donor's stool. 7 electroporation of plasmids was performed to localize the gene conferring resistance to colistin and neomycin and molecular typing of the electroporants was performed using pcr based replicon typing (pbrt). ✩ université de paris, iame, inserm, umr-1137 no patient or donor included in the trial carried cr isolates on v0. among the 15 patients in the intervention group two (13.3%, [ic90 −1; 3], p = 0.24) carried cr isolates at least at one visit after the intervention ( fig. 1 ) . no cr-enterobacterales was detected in the stools of subjects from the control group. among both subjects with cr-enterobacterales, one carried 10 log cfu/g of hafnia paralvei , a species which is intrinsically resistant to colistin (mic = 8 mg/l), also resistant to neomycin (mic = 32 mg/l) on visit 4 and the other carried 1 log cfu/g and 3 log cfu/g cr-e. coli at visits 4 and 5, respectively, with a colistin mic at 8 mg/l. relative abundance of cr-e. coli increased between v4 and v5 from 0.01% to 1% of the total enterobacterales population. the cr-e. coli recovered at v4 and v5 both belonged to phylogroup c st23 group and carried the serotype o176:h9. a plasmid-borne mcr-1.1 gene encoding for cr as well as a aph(3 )-ia gene conferring resistance to neomycin were identified, both being co-located on the same inchi2 plasmid. in addition, resistance genes conferring resistance to hygromycin b ( aph(4)-ia ), sulfonamides ( sul2 ), tetracyclines ( tet(a) ) and phenicols ( flor and cata1 ), all antibiotics used in veterinary medicine, were evidenced. for both subjects, cr strains could not be retrieved in the initial stool of the subject or in the donor's stool. pcr experiments performed with specific primers to detect mcr-1 gene directly on the pre-therapeutic stool were also negative. to our knowledge, this is the first report of the in-vivo selection of cr-enterobacterales in the gut microbiota of patients after oral decontamination by colistin. the selection of cr strains (a naturally-resistant h. paralvei and a mcr-1 producing e. coli ), both resistant to colistin and neomycin, may be the result either of the enrichment process by sod of preexisting cr strains that had not been initially detected because of very low abundances, or of an exogenous acquisition, either from other individuals or through fmt. 8 indeed the transmission from fmt of mdr strains from positive donors is a potential risk. 8 despite our efforts to decrease the limit of detection of mcr producers by using a pcr technique directly on the pre-therapeutic stool sample and the donors' stools, we failed to detect the parental strain, either because cr strains were in intestinal niches, the limit of detection remained too high, or the strain was acquired exogenously. however, the mcr-1 -positive e. coli is likely of animal origin according to its genetic features and its co-resistance profile. 9 indeed, phylogroup st23 is frequently encountered among avian pathogenic e. coli (apec) and co-resistances to many antibiotics used specifically in veterinary medicine is striking. 10 furthermore, the aph(3 )-ia gene confers resistance to neomycin and paromomycin, the latter commonly used in cattle and pigs. the selection of the mcr-1 producer is an illustration of the "one health" problem of resistance: a strain likely to have been selected by veterinary antibiotics among animals ended up in a patient's gut, later enriched by the use of colistin and neomycin as decontaminant. although the small number of subjects is a clear limitation, this observation is a "proof-of-concept" of the risk of selection of cr-enterobacterales after oral colistin treatment and fmt, at a time when colistin is one of the last resort antibiotics to treat mdr-enterobacterales infections. the selection of commensal cr-e. coli is especially worrying, given the pathogenic potential of e. coli and its ability to widely colonize animals and humans. given the controversial results of oral decontamination by colistin, we believe it should only be used with precautions and with thorough monitoring of cr. we read with interest a recent paper in this journal by luzatti and colleagues, 1 who explored the significance of the presence of herpes simplex virus (hsv) dna in lower respiratory tract (lrt) specimens for the diagnosis of hsv pneumonia in immunocompromised patients. the authors underlined the difficulty in gauging the clinical relevance of such a laboratory finding in the absence of histopathological data, as hsv shedding in the lrt may occur in the absence of disease. the interpretation of real-time pcr results for diagnosis of pneumocystis jirovecii (pj) pneumonia (pjp) faces an analogous challenge, since the presence of pj dna in lrt may reflect colonization (carriage) rather than infection. 2 there is limited information on the clinical value of pj real-time pcr in diagnosing pjp in patients with hematological diseases; 3-6 this is exceedingly challenging as the sensitivity of direct examination procedures is suboptimal due to low fungal burdens. 3 here, we report on our experience on this matter. a total of 219 episodes of pneumonia occurring in 192 consecutive patients with hematological disorders in which pjp was considered in the differential etiological diagnosis were included. of these, 127 episodes developed in patients undergoing either allogeneic hematopoietic stem cell transplantation-allo-hsct-( n = 86) or autologous-hsct ( n = 19), and 92 in non-transplant patients (acute leukemia, n = 61; lymphoma, n = 16; chronic leukemia, n = 8; others, n = 2). the patients were attended at the hospital clínico universitario-hcu-( n = 100) or at the hospital universitario politécnico "la fe" -hlf-( n = 92) between june 2014 and august 2019. no patients in the cohort tested positive for hiv. this study was approved by the respective hospital ethics committee and informed consent was obtained from all patients. a single specimen per episode was available for diagnosis (bal fluids, n = 179; sputa, n = 22; ta, n = 17 and bronchial biopsy, n = 1). the realcycler pjir kit r (progenie molecular, spain) was used at hcu, and the pneumocystis jirovecii real time pcr detection (certest biotech; zaragoza, spain) was employed at hlf (see footnote in table 1 ). both assays target the large sub-unit of ribosomal (mtlsu) rna gene. preliminary experiments using 5 bal specimens indicated that both assays yield comparable pcr cycle thresholds (c t s) (median, 28.2, range, 26.4-32.3 vs. median 27.5; range, 26.3-33.1, respectively; p = 0.89). all specimens tested negative by direct examination for pj, whereas 27 were positive by real-time pcr (bal, n = 18; sputa, n = 7, and ta, n = 2); following stringent clinical, microbiological and imaging criteria ( table 1 ) , pjp was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. no histopathological confirmation of pjp was available for any patient. pcr c t values inversely correlate with fungal burden in the sample. 6 which is higher in patients with pjp than in colonized individuals. 2 here, overall, pj pcr c t s in specimens from patients with pjp tended to be lower than in pj carriers ( p = 0.39); when only bal fluid specimens were considered, the difference reached statistical significance (median, 29.0; range, 26.4-34.7 vs. median 34.6; range, 30.0-41.0; p = 0.04). this finding is likely related to use of more standardized procedures for bal fluid sampling. receiver operating characteristic (roc) curve analysis showed that a threshold c t value of 30.0 in bal specimens displayed a sensitivity of 85.7% (95% ci, 45.0-100%) and a specificity of 80% (95% ci, 40.8-100%) for pjp diagnosis. a number of studies have established different c t s cut-offs for that purpose, [6] [7] [8] [9] . in our view, however, the variability in the performance of different pcr assays and sampling conditions, heterogeneity of patient populations, and in particular the lack of a pj international standard material for pcr result normalization precludes defining a consensus universal threshold nowadays. the absence of anti-pj prophylaxis, treatment with corticosteroids and serum ldh levels ≥400 u/l have been shown to be associated with pjp. 3 here, patients not undergoing anti-pj prophylaxis were more likely to display a clinically significant pj pcr result ( table 1 ). in turn, roc curve analysis indicated that a cut-off ldh value ≥400 u/l had a sensitivity of 81.8% (ci 95%, 59.0-100%) and specificity of 67% (95% ci, 34.0-99.3%) for pjp diagnosis. in univariate regression logistic models, serum ldh values ≥400 u/l were associated with a clinically significant positive pcr pj result (or, 9.0; 95% ci, 1.2-63.8; p = 0.02). in contrast, corticosteroid use within the month before sampling was not different between the probability of pneumocystis jirovecii (pj) pneumonia (pjp) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented pj presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-pjp treatment; (v) absence of alternative diagnosis. the efficacy of therapy was assessed on a daily basis. pjp was ruled out if real-time pcr for pj tested negative, or if clinical recovery occurred in the absence of pj-targeted antimicrobial therapy. pj colonization (carriage) was the most likely possibility when patients did not meet the above criteria and an alternate diagnosis was made. b frequencies were compared using the χ 2 test (fisher exact test) for categorical variables. two-sided exact p values were reported and p values ≤ 0.05 were considered statistically significant. the data were analyzed with the spss (version 20.0) statistical package. c respiratory tract specimens were obtained following conventional procedures. specimens were examined for presence of ascus or trophic forms of pj by microscopy following blue toluidine, calcofluor white or grocott's methenamine silver staining. cytospin preparations were prepared from bal specimens for direct examination. sputa and ta samples were mixed v/v with sputasol (oxoid, uk) and vortexed for 5 min. all samples were centrifuged at 30 0 0 g for 10 min, and the pellets were resuspended 1/10 in 0.9% nacl for further processing. for real-time pcr, dna was extracted from 200 μl of specimens using the qiaamp dna blood mini kit (qiagen, hilden, germany) on either qia symphony or ez-1 platforms (qiagen), following the manufacturer's instructions. at hcu, a commercially-available real-time pcr assay previously evaluated by others, the realcycler pjir kit r (progenie molecular, spain), which targets the mitochondrial large sub-unit of ribosomal (mtlsu) rna gene, was used according to the manufacturer's instructions ( http://www.progenie-molecular.com/pjir-u-in.pdf ). at hlf, the commercially-available pneumocystis jirovecii real time pcr detection. (certest biotech; zaragoza, spain), which also targets the large sub-unit of ribosomal (mtlsu) rna gene, was employed following the manufacturer instructions ( https://www.certest. es/wpontent/uploads/2019/02/viasure _ real _ time _ pcr _ pneumocystis _ jirovecii _ sp1.pdf ). at both centers pcr were performed in the applied biosystems 7500 fast real-time pcr platform (applied biosystems, ca, usa). pcr results were reported as positive or negative. for positive samples, threshold cycle (c t ) values were also recorded. no standard curve was generated with a positive control for quantitative estimations. d antimicrobial prophylaxis for pjp was performed with trimethoprim-sulfamethoxazole (tmp/smx), one double-strength tablet (160 mg tmp/800 mg smx) given 2 (in allogeneic hsct patients) or 3 times a week with oral folic acid (15, 16) . patients with suspicion of pjp according to the attending physician were treated with tmp/smx 15-20 mg/kg (tmp) 75-100 mg/kg (smx) per day for 2-3 weeks. e in all these cases, death was attributable to pjp. patients with clinically significant pj detection and pj carriers ( table 1 ) . detection or recovery of other microbial agents (one or more) was documented in 17 of the 27 specimens testing positive by pj pcr ( table 2 ). in line with a previous report, 9 this microbiological finding was significantly less frequent ( p = 0.001) in specimens from patients with pjp than in colonized patients; in fact, microbial co-detection was inversely associated with pjp in univariate logistic regression models (or, 0.024; 95% ci, 0.002-0.26; p = 0.002). strengths of the current study are the following: (i) clinical categorization of pjp was based upon stringent criteria defined by a multidisciplinary team; (ii) only hematological patients were included; (iii) a comprehensive routine investigation of microbial causes of pneumonia other than pj was conducted; (iv) the experience of two centers was collected. in addition to its retrospective nature, our study also has some limitations: (i) we cannot completely rule out that some patients categorized as being pj carriers did in fact have pjp, as most of these patients received full courses of tmp/smx in combination with antimicrobials targeting other microbial agents. the lack of standardized criteria for pjp diagnosis makes clinical misclassification of patients a potential drawback in studies such as ours, particularly when no positive microscopy or histopathology findings are available; (ii) although we evaluated bal, bronchoalveolar lavage; pjp, pneumocysis jirovecii pneumonia; ta, tracheal aspirate. a as per our routine protocol, all specimens were examined by gram and acid-fast bacilli stain. samples were also examined for presence of respiratory viruses (rvs) using either the luminex xtag rvp fast assay (luminex molecular diagnostics, austin, tx,usa) at hcu, or the clart® pneumovir assay (genomica, coslada, spain) at both centers, as previously reported. 10 semiquantitative (sputa) and quantitative (bal and ta) cultures for bacteria were performed on conventional media: bacterial loads > 10 4 cfu/ml or > 10 5 cfu/ml were deemed to be clinically relevant on bal fluids and ta samples, respectively. specimens were cultured on bcye-alpha agar, bd (becton dickinson) mgit® ( mycobacteria growth indicator tube)/lowenstein-jensen agar slants and sabouraud agar for recovery of legionella pneumophila, mycobacterium spp., and other fungal organisms, respectively. the platelia tm aspergillus ag kit (bio-rad, hercules, ca, usa) was used for quantitation of aspergillus spp. galactomannan in bal fluid and serum specimens. all bal fluid specimens underwent cytomegalovirus (cmv) pcr testing using the realtime cmv pcr assay (abbott molecular) at hcu or the cmv r-gene® assay (biomerieux) at hlf, as previously reported. 10 over 200 patients, only 12 presumptively had pjp; (iii) two different commercially-available pcr assays were used across centers. nevertheless, we found them to yield rather comparable c t s. in summary, we found that a positive pj pcr result in respiratory specimens from transplant and non-transplant hematological patients with pneumonia frequently reflects colonization rather than infection; pcr c t values in bal fluids, serum ldh levels and lack of co-detection of other microorganisms potentially involved may be helpful in clinical categorization in the absence of positive by pj microcopy results. we have no conflict of interest to declare. dear editor , poller et al., in this journal, provided a useful consensus for use of personal protective equipment for managing high consequence infectious disease 1 . although this was driven largely by recent ebola virus disease emergencies, we should remind your readers of the continuing problem of lassa fever (lf) in west africa. lf is a febrile infectious disease caused by lassa virus. the clinical presentation of the disease is nonspecific and includes fever, fatigue, hemorrhage, gastrointestinal symptoms, respiratory symptoms, and neurological symptoms 2 . the observed case fatality rate among patients hospitalized with severe lf is 15-20% 3 , 4 . the disease is mainly spread to humans through contamination with the urine or faeces of infected rats 2 . human-to-human transmission can occur through contact with the body fluids of infected per-sons. therefore, health care workers are at high risk for infection when the standard precautions for infection prevention and control including appropriate personal protective equipment are inadequate 5 . it is estimated that there are approximately 30 0,0 0 0 lf cases annually, resulting in approximately 50 0 0 deaths in west african countries 4 . in 2018, nigeria had a large lf outbreak, and we previously reported epidemiological characteristics of the outbreak, analyzing data collected between january and may 2018. 6 however, information on laboratory-negative suspected cases was not enough to conduct a case-control study to fully determine the risk factors and clinical characteristics of the disease. nigeria had a lf outbreak in 2019 as well. 7 here we report the epidemiological and clinical characteristics of the outbreak including case-control analysis against laboratory-negative suspected cases using data collected between 1st january 2018 and 6th october 2019. from january to december 2018, there were 3498 suspected cases, including 633 laboratory-confirmed lf cases. in 2019, there were 4019 suspected cases reported by 6th october, including 721 laboratory-confirmed lf cases. details on the case definition, laboratory test, surveillance, and data collection have been described previously. 6 of the confirmed lf cases, there were 171 fatalities (case fatality rate, 27.0%) in 2018 and 154 fatalities (case fatality rate, 21.4%) in 2019. the number of laboratory-confirmed lf cases and positivity rate peaked in the dry season (january-march) in both 2018 and 2019 ( fig. 1 (a) ). the largest number of laboratory-confirmed lf cases were reported from the neighboring edo and ondo states in both 2018 and 2019 ( fig. 1 (b) ). there were laboratory-confirmed lf cases in states such as kebbi and zamfara that had no reported cases previously, in 2019. during the study period, the detailed demographic and clinical information was collected for 1305 laboratory-confirmed lf cases (of 1354 cases, 96.4%) and 3350 laboratory-negative suspected cases (of 6163 cases, 54.4%). chi-square tests were conducted to compare the distribution of age, sex, and each symptom between the laboratory-confirmed lf cases and laboratory-negative suspected cases ( table 1 ). the proportion of children was significantly lower in laboratory-confirmed lf cases compared with that in laboratory-negative suspected cases. the proportion of males was significantly higher in laboratory-confirmed lf cases than that in laboratory-negative suspected cases. fever was the most prevalent symptom in both laboratoryconfirmed lf cases and laboratory-negative suspected cases, followed by headache ( table 1 ) . gastrointestinal symptoms, such as abdominal pain, vomiting, and diarrhea, were observed in more than 30% of laboratory-confirmed lf cases, whereas hemorrhaging was observed in 21.1% of laboratory-confirmed lf cases. while the prevalence of face/neck edema was low even in laboratoryconfirmed lf cases (6.4%), nonetheless, the odds ratio of having face/neck edema was 6.0 times high for laboratory-confirmed lf cases. we here reported the lf outbreak in 2018-2019 largest recorded in history. while previous studies have focused on laboratory-confirmed lf cases and mainly compared fatal cases and survived cases, 6 , 8 , 9 our observation revealed the difference between laboratory-confirmed lf cases and laboratory-negative suspected cases. the age and sex distribution differed significantly between laboratory-confirmed lf cases and laboratory-negative suspected cases. fever, headache, and gastrointestinal symptoms were the most common symptoms in laboratory-confirmed lf cases, which are similar to those reported previously. 6 , 8 however, these symptoms were also prevalent in laboratory-negative suspected cases. clinical guidelines for lf state that edema in the face and neck is a specific sign of the disease. 10 the present study found that the symptom had a significantly high odds ratio for confirmed lf although the prevalence of this symptom was low. unfortunately, we did not determine the differential diagnosis for the laboratory-negative suspected cases. laboratory tests for the differential diagnoses are now underway for the lf-negative samples collected during the outbreak. the results would provide us further insight for better clinical management of patients with febrile illnesses in lf-endemic areas. in addition to the standard precautions for infection prevention and control including appropriate personal protective equipment pointed out by poller et al., 1 it is important to know epidemiological and clinical characteristics of high consequence infectious diseases such as lf. that would help healthcare workers and public health officers increase an index of suspicion of the diseases, further leading to better clinical management and surveillance. the authors have declared that no conflicts of interest exist. this work was partially supported by the leading initiative for excellent young researchers from the ministry of education , culture, sport, science & technology of japan and the japan society for the promotion of science (grant number, 16809810 ). the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 1 these authors contributed equally to this article. accepted 31 december 2019 available online 15 january 2020 https://doi.org/10.1016/j.jinf.2019.12.020 © 2020 the british infection association. published by elsevier ltd. all rights reserved. recently, several studies in this journal have demonstrated the threat of animal-derived viruses to humans. [1] [2] [3] since 2018, an increase in human pseudorabies virus (prv) infection cases has been reported in china, indicating a new animal-derived virus threat to human health. porcine pseudorabies (pr), also known as aujeszky's disease, is one of the most economically important viral diseases in pigs globally. its causative agent is prv, which is classified into the genus varicellovirus of subfamily alphaherpesvirinae , family herpesviridae . prv is almost always fatal in newborn piglets, is frequently accompanied by neurological symptoms, and may cause abortions and/or stillbirths in pregnant sows. prv primarily infects members of the suidae family and can also infect other domestic and wild mammals, including horses, cattle, sheep, goats, dogs, cats, etc. currently, vaccination is the most effective strategy for pr prevention and control in pigs worldwide. in china, prv infections in pigs were first recorded in 1947. in the 1970s, an inactivated vaccine consisting of the bartha-k61 vaccine strain was imported into china. since then, this vaccine has been widely used in pig vaccination for pr prevention and control. before 2011, no large pr outbreaks were reported in pigs in china. however, after late 2011, novel prv wild-type variants emerged in nearly all regions of china and affected a number of swine herds vaccinated regularly with the bartha-k61 vaccine, resulting in significant economic losses. 4 subsequent animal experiments indicated that the bartha-k61 vaccine could not provide complete protection for pigs against a challenge with novel prv wild-type variants in china. for control and eradication of pr, the disease was listed in the "mid-and long-term animal disease prevention and control program in china (2012-2020)" by the chinese government, with the aim of eliminating pr in china by 2020 ( http://www.gov.cn/zwgk/2012-05/25/content _ 2145581.htm ). however, vaccination for prv is still voluntary and not required in china. a nationwide epidemiological investigation in 2014 demonstrated a high prevalence of 23.26% of prv among swine herds in china. 5 humans were previously regarded as refractory for prv infection, although serological prv antibody positivity was found in three cases. in 2018, the first human prv infection case with direct molecular evidence was reported in china (case 1, table 1 ). 6 in this case, the eyes of a 46-year-old woman were directly exposed to sewage on a hog farm. in the following two weeks, symptoms of fever, headache, coma, and endophthalmitis were observed in the patient. next-generation sequencing (ngs) indicated that prv dna was detected in her vitreous humor samples but not in her cerebrospinal fluid (csf). after surgery, the patient was discharged, but her vision remained impaired. in a subsequent study, zhao et al. table 1 clinical characteristics and other information on the twelve human prv infection cases in china. analyzed csf samples from four patients with encephalitis of unknown etiology using ngs (cases 2-5, table 1 ) and found molecular evidence of prv infection. 7 in addition, retinitis and blindness was observed in two cases (cases 2, 5, table 1 ), and the patient in case 3 died. the occupation of the four patients was all associated with pork production/sale/cooking. in 2019, six other human prv infection cases involving encephalitis were reported in china, and all patients were pork/pig handlers or veterinarians. [8] [9] [10] it was noted that all patients still suffered from various sequelae after discharge, except for in one case where the patient died. increasing reports on human prv infection cases in china have recently indicated that prv poses a significant threat to public health in china, especially in people in close contact with sick pigs and/or related pork products/contaminants. to reduce the risk of prv infection in susceptible workers, it is necessary to promulgate relevant policies by the chinese government to promote pr vaccine development to protect pigs from infection with novel prv wild-type variants currently circulating in china. in addition, relevant policies should be updated by the chinese government to monitor vaccination status and virus variation in pigs nationwide. moreover, it seems that prv can infect humans via injury to the skin or eyes. until now, no effective drugs to prevent the progression of the disease caused by prv infection have been reported. therefore, it is necessary to improve biosafety and self-protection awareness in susceptible populations that have contact with sick pigs and work in jobs related to handling pork products/contaminants. promoting drug development for curing prv-related disease in infected patients may also help reduce the currently increasing threat of prv to human health in china. all authors declare that they have no competing interests. dear editor, the emergence and spread of gram-negative bacteria, for example, klebsiella pneumoniae , co-producing carbapenemases and mobilized colistin resistance ( mcr ) genes limit our choice for treating multidrug-resistant infections, posing significant threats to public health. herein, we reported the discovery of mcr-9 gene in 28 k. pneumoniae strains isolated from patients in eight european countries, including belgium ( n = 2), denmark ( n = 1), montenegro ( n = 13), poland ( n = 1), romania ( n = 1), serbia ( n = 1), slovenia ( n = 1), and spain ( n = 7). notably, the co-existence of mcr-9 and the carbapenemase-encoding genes, ndm-1, vim-1, and oxa-48 were confirmed in k. pneumoniae isolates of human origin. phylogenetic analysis suggested that mcr-9 -carrying k. pneumoniae isolates, including 23 carbapenem-resistant and five susceptible k. pneumoniae strains, show a highly geographically clustered pattern. genetic environment analysis revealed the presence of insertion element is903, is1 or a cupin fold metalloprotein, wbuc, in the mcr-9 flanking. taken together, these findings indicated that mcr-9 has existed for a long time and already spread among crkp isolates of human origin in europe since 2013, further increasing the significant threat of public health through either the nosocomial spread or environmental routes. the mobilized colistin resistance ( mcr ) gene mcr-9 was detected in 28 human gut microbiomes, which has been disseminating across three continents, including asia, europe and america, recently published in the journal of infection. 1 the rapid increase in carbapenem resistance among gram-negative bacteria worldwide has greatly compromised the efficacy of carbapenem antibiotics, which has gotten renewed attention to the importance of polymyxin antibiotics for multidrug-resistant (mdr) infections. recently, sophia david and colleagues 2 reported the epidemic of carbapenem-resistant klebsiella pneumoniae (crkp) in europe, which raised concern that mobile carbapenemase resistance determinants were widely spread in european hospital settings, and inter-hospital spread is far more frequent within, rather than between, countries. however, limited information regarding the co-occurrence of carbapenemases and mcr genes in the klebsiella pneumoniae ( k. pneumoniae ) isolates have been provided. plasmid-mediated resistance genes mcr as well as tet (x3/x4) have been widespread in bacterial species of animal, human, and environment origin as well as human and animal gut microbiomes worldwide, where is a huge arg reservoir with a high horizontal gene transfer possibility. 1 , 3 -5 several studies 6 -8 illustrated that the newly described mcr-9 has spread beyond the united states into europe and asia, and into other enterobacteriaceae species. of clinical concern is the inevitable spread of a plasmid harboring the mcr-9 gene into a crkp isolate, which has been listed by the world health organization as a critical priority antibiotic-resistant bacterial pathogen for which new antibiotics are urgently needed. 9 in response to this potential clinical problem, we download > 1717 k. pneumoniae genomes isolated from 244 hospitals in 32 european countries 2 and the 14,764 complete bacterial genome sequence (accessed 26 july 2019), and explored the distribution of plasmid-mediated resistance genes mcr and tet (x3/x4). we are surprised to find that the complete mcr-9 gene (nucleotide = 100%) was present in 28 k. pneumoniae isolates of 1717 k. pneumoniae strains from belgium ( n = 2), denmark ( n = 1), montenegro ( n = 13), poland ( n = 1), romania ( n = 2), serbia ( n = 1), slovenia ( n = 1), and spain ( n = 7) (table s1 ). additionally, 23 of the 28 k. pneumoniae isolates of human origin were crkp strains and only five were carbapenem-susceptive isolates (table s1 ). as reported, these mcr-9 -harbouring strains were isolated from patients in europe between 2013 and 2014. these results suggest that mcr-9 gene might have been presented in europe for a long time and already spread to the crkp isolates, which is a major cause of both hospital-and community-acquired infections. 2 to further analyze these mcr-9 -positive k. pneumoniae isolates, the resistome of the draft genome was analyzed using the comprehensive antibiotic resistance database. 10 interestingly, the mcr-9 gene was co-existed with various carbapenemase-encoding genes: in eleven isolates with ndm-1, eight with vim-1, and two with oxa-48 ( fig. 1 (a) ). it should be noted that the mcr-9 -and ndm-1-carrying isolates were distributed in denmark ( n = 1), montenegro ( n = 8), romania ( n = 1), and serbia ( n = 1), as well as several other beta-lactam resistance determinants (for example, tem-1, cmy-16, oxa-10 and shv-11) ( fig. 1 (a) and table s1 ). moreover, the mcr-9 -and vim-1-harbouring isolates were dominant in spain ( n = 7) and slovenia ( n = 1), as well as two beta-lactamase-encoding genes (non-carbapenemases) (ctx-m-9 and shv-11) ( fig. 1 (a) and table s1 ). it is worrying that a crkp isolate from spain in 2014 was carrying mcr-9 , vim-1, and oxa-48 genes simultaneously. the presence of mcr-9 in crkp isolates from patients is of critical importance as mcr-9 could be present in hospital-borne outbreaks cre strains in the future. from whole-genome shotgun (wgs) data of the 28 mcr-9 -positive k. pneumoniae isolates, sequences types (sts) were extracted and assigned to nine different types, i.e. , 274, 461, 15, 16, 416, 1890, 37, 1942, and 147 ( fig. 1 (a) ). phylogenetic analysis suggested that mcr-9 -carrying k. pneumoniae isolates show a highly geographical clustering pattern 2 ( fig. 1 (a) ). isolates from patients in the same hospital were clustered into one clade, for example, in spain and montenegro. overall, the k. pneumoniae isolates from different countries were genetically diverse, suggesting that the mcr-9 -positive k. pneumoniae isolates were also genetically diverse and that mcr-9 could disseminate among different k. pneumoniae isolates, mainly by nosocomial transmission. 2 nowadays, all known mcr genes have been detected in various gram-negative bacterial species, whereas a small number of studies have shown the presence of mcr-1, mcr-3, mcr-7 , and mcr-8 in k. pneumoniae isolates from animal and human origin at relatively low detection rate. 11 -14 the presence of mcr-9 in the crkp isolates indicated that this novel mcr gene may already be widely spread among k. pneumoniae isolates of human origin in europe. we subsequently searched mcr-9 gene in 14,764 complete bacterial genome sequence and ncbi-nr database (14 october 2019) in the ncbi, to fully understand the prevalence of mcr-9 gene in klebsiella species isolates. interestingly, the mcr-9 gene (identity > 99% and 100% query coverage) was present in various bacterial genomes, including three klebsiella species isolates consisting of k. pneumoniae ( n = 4), k. quasipneumoniae ( n = 1), and k. oxytoca ( n = 3) (table s3) . therefore, further studies focusing on the epidemiology and transmission mechanism of mcr genes, in particular mcr-9 in klebsiella species of human origin are warranted to better understand the public health threat of emergence of antibiotic resistance among clinical k. pneumoniae . contigs carrying mcr-9 in 28 k. pneumoniae isolates could be classified into two groups (for example, gca_900513855.1 and gca_900501685.1) (table s2) . genetic environments analysis indicated that the presence of insertion element is903 and wbuc (a cupin fold metalloprotein), in the mcr-9 (gca_900513855.1, ∼28 kb) upstream and downstream flanking, respectively, similar to (identity > 99%) the plasmid sequences of pme-1a, pctxm9_020038, and pmrvim0813, and contigs from of e. coli isolate 68a and nz_naan010 0 0 063 from salmonella 15 ( fig. 1 (b) ). additionally, mcr-9 in another contig ∼8.7 kb was in the upstream of two insertion element is1 and is30 0 0, as well as a beta-lactamase-encoding resistance gene ctx-m-9, which similar to the plasmid sequence of pmrvim0813. we did not detect the downstream regulatory genes (qsec and qseb) found in the isolates that harbor mcr-9 . 8 , 16 moreover, we were unable to determine whether a complete is903 element is upstream due to a short mcr-9 -bearing contig that is available for comparison ( fig. 1 (b) ). therefore, a long-read sequencing coupled with a hybrid assembly method is needed to fully evaluate and monitor the transfer and development of args, especially mcr-9 among crkp isolates. although two unique plasmid-mediated tigecycline resistance genes firstly discovered in bacteria of animal origin in china and subsequently identified in many bacterial isolates of human, animal and environment origin, including klebsiella species, as well as human and animal gut microbiomes, 1 , 4 , 5 none of them was detected in the 1717 k. pneumoniae strains in europe. in summary, we reported the discovery of mcr-9 gene in 28 clinical k. pneumoniae strains of human origin in eight european countries. importantly, the mcr-9 gene was co-existed with different carbapenemase-encoding genes in the same strains. the spread of mcr-9 , ndm-1, vim-1, and oxa-48 and other beta-lactam resistance determinants (non-carbapenemase) carrying by crkp appears likely to be by plasmid dissemination, as the genes identified in isolates belonging to a diverse set of sts distributed in different hospitals in europe. it is noteworthy that all these mcr-9 -positive crkp strains were isolated between 2013 and 2014, highlighting an earlier presence of mcr-9 among crkp around the world than previously known. these findings raise the likelihood of ongoing undetected mcr-9 gene spread among cre strains. therefore, further study is urgently needed to understand the prevalence and dissemination of mcr-9 , especially in cre and crkp strains, and effective measures should be taken to control its spread. g.f.g. designed the study. y.n.w. and f.l. collected and downloaded the datasets. y.n.w., f.l., y.f.h., b.l.z., g.p.z., and g.f.g. analyzed and interpreted the data. y.n.w. and g.f.g. wrote the draft of the manuscript. all authors discussed, reviewed and approved the final report. supplementary information is available for this paper. correspondence and requests for materials should be addressed to g.f.g. the authors declare no competing interests. the interesting systematic review by amin-chowdhury and colleagues provides information about outbreaks of severe pneumococcal disease (spd) in closed settings that occurred in the conjugate vaccines era 1 . it shows that vaccine-type spd outbreaks are still occurring and it highlights the lack of consensus on how to manage such outbreaks. in the following, we will describe how we managed a recent outbreak of spd in norway. in march 2019, møre and romsdal hospital trust notified the norwegian institute of public health (niph) about a cluster of spd amongst men working in shipyards in møre and romsdal county. serotype data from niph were available for nine of the cases -all were serotype 4. the majority of cases had been working at one specific shipyard. municipal medical officers (mmo), the norwegian labour inspection authority (nlia), and niph formed a multidisciplinary outbreak team to investigate and control the outbreak. we formed specific case definitions: each case had to have resided in møre and romsdal county in the period from 1. january 2019 onwards and: confirmed : had invasive pneumococcal disease (ipd) with serotype 4 isolated from a normally sterile site. probable : worked at the specific shipyard and had a clinical presentation compatible with lower respiratory tract infection or ipd, but without microbiological confirmation or serotype 4 isolated from a non-sterile medium (e.g. nasopharyngeal swab or sputum culture). we identified 20 cases, ten confirmed and ten probable in the period between 28. january and 3. april ( fig. 1 ). all available isolates were serotype 4 (10 confirmed, 7 probable) and were susceptible to penicillin. fifteen isolates were sequence type (st) 801, while two were a single locus variant of 801, st 15,063. all cases were men between 20 and 60 years, with a mean age of 47 years. fifteen were hospitalized. four were norwegian citizens, the remaining came from other european countries. seven cases smoked. one case had an underlying medical risk condition. immunization history against pneumococci were unknown for all. the cases had several professions; mostly related to interior outfitting and metal welding. approximately 1800 individuals worked at the shipyard in the time period. many of them lived in temporary accommodation. at an on-site inspection of the shipyard, nlia observed a polluted atmospheric work environment and little use of personal protective equipment. several measures were put in place to control the outbreak, including information and advice to raise symptom awareness and to reinforce hand and respiratory hygiene, vaccination and occupational corrections. local medical clinics and hospital were alerted about the outbreak and advised to have a low threshold to admit and treat suspected cases. mmo held information meetings with shift leaders, and written information about spd in several languages was distributed to workers to increase spd awareness. intensified hygiene measures were implemented at the ship yard and housing quarters. nlia ordered immediate occupational corrections related to controlling the atmospheric work environment. niph recommended vaccination with the 13-valent conjugate vaccine (pcv13) to interrupt transmission and prevent disease. both the pcv13 and the 23-valent polysaccharide vaccine provide protection against serotype 4, but pcv13 was preferred as this may also affect colonization. as several work tasks were conducted in parallel process in confined spaces with suboptimal ventilation, we were unable to identify a single target group for vaccination. hence, the shipyard offered vaccination to all workers. occupational health service promptly vaccinated all workers during a four-day period. contrary to the majority of studies included in the systematic review, niph did not recommend chemoprophylaxis. as the workers were otherwise healthy (i.e. no high risk group like old age, immunocompromising conditions etc.), and since it was impossible to target a specific group of workers, niph deemed it undesirable to distribute antibiotics to 1800 asymptomatic workers, with the possibility of inducing antimicrobial resistance and possible side effects. due to high turnover of personnel it was not possible to calculate an attack rate. we did not find any new cases after control measures were implemented. no deaths have been reported in relation to the outbreak. this outbreak closely resembles one of the outbreaks described in the systematic review; between april and june 2015, an outbreak with serotype 4, st 801 occurred at a shipyard in belfast 2 . we are also aware of an outbreak this fall, 2019, at a shipyard in finland with serotype 4 (st 801), 8 and 12f 3 . although welders are a known risk group for spd, 4 in all these three outbreaks, people who worked closely alongside welders were also infected. in addition to exposure to welding fumes, the crammed and poorly ventilated working conditions, and possibly housing conditions, may have increased the risk of developing spd and facilitated the transmission of pneumococci in this closed setting. overall, this norwegian outbreak extends the knowledge about how to manage and control outbreaks of spd in closed settings. none. in this journal brunet and colleagues 1 discussed reactivation of latent infections in the context of chronic disease, solid organ transplantation or long-term immunosuppressive treatment. we recently observed the reactivation of leishmania infection in a 46-year-old patient receiving methotrexate for psoriasis, who was diagnosed with visceral leishmaniasis (vl) showing a mucocutaneous involvement. we analyzed the epidemiologic and clinical characteristics of all cases of leishmaniasis in patients with psoriasis found through a review of the literature. our patient was admitted into the infectious disease unit of paolo giaccone hospital, in palermo, with a painless and ulcerated lesion onto the oral mucosa ( fig. 1a ) , two nodular ulcerated lesions on the right knee and another one on instep of the right foot appeared one month before ( fig. 1b ) . the patient did not travel outside italy during the last year. he had been suffering from lowgrade fever in the last month. considering the above findings leishmaniasis was suspected and a needle aspiration of oral and cutaneous lesions was arranged in order to perform microscopy and leishmania-pcr, which were positive for leishmania. laboratory tests exhibited: wbc 4970/mmc, hb 13.9 g/dl, c reactive protein, 26.9 mg/l; positive serology for leishmania (igg 1/3200) and positive leishmania-pcr test on peripheral blood. abdominal us examination revealed splenomegaly (14 cm); methotrexate was suspended and liposomal amphotericin b, 4 mg/kg per day for 10 days, followed by two further administrations two weeks later was started. cutaneous and mucosal lesions improved at the end of the first 10 days of therapy and completely vanished after two further administrations, 40 days from the beginning of treatment. leishmania-pcr on peripheral blood after 10 days of therapy was negative. table 1 shows the literature data about characteristics, therapy and outcome of patients with psoriasis and leishmaniasis. leishmaniasis is a vector-born chronic infectious disease caused by protozoa of the genus leishmania and transmitted to humans by the bite of phlebotomine sandflies. in europe, the mediterranean countries are the most affected areas. leishmania parasite establishes chronic intracellular parasitism, survives for an infected person's lifetime and, in the event of major immune deficiency, may be reactivated from sites of latency. leishmaniasis can present with a spectrum of clinical manifestations and three patterns of infection are described: cutaneous (cl), mucosal or mucocutaneous (ml or mcl) and visceral leishmaniasis (vl). the infecting species of leishmania is very important in determining the clinical manifestations and the host immune response is crucial in determining the clinical outcome of infection 2 . today, non-hiv related immunosuppressive conditions are becoming increasingly prevalent, mainly because of better medical care of patients with chronic illnesses and the therapeutic use of immunosuppressive drugs. in the field of rheumatology, leishmaniasis has been reported in association with the use of various immunosuppressive drugs. 3 the introduction of tumor necrosis factor-alpha (tnf-α) antagonist drugs has received much attention recently and several cases of vl have been reported in rheumatic patients who do anti-tnf α drugs. 4 psoriasis is a chronic inflammatory autoimmune disease affecting 2-3% of the world's population and characterized by an aberrant hyper-proliferation of keratinocytes. the pathogenesis of psoriasis is complex. genetic susceptibility, environmental triggering factors and an over-reaction of local innate immune response initiate inflammation. subsequent involvement of adaptive immune response with production of th 1 cytokines, chemokines and growth factors lead to epidermal hyperplasia. 5 recently, a functional role of interleukin-17-producing t helper cells (th17) in psoriasis has been suggested by their reduction during successful anti-tnf treatment. 6 it is also known that th17 lymphocytes play an essential role in protecting against intracellular protozoa and in the successful clearance of leishmania by strengthening the th1 response. 7 in view of this, it could be argued that psoriasis may represent a protective factor for leishmania infection. indeed, in our review we did not found any case of leishmaniasis in psoriatic subjects who were not under immunosuppressive therapies. biological agents, which are powerful immunosuppressive drugs, have been more and more used in rheumatic patients and leishmania infections have been reported among anti-tnf-agents users. 8 recently maritati et al. found higher prevalence of subclinical leishmaniasis in patients with inflammatory rheumatic diseases receiving biological drugs than those treated with other immunosuppressive drugs. 9 however, leishmaniasis has also been reported in psoriatic patients not receiving biological drugs, as occurred to our patient ( table 1 ) . diagnosis of cl in psoriatic patients is challenging, as it mimics many other infections or a flare-up of psoriasis itself that can lead to ineffective and harmful changes of therapy. immunosuppressive therapies cause atypical manifestations of leishmaniasis with large lesions spread over large cutaneous areas and associated to a possible mucosal involvement. ml by l. infantum is very rare and only sporadically described in patients receiving powerful immunosuppressive therapies or in hiv-coinfected patients. mcl is mostly observed in latin america where l. braziliensis accounts for most cases, but l. panamensis, l. guyanensis, and l. amazonensis have also been implicated. only rarely cutaneous lesions extend to areas of skin distant from the mucosa involved, as in our case in which two lesions on the foot and knee were associated with the oral lesion. in the context of impaired immunity, it is also advisable to rule out vl by pcr-leismania on peripheral blood so as to establish the most appropriate therapy: intralesional or intravenous. finally, there is no agreement on appropriate screening for leishmaniasis before immunosuppressive treatments and on the strategy to be followed after the diagnosis of leishmaniasis in rheumatic patients taking immunosuppressive drugs. 10 molecular methods are highly sensitive and specific tools for the diagnosis of visceral leishmaniasis and a screening with leishmania-pcr in immunosuppressed patients living in endemic areas could be useful to identify patients at highest risk of reactivation. 9 specific leishmaniasis treatment followed by suspension of the immunosuppressive therapy was adopted by most of the authors. overall even if the treatment response is not as good as seen in the immunocompetent population, our review reports a good outcome in all cases and patients remained relapse-free without maintenance therapy and despite the ongoing use of immunosuppressive medication. in conclusion physicians must be alert to the possibility of development of leishmaniasis in immunosuppressed rheumatic patients. adequate screening for vl should be incorporated into the list of baseline studies to carry out before initiating biologic therapies, at least in endemic areas. the authors declare that there is no conflict of interest. as demonstrated in several studies in journal of infection , herpesviruses pose an increasing threat to human health. [1] [2] [3] according to international committee on taxonomy of viruses (ictv), equine herpesviruses (ehvs) belong to the family herpesviridae . until now, a total of 9 ehv species types have been determined in equines, viz. ehv1-ehv9. 4 among them, ehv1 and ehv4 are the most relevant herpesviruses affecting equines. both ehv1 and ehv4 infection are associated with upper respiratory tract disease, but only ehv1 infection could cause abortion and myeloencephalitis. ehv1 and ehv4 are prevalent in equines on all continents and have considerable economic impact on the horse industry. 5 in china, the number of equines is very large, reaching to be ∼ 6.8 million in 2018 ( http://www.stats.gov.cn/tjsj/zxfb/ ). ehv infection in equines was first reported in china in 1980, and the epidemiological investigation since then indicated ehv was prevalent in the equine population in all the studied 16 provinces in mainland china, with a seroprevalence ranging 8% −92%. [6] [7] [8] vaccination is commonly used to prevent and control ehv. however, china has not developed a commercially available ehv vaccine so far. ehv vaccine has a limited market application potential in china currently. due to the lack of relevant knowledge on ehv, most of the chinese horse owners always erroneously identified it as other common pathogen of equine respiratory diseases, and didn't realize its potential threat to equine health and reproduction. although the number of equines in china is large, most of them are labor/farming horses. to the best of our knowledge, even for racehorses, vaccination with ehv vaccine has not been performed in mainland china. considering the wide distribution and high prevalence of ehv in china, it is urgently to popularize knowledge on ehv in horse owners and promote market application prospects of ehv vaccine. in china, few veterinary researchers are currently investigating equine virus, including ehv. this is mainly caused by the change of equines' historical role. in the last century, a great number of equines were used for military in china. however, there is only one military equine farm in mainland china at present. considering a more important economic role of other domestic animals (e.g., pigs, chickens, and cattle) compared with equines, investigating equine virus (including ehv) is not a priority in the related guide policies issued by the chinese government. though epidemiological studies on ehv in china are limited, it still could be concluded that epidemic status of ehv is very complicated in china, which increases the difficulty in ehv vaccine development. in most provinces, ehv1 and ehv4 were co-circulating in equines with a high seroprevalence. 8 until now, a total of 7 ehv1 strains have been isolated from tissue samples of aborted equine fetuses (5 from farming horses in northeast china in 1980, 1 from asian wild horses in western china in 1999, 1 from farming horses in western china in 2016). 6 , 8 in addition, a novel ehv8 strain was isolated from one horse with serious respiratory disease in northern china in 2010. 9 recently, our laboratory firstly determined the molecule evinces for ehv4 and ehv5 in racehorses in sothern china (data not shown). however, a more large-scale and surveillance of ehv in equines is necessary to fully understand epidemic status of ehv in china, which could establish a foundation for updating the composition of ehv vaccine developed in china in future. in other countries, much effort has been made to develop ehv vaccine, and modified-live and inactivated virus vaccines have been registered for sale. 10 before an ehv vaccine is developed successfully in china by itself, it is necessary to vaccinate the susceptible equine population with an ehv vaccine commercially available from other countries to prevent and control ehv in china. however, a well-designed case-control animal challenge study still needs to estimate the protective efficacy of different vaccines against the field prevalent ehv strains in china. all authors declare that they have no competing interests. a recent review article on the treatment of hepatitis c with directly-acting antiviral (daa) drugs, makes numerous recommendations for baseline drug resistance testing. 1 in our local practice, we have been performing baseline drug resistance testing for some years now, prior to the publication of these guidelines. we present a recent retrospective hcv kinetics analysis of these patients' changing viral loads in response to daa therapy below. such studies have been used previously to compare viral suppressive responses in different hcv genotypes and treatment regimens. 2 , 3 the patients were a mixture of treatment-naive and treatment-experienced (including with interferon-based, ns3 protease inhibitor-based and daa-based regimens) cases. the current standard of care for hepatitis (hcv) patients is a combination of direct acting antivirals (daas), for which there are three different hcv viral protein targets (ns3, ns5a and ns5b). table 1 ns3, ns5a, ns5b resistance associated substitutions (ras), by hcv genotype, found in this patient cohort at baseline drug resistance testing (viral sequencing performed at imperial college, london, uk). the patients included a mixture of treatment-naïve and treatment experienced (i.e. interferon-based, ns3 protease inhibitor-based and more recent daa-based regimens) cases. resistance associated substitution (ras) by hcv genotype treatment with daas cure the vast majority of hcv-infected patients, with oral regimens having > 95% efficacy in most patient groups. 1 , 4 , 5 treatment failure currently affects approximately 5% of treated patients and is often associated with the selection of resistance associated substitutions (ras). 1 we performed hcv drug resistance testing both retrospectively (following treatment failures) and prospectively (prior to treatment) in our cohort of hcv genotype (g) 1-3-infected patients, during march 2015-june 2018. viral extraction, pcr and sequencing were performed at imperial college, using qiagen viral rna mini kits (qiagen pn:52906, qiagen ltd., manchester, uk), and inhouse pcr and sanger sequencing methods on an abi prism 3100-avant genetic analyser (thermo fischer scientific, loughborough, uk). the prediction of hcv genotype and drug sensitivities is derived from the geno2pheno algorithm [ www.geno2pheno.org ]. 6 treatment regimens used during this period complied with contemporaneous nhs rate cards: for non-cirrhotic or compensated cirrhotic patients: g1-treatment-naive: omb/par/rit + das + r; g1-treatment-experienced: elb/grz + /-r; g2-treatmentnaive/experienced: gle/pib; g3-treatment-naive/experienced: gle/ pib; g1-decompensated cirrhotic patients sof/led + r; g2/g3decompensated cirrhotic patients: sof/vel + r. we assessed the impact of any ras across g1-g3 on hcv rna kinetics by analysing viral load (realtime hcv viral load, abbott m20 0 0, abbott molecular uk, maidenhead, england) decline rates. we applied linear mixed regression to model the viral loads and assumed a linear decline (log 10 scale) over time, using sas statistical software (sas institute inc., nc, usa). in this cohort of 54 patients (n: g1 = 21, g2 = 6, g3 = 27), hcv ras were found as shown in table 1 . hcv rna viral load decline rates were found to be similar and not statistically different ( p = 0.760) at: −2 log 10 and −1.8 log 10 per month, respectively, for g1 and g2/g3 ( fig. 1 ). this suggests that these viral load decline rates were similar across g1-g3 infections despite baseline differences in viral load, ras profile, or a history of any previous treatment (i.e. interferon-based, older ns3 protease inhibitor-based, or more recent daa regimens). these results demonstrate similar hcv rna clearance efficacies of the various daa treatment regimens for g1-g3, in this patient cohort. although other studies on hcv kinetics have been published, they do not usually compare multiple hcv genotypes. 7 similar studies on patients infected with g4-6 viruses, and/or undergoing other daa treatment or retreatment combinations, 8 , 9 will be with great interest we have read the report of zhang et al. concerning the increased susceptibility to pertussis in chinese adults at childbearing age, as determined in a comparative seroprevalence study using samples collected from 2010 to 2016. 1 the authors describe that about 5% of the individuals had pt-igg antibodies, which is indicative of a recent infection. in the adults 20-39 years of age, 29.1% subjects had undetectable pt-igg antibodies in 2010 but 57.4% in 2015/2016. it is well known that adolescents and adults have become the reservoir of pertussis and an important source of transmission to vulnerable infants. bordetella pertussis is commonly associated with atypical pneumonia as determined in hospitalized children. 2 several seroprevalence studies conducted in different regions of china indicate that the incidence of pertussis is most likely underestimated. 3 , 4 this may be due to the use of insensitive diagnostics. at present, the diagnosis of pertussis in china is mainly based on culture. however, both the cdc and the world health organization (who) use pcr as the gold standard for diagnosis, in addition to culture. 3 oropharyngeal or nasopharyngeal swabs were obtained from 17,104 inpatients aged between 10 days and 14 years of age with clinical suspicion of pertussis, enrolled from march 2014 to february 2018 in shenzhen children's hospital. more than 50% of all patients were younger than 6 months of age. the hospitalized patients included 10,894 males and 6210 females (sex ratio, 1.75). all patients recovered after the treatment. a real time pcr assay targeting ptxa-pr was used to detect b. pertussis . of the 17,104 samples, 772 (4.51%) tested positive for b. pertussis by rt-pcr. our results indicate that despite vaccination pertussis remains a major health problem in china, since the prevalence of infection by b. pertussis in hospitalized children was high. the majority of patients were admitted because of pneumonia. the detection rate in hospitalized patients was lower than the rates reported earlier in shanghai and ji'nan. 3 , 4 this may be due to lower number of samples collected in these studies and due to the use of serology or culture methods. the overall prevalence rates were 3.97% and 5.48%, respectively. however, b. pertussis infection in female patients was significantly higher than in male patients (x 2 = 20.913, p < 0.001). this has earlier been reported by the ecdc 5 and haberling et al. 6 and may point to a genetic association with susceptibility to b. pertussis . the detection rates were dependent on age in patients (x 2 = 139.8, p < 0.001). the prevalence decreased with age: 8.71% newborns, 5.33% in infants, 2.39% in toddlers, 1.28% in (pre-) schoolers ( fig. 1 ) . the high vulnerability of newborns and young infants for b. pertussis infection may be related to a combination of insufficient herd immunity and suboptimal protection against b. pertussis infection in children too young to be fully vaccinated. since vaccination rates in infants are already at 99%, it will be difficult to improve this further. therefore, other measures must be considered, including booster vaccination at pre-school age and vaccination during pregnancy. because young infants are mainly cared for by mothers and other adults, the most important cause of infection with b. pertussis is their close contact with parents and siblings. 7 in general, b. pertussis was detected more often during seasonal changes, especially from late summer to early autumn. in hospitalized children the number of b. pertussis infections increased in march and september as compared to other months ( fig. 2 ) . the seasonal infection rates were 4.66% in spring, 4.75% in summer, 4.62% in autumn and 4.00% in winter, respectively. the prevalence in the winter season was lower but not statistically different than in other seasons (x 2 = 3.388, p = 0.336). in this study, we used real-time pcr, the most accurate method to detect b. pertussis . the detection rate may be significantly lower than the actual level, because oropharyngeal samples in most patients were collected instead of nasopharyngeal samples, and the pcr target gene was ptxa-pr instead of is4 81. is4 81 is present in high-copy numbers in b. pertussis whereas ptxa-pr is a single-copy target. however, the ptxa-pr pcr is more specific and will not detect b. parapertussis , which contributes to more than 5% of pertussis cases. 8 many studies have shown that adolescents and adults with b. pertussis infections, causing chronic cough, are an important reservoir for transmission, putting newborns at high risk. 9 maternal pertussis immunization prevents infant pertussis, as recently shown by amirthalingam et al. vaccine effectiveness against infant deaths was estimated at 95%, and disease incidence in infants < 3 months of age has remained low. 10 according to our results, vaccination of pregnant women and adults, especially those in close contact with infants and young children, may help to prevent pertussis in infants and young children in china. the authors have declared that no competing interests exist. this study was supported by the sanming project of medicine in shenzhen ( szsm201512030 ) and by the shenzhen science and technology project ( jcyj20170303155012371 ). tang and colleagues reported in this journal their experience with covid-19 disease 1 , the outbreak of which began in december 2019 in wuhan, hubei province, china 2 , 3 with spread to 33 additional countries 4-8 as of the 21st february 2020. here we report the clinical features and outcome of the first two cases of disease caused by sars-cov-2 infection in the united kingdom (uk) -the first imported and the second associated with probable person-toperson transmission within the uk. public health management will be reported separately. the index case (a) entered the uk on 23/01/20 from hubei province in china. initially asymptomatic, this individual, a 50 year-old female with no past medical history and on no regular medications, developed symptoms of fever and malaise on 26/01/20, accompanied by sore throat and dry cough. she had travelled with her partner and reported no infectious contacts prior to travel. on 28/01/20, a close household contact of the index case, a resident of the uk, developed symptoms of fever (38.5 °c), followed the next day by diffuse myalgia and a dry cough. this patient (case b) is a previously fit and well 23 year-old male. he had returned to the uk from hubei province on 06/01/20. case b promptly sought advice via the national health service (nhs) self-referral service nhs 111, and he and case a were assessed as being possibly at risk of covid-19, and were admitted to the regional infectious diseases unit at castle hill hospital, hull university teaching hospitals for isolation, assessment and diagnostic sampling. they were managed in separate negative pressure cubicles with anterooms. nursing and medical staff donned personal protective equipment (ppe) as recommended by public health england (phe). the clinical observations of each of the patients, together with their initial blood tests, are shown in table 1 . ( fig. 1 ) . clinical examination findings were unremarkable. initial investigations revealed only mild lymphopenia and elevation of crp, with mild neutrophilia in case b. periodic fever of 38-38.5 °c was observed in case b until d3 of admission. repeat blood tests in this individual on d3 demonstrated mild acute kidney injury (aki, serum creatinine 144 μmol/l). the aki was thought most likely due to dehydration, and resolved within 24 h with administration of intravenous infusion of crystalloid at 125 ml/h. cxr was normal. empirical oral antibiotic therapy (co-amoxyclav 500/125 mg p.o. t.d.s.) was administered on d3, to cover the possibility of secondary bacterial infection, but was subsequently discontinued. symptoms resolved in case a by d3 and in case b by d4 of admission. pcr testing of sars-cov-2 from nose and throat swabs taken daily was negative from d2 onwards in case a and from d5 in case b (throat swabs from this individual were negative throughout). there was no clinical indication for the use of experimental antiviral therapies. patients were deisolated according to current phe guidance, based on complete resolution of symptoms and two sequential negative respiratory pcr tests at least 24 h apart. rooms were decontaminated with 0.1% hypochlorite followed by uv light treatment. the contact of these individuals remained asymptomatic throughout the 14 days incubation period but was isolated as a precaution and to be close to family these first cases of sars-cov-2 are informative for clinicians caring for suspected and confirmed cases in the uk and elsewhere. reassuringly, illness in both individuals was relatively mild and short-lived, with no evidence of parenchymal lung disease (reflected by normal oxygenation and the absence of radiological infiltrates) or of the late-stage deterioration that has been reported in case series 9 , possibly due to the absence of comorbidities. experimental antiviral therapeutic options for severe disease were not considered necessary given the mild clinical nature of the illness. clinical illness correlated with the presence of viral rna in upper airway samples ( fig. 1 ) , with no evidence of prolonged asymptomatic shedding, although discordance between nose and throat samples in case b highlights the need to sample both areas. it was reasonably assumed that the source of infection in case b was close contact with symptomatic case a, given that the time from travel to china to onset of symptoms in case b was 22 days, although this cannot be proven. based on this assumption, the period from exposure to disease onset appeared short, at approximately 48 h, consistent with recent reports of the incubation period of sars-cov-2 6 . co-occurrence of respiratory viral infection, as we observed in case b with rhinovirus, has been described in the context of sars-cov-2 ( https://www.medrxiv.org/ content/10.1101/2020.02.12.20022327v1 ) as it has with many other respiratory viruses spread by similar routes, and may have contributed to the increased symptomatology in case b. interestingly the partner of case a, who was a close household contact, remained asymptomatic throughout and had negative tests for sars-cov-2 shedding. it will be of interest to investigate the serological responses in this individual to ascertain evidence of subclinical infection. isolation, minimisation of contacts and use of appropriate ppe is a cornerstone of management of high consequence respiratory viral infection. in the cases reported here, phe recommendations for ppe were followed 10 and there were no breeches in ppe or nosocomial transmission. this should provide reassurance to healthcare workers managing patients with suspected covid-19 in the uk that current ppe is both feasible and effective. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. dear editor , as reported in this journal 1 and elsewhere, 2 an outbreak of atypical pneumonia caused by the zoonotic 2019 novel coronavirus (sars-cov-2) is on-going in china and has spread to the world. as of feb 16, 2020 (24:00, gmt + 8), there have been 70,548 confirmed patients and more than 1700 deaths from sars-cov-2 infection in china, and 58,182 confirmed patients and 1696 deaths in the most affected province, hubei province. much research progress has been made in dissecting the evolution and origin of sars-cov-2 and characterizing its clinical features. [3] [4] [5] [6] [7] while the outbreak is on-going, people raise grave concerns about the future trajectory of the outbreak, especially given that the working and schooling time has been already dramatically postponed after the chinese lunar new year holiday was over (scheduled on jan 31). in particular, a precise estimation of the potential total number of infected cases and/or confirmed cases is highly demanding. earlier studies based on susceptible-exposed-infectious-recovered metapopulation and susceptible-infected-recovered-dead models revealed the number of potentially infected cases and the basic reproductive number of sars-cov-2. 3 , 8 , 9 these traditional epidemiological models apparently require much detailed data for analysis. 3 , 8 here we explored a simple data-driven, boltzmann functionbased approach for estimation only based on the daily cumulative number of confirmed cases of sars-cov-2 (note: the rational for boltzmann function-based regression analysis is presented in supporting information (si) file). we decided to collect data (initially from jan 21 to feb 10, 2020) in several typical regions of china, including the center of the outbreak (i.e. wuhan city and hubei province), other four most affected provinces (i.e., guangdong, zhejiang, henan, hunan) and top-4 major cities in china (i.e., beijing, shanghai, guangzhou, shenzhen). during data analysis on feb 13, 2020, the number of new confirmed cases on feb 12 in hubei province and wuhan city suddenly increased by 14,840 and 13,436, respectively, of which 13,332 and 12,364 are those confirmed by clinical features (note: all the number of confirmed cases released by feb 12 were counted according to the result of viral nucleic acid detection rather than by referring to clinical features). we thus arbitrarily distributed these suddenly added cases to the reported cumulative number of confirmed cases from jan 21 to feb 14 for hubei province by a fixed factor (refer to table s1 ), assuming that they were linearly accumulative in those days. it is the same forth with the data for wuhan city. regression analyses indicate that all sets of data were well fitted with the boltzmann function (all r 2 values being close to 0.999; figs. 1 a, b, s1 , and table 1 ). the potential total number of confirmed cases for mainland china, hubei province, wuhan city, and other provinces were estimated as 72,80 0 ±60 0, 59,30 0 ±60 0, 42,10 0 ±70 0 and 12,80 0 ±10 0; respectively; those for provinces guangdong, zhejiang, henan and hunan were 1300 ±10, 1170 ±10, 1260 ±10, 1050 ±10, 1020 ±10 and 940 ±10, respectively ( table 1 ) ; those for beijing, shanghai, guangzhou and shenzhen were 394 ±4, 328 ±3, 337 ±3 and 397 ±4, respectively. in addition, we estimated the key date, on which the number of daily new confirmed cases is lower than 0.1% of the potential total number as defined by us subjectively (refer to table 1 ). the above analyses were performed assuming that the released data on the confirmed cases are precise. however, there is a health commission, the state administration of traditional chinese medicine, the academy of chinese medical sciences, 29 provinces and cities, as well as the army ( fig. 1 ) . huoshenshan hospital is a specialized hospital established in the wuhan staff sanatorium. patients with confirmed coronavirus pneumonia have been admitted to our hospital. it has a total of 10 0 0 beds, and includes an intensive care unit, an ordinary care unit, a laboratory, and radiology and other auxiliary departments. according to the national health commission of the people's republic of china, the related design scheme of the institute was completed on january 24, 2020. construction of the hospital began on january 29th, and the hospital was completed and put into use on february 2nd. the chinese people's liberation army has transferred 1400 medical personnel to undertake the task of helping people infected with the virus. we firmly believe that chinese medical 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www.gov.uk/government/publications/wuhan-novelcoronavirus-infection-prevention-and-control/wuhan-novel-coronavirus-wncov-infection-prevention-and-control-guidance accessed 3rd emergence of a novel coronavirus causing respiratory illness from wuhan a novel coronavirus outbreak of global health concern epidemiological and clinical features of the 2019 novel coronavirus outbreak in china a new coronavirus associated with human respiratory disease in china a pneumonia outbreak associated with a new coronavirus of probable bat origin genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding clinical characteristics of 2019 novel coronavirus infection in china nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study data-based analysis, modelling and forecasting of the novel coronavirus (2019-ncov) outbreak a data driven time-dependent transmission rate for tracking an epidemic: a case study of 2019-ncov emergence of a novel coronavirus causing respiratory illness from wuhan early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features of patients infected with 2019 novel coronavirus in wuhan the novel coronavirus originating in wuhan. china: challenges for global health governance emergence of sars-like coronavirus poses new challenge in china we are indebted to all colleagues who contributed to this substudy in paris and geneva. in particular, we would like to thank no public or private funds were used for the current study. eliseo albert holds a río hortega research contract from the carlos iii health institute (ref. cm18/00221 ). estela giménez holds a juan rodés research contract from the carlos iii health institute (ref. jr18/0 0 053 ). we thank all the staff of the domestic and international organizations who fought against this outbreak, including those at the various health care facilities, lassa fever diagnostic laborato-ries, nigeria centre for disease control, world health organization, african field epidemiology network, public health england, ehealth africa, pro health international, university of maryland baltimore, us centers for disease control and prevention, alliance for international medical action, médecins sans frontières, and numerous other partners. we also express our sincerest condolences to the families and friends of those who died during the outbreak. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2019.12.016 . this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sector. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2020.01.019 . this work was supported by the national natural science foundation of china ( 31702271 ), and the guangdong provincial natural science foundation ( 2017a030310367 ). we are grateful to the patients for providing their written informed consent to publish this report. our thanks go to nursing, laboratory and medical colleagues in hull university teaching hospitals nhs trust and the newcastle upon tyne hospitals nhs foundation trust who contributed directly and indirectly to patient care, and to many colleagues in public health england and across the hcid network who contributed their time and expertise to the management of these cases. cjad is supported by a clinical research career development fellowship from the wellcome trust ( 211153/z/18/z ). we thank graduate students (boyan lv, zhongyan li, zhongyu chen, yu cheng, mengmeng bian, shuang zhang, zuqin zhang, and wei yao; all from prof. xinmiao fu's research group at fujian normal university) for data collection. this work is support by the national natural science foundation of china (no. 31972918 and 31770830 to xf). the reported cumulative number of confirmed cases may have uncertainty. assuming the relative uncertainty follows a single-sided normal distribution with a mean of 1.0 and a standard deviation of 10%, the potential total number and key dates were estimated at 95% ci. for detail, refer to the methods section and figs. 1 c, d, s2 and s3.b key date is determined when the number of daily new confirmed cases is less than 0.1% of the potential total number. tendency to miss-report some positive cases such that the reported numbers represent a lower limit. one typical example indicating this uncertainty is the sudden increase of more than 14 0 0 0 new confirmed cases in hubei province on feb 12 after clinical features were officially accepted as a standard for infection confirmation.another uncertainty might result from insufficient kits for viral nucleic acid detection at the early stage of the outbreak. we thus examined the effects of such uncertainty using a monte carlo method (for detail, refer to the methods section in si file). for simplicity, we assumed that the relative uncertainty of the reported data follows a single-sided normal distribution with a mean of 1.0 and a standard deviation of 10%. under the above conditions, the potential total numbers of confirmed cases of sars-cov-2 for different regions were estimated ( figs. 1 c, d, s2 and s3 ) and summarized in table 1 16 ,092), respectively, indicating that overall the outbreak may not be so bad as previously estimated. 9 such uncertainty analysis also allowed us to estimate the key dates at 95% ci. as summarized in table 1 , the key dates for mainland china, hubei province, wuhan city, and other provinces would fall in (2/28, 3/10), (2/27, 3/10), (2/28, 3/10) and (2/27, 3/13), respectively.finally, the ongoing sars-cov-2 outbreak has undoubtedly caused us the memories of the sars-cov outbreak in 2003. we thus collected the data from the who officiate website for analysis, and found that the cumulative numbers of confirmed cases of 2003 sars-cov both in china and worldwide were fitted well with the boltzmann function, with r 2 being 0.999 and 0.998, respectively ( figs. 1 e and f) .in summary, we found that all data sets, including both the on-going outbreak of sars-cov-2 in china and the 2003 sars-cov epidemic in china and worldwide, were well fitted to the boltzmann function ( fig. 1 and s1 ). these results strongly suggest that the boltzmann function is suitable for analyzing the epidemics of coronaviruses like sars-cov and sars-cov-2. one advantage of this model is that it only needs the cumulative number of confirmed cases, somehow as simple as the recently proposed model. 10 in addition, the estimated potential total numbers of confirmed cases and key dates may provide valuable guidance for chinese central and local governments to deal with this emerging threat at current critical stage. none. supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.jinf.2020.02.019 . we appreciate the work tang et al. have report emergence of a novel coronavirus in china. 1 the 2019-ncov broke out in wuhan, china at the end of 2019, and has attracted worldwide attention. [2] [3] [4] although the chinese government has taken active measures to control this epidemic, the virus is very infectious. according to the real-time data of the national health commission of the people's republic of china up until february 5, 2020, within a short period of half a month, the number of confirmed cases and the number of deaths were 24,443 and 493, respectively. the epidemic is progressing rapidly. 2019-ncov poses new public health challenges in china. 5 in wuhan, china, the number of local medical staff is insufficient for the demand resulting from the explosive increase in the number of infected patients. therefore, many medical personnel are needed to devote themselves to the front line of combating the virus.medical personnel throughout the country are led under the unified leadership of the chinese government. although the epidemic in wuhan is serious, a large number of medical staff rushed to wuhan to supplement the shortage of manpower in wuhan hospitals. this is a battle without smoke, the heroes of which are our medical staff. according to the national health commission of the people's republic of china, as of january 30, 2020, hubei province opened 11,0 0 0 isolated patient beds, and about 170,0 0 0 healthcare professionals from all kinds of medical institutions are working on the front lines and providing care for patients with fevers, and for suspected or confirmed patients. in this time of emergency, under the unified deployment of the chinese government, there are 52 medical teams including 6097 medical personnel from the national key: cord-320953-1st77mvh authors: overton, christophere.; stage, helenab.; ahmad, shazaad; curran-sebastian, jacob; dark, paul; das, rajenki; fearon, elizabeth; felton, timothy; fyles, martyn; gent, nick; hall, ian; house, thomas; lewkowicz, hugo; pang, xiaoxi; pellis, lorenzo; sawko, robert; ustianowski, andrew; vekaria, bindu; webb, luke title: using statistics and mathematical modelling to understand infectious disease outbreaks: covid-19 as an example date: 2020-07-04 journal: infect dis model doi: 10.1016/j.idm.2020.06.008 sha: doc_id: 320953 cord_uid: 1st77mvh during an infectious disease outbreak, biases in the data and complexities of the underlying dynamics pose significant challenges in mathematically modelling the outbreak and designing policy. motivated by the ongoing response to covid-19, we provide a toolkit of statistical and mathematical models beyond the simple sir-type differential equation models for analysing the early stages of an outbreak and assessing interventions. in particular, we focus on parameter estimation in the presence of known biases in the data, and the effect of non-pharmaceutical interventions in enclosed subpopulations, such as households and care homes. we illustrate these methods by applying them to the covid-19 pandemic. mathematical epidemiology is a well-developed field. since the pioneering work of ross in malaria modelling [67] and kermack and mckendrick's general epidemic models [40] , there has been gathering interest in using mathematical tools to investigate infectious diseases. the allure is clear, since mathematical models can provide powerful insight into how these complex systems behave, which in turn can enable these problems to be better controlled/prevented. not only is the power of the mathematical tools increasing, but the availability of data on infectious diseases, whether this be a rapid release of data during an outbreak or detailed collection of data for endemic pathogens, is increasing. rapid interpretation of epidemiological data is critical for the development of effective containment, suppression and mitigation interventions, but there are many difficulties to interpreting case data in real-time. these include interpreting symptom progression and fatality ratios with delay distributions and right-censoring, exacerbated by exponential growth in cases leading to the majority of case data being on recently infected individuals; lack of clarity and consistency in denominators; inconsistency of case definitions over time and the eventual impact of interventions and changes to behaviour on transmission dynamics. mathematical and statistical techniques can help overcome some of these challenges to interpretation, aiding in the development of intervention strategies and management of care. examining key epidemiological quantities alongside each other in a transmission model can provide quantitative insights into the outbreak, testing the potential impact of intervention strategies and predicting the risk posed to the human (or animal) host population and healthcare preparedness. mathematical modelling has been used as part of the planning process during outbreak response by governments worldwide for many recent outbreaks. for example the uk department of health has a long established committee scientific pandemic influenza group on modelling, or spi-m to advise on new and emerging respiratory infections [22] . one of the largest instances of such an outbreak in recent history was the 2009 h1n1 pandemic. the world health organisation developed a network of modelling groups and public health experts to work on exploring various characteristic of the outbreak [12, 78] . these ranged from characterising the dynamics of the outbreak to investigating the effectiveness of different intervention strategies. this integration of mathematics into policy design indicates the important insights that modelling and statistics can provide. this paper is a collection of work-streams addressing various technical questions faced by the group as part of the ongoing response to covid-19, and as such is written to be reflective of the experience we have gone and are currently going through. therefore, to aid the reader each section includes results and a short discussion. many of the questions and techniques presented here can be further developed as the availability of data and research interests evolves, but are compiled into this manuscript as an overview of methodology and scientific approaches beyond the standard sir textbook model that benefit the ongoing efforts in tackling this and other outbreaks. first documented in december 2019, an outbreak of community-acquired pneumonia began in wuhan, hubei province, china. in january, this outbreak was attributed to a novel coronavirus, sars-cov-2. the initial spread of the pathogen in wuhan was fast, and after a period of case-finding and contact tracing, china moved to implement a 'shutdown' of wuhan on january 23, and other cities in china the following days, to try to suppress the growth of the epidemic. these measures may have succeeded at slowing down the rate at which cases have been seeded elsewhere, but in many countries initial importation of cases and transmission has not been contained. countries around the world are now seeing outbreaks that are overwhelming, or have the potential to overwhelm, healthcare systems and cause a high number of deaths even in high-income countries [64] . while the majority of documented symptomatic cases are mild, characterised in many reports by a persistent cough and fever, a significant proportion of these individuals go on to develop pneumonia, with some then developing acute respiratory failure and a small proportion of overall cases becoming fatal. severity of symptoms has been observed to increase with age and with the presence of underlying health conditions such as diabetes [23] and cardiac conditions, with some evidence that severity of symptoms might depend on gender and ethnicity [31, 65, 82, 83, 85] . sars-cov-2 has a fast doubling time (the time it takes for the number of cases in the region to double, estimated at approximately 3 days [63] ) and, potentially, a very large 0 r (the average number of infections caused by each infected individual, with estimates ranging from 1.4 to 6.47 [48, 50, 51, 59] ). it is possible that there is a significant degree of asymptomatic and/or pre-symptomatic transmission [46, 52, 56] , though without robust serosurveys, this is difficult to quantify with certainty. these characteristics result in the pathogen being able to spread widely, rapidly and undetected, presenting a significant risk to public health. typically, the aim of an intervention strategy would be to push and keep the reproduction number t r , defined as the average number of cases generated by a typical infective at time t, below 1. at this point each infected individual subsequently infects, on average, less than one individual, such that the number of cases should decline. the basic reproduction number, 0 r , represents the initial value of t r , before any intervention is put in place and the population can be assumed to be fully susceptible. high 0 r , fast growth, and possible pre-or asymptomatic infection make the design of potential interventions, and the modelling that would inform them, particularly challenging. large values of 0 r mean a substantial amount of transmission needs to be halted; fast growth causes the number of cases in the absence of interventions to rise rapidly, so that the time scale of interventions to reduce 0 r must also be fast in order to effect substantive early changes on a population level; finally, the resulting interventions must encompass possible pre-and asymptomatic cases, a challenging prospect when in many instances these individuals are indistinguishable from healthy individuals. consequently, we must consider the possibility of interventions that are massively disruptive to society and may have to be sustained for a long period of time in order to cause the number of infections to decline towards zero [25] . if infections remain, and the susceptible proportion of the population remains above the herd immunity threshold, these interventions must be upheld to prevent a second wave of the epidemic. there is not yet conclusive evidence as to the degree and duration of immunity conferred by infection with sars-cov-2 nor the feasibility of a vaccine, the timeline for which is unlikely to be any time shorter than 18 months away at the time of writing [35] . therefore, short term extreme interventions are not as effective as they might be in other circumstances, since after their removal there remains a long period of time in which cases can rise again. the longer these significantly suppressive and disruptive interventions are in effect, the more severe the effect on the economy, and broader societal health and well-being. furthermore, adherence to interventions will likely vary with their duration and severity. we are further challenged by the lack of transferable intuition. early work looked at intuition gained from sars and mers outbreaks, also caused by coronaviruses. some parameters do appear to be similar to these pathogens, such as the average length of the incubation period [44, 79, 80] . however, there are also clear differences, with both sars and mers being more fatal, but seemingly less efficient at spreading since they did not seed major global pandemics. another complication is the spread of the infection during the chinese spring festival, a time period during which movement, social, and contact patterns vary significantly. this presents significant challenges as experience and intuition from other studies regarding population mixing and spatial patterns must either be modified or are invalid. furthermore, the pandemic has received a proportionately larger level of public attention than e.g. the 2009 h1n1 pandemic [19, 68] , largely boosted by social media. this greater level of public awareness, and the successive, staggered interventions placed to prevent disease spread are responsible for significant variations in behaviour [16, 27] and adherence to public guidance both in china and abroad. the structure of this paper follows two main themes. in section 2, we discuss various biases that are present in outbreak data and techniques for estimating epidemiological parameters. accounting for biases and producing robust parameter estimates is important throughout the duration of an epidemic, both for increasing our understanding of the underlying dynamics, and for feeding into models. firstly, we discuss a bias-corrected method for estimating the incubation period, which can also be applied to serial intervals, onset-to-death time, and other delay distributions. we then present a method for estimating the true growth rate of the epidemic, accounting for the bias encountered since infected individuals may be exported from the region. our next method is a tool for estimating the expected size of the next generation of infectives based on the rate of observed cases. this tool provides insight into the size of small outbreaks, which can inform decision making when trying to prevent a major outbreak taking off. in section 3, we propose a variety of mathematical models looking at disease impact and intervention strategies, with particular focus on non-pharmaceutical interventions due to the current lack of widely deployable, targeted pharmaceutical treatments. these models focus on enclosed populations, since this is the level at which most interventions are implemented. since the disease is particularly fatal in the elderly and other at-risk groups, we develop a care home model to investigate how the pathogen may spread through care homes. we also develop household models to investigate the impact of different intervention/control strategies. these models can inform policy design for mitigating or controlling epidemic spread. finally, in the context of relaxing strong social distancing policies, we investigate the extinction probability of the pathogen. we first consider the extinction probability after lifting restrictions. we then develop a household-based contact tracing model, with which we investigate the extinction probability under weaker isolation policies paired with contact tracing, thus shedding light on possible combinations of interventions that allow us to feasibly manage the infection while minimising the social impact of control policies. 2 . biases and estimation during outbreaks 2.1 . potential biases in the outbreak data techniques are constantly developing that enable higher volumes of more accurate data to be collected real-time during an epidemic. these data present a large opportunity for analysis to gain insight into the pathogen and the dynamics of the outbreak. however, although the quality of the data is constantly increasing, there are still many biases present. some of these are due to the data collection methods, and in an ideal world we would be able to eliminate them, and some are simply due to the nature of the outbreak, and will be present regardless of data collection methods. during an outbreak, many parameters depend on delay distributions (the length of time between two events), such as the time from infection to symptom onset (the incubation period). if an individual can be followed indefinitely, it is easy to determine the length of these events. however, in reality only events that occur before a given date are observed. therefore, the data is subject to censoring and truncation issues. in the incubation period, for example, censoring comes into play since, if we have observed an infection but the individual has not yet developed symptoms, we only have a lower bound on how long it will take them to develop symptoms. to account for this, we can instead condition on observing symptom onset before the cut-off date. however, this leads to a truncation issue, since individuals who were infected close to the cut-off date will only be observed if they have a short incubation period, which leads to an overexpression of short delays. the number of cases tends to grow exponentially during the early stages of an outbreak, causing the force of infection and the number of reported cases to increase with time. this further complicates the truncation issue since not only are recent cases truncated but they also account for the majority of cases. the growing force of infection also needs to be accounted for, since if the potential time of infection is interval-censored rather than observed directly, the probability that the case was infected in each day of that interval is not constant. in theory, both of these biases are relatively straightforward to account for. in practice however, there are other biases in the data. one of the major biases is the reporting rate. although the total number of cases may be reasonably described as growing exponentially with a constant rate in the early stages of an outbreak, high-resolution data may exhibit more complex behaviour. this can be due to a variety of reasons, such as the workload becoming overwhelming, the availability of individual-level data decreasing, the laboratories or offices slowing down activity over the weekend, the case definition changing, the testing capabilities increasing, and so on. another uncertainty arises since generally only the date of each event is recorded rather than the time. this presents a large window of uncertainty in the length of the delay, since the time of each event can vary up to 24 hours, and for a delay distribution, which depend on two events, it could vary by up to 48 hours. travel rate is another bias present in the data. for example, this changes the density of observed cases in a region, which can change the apparent growth rate. intervention strategies present a further bias because this can change the growth rate of the epidemic and the reporting rate. additionally, estimates of certain parameters may vary depending on the interventions that are implemented, so these need to be considered carefully. to model the incubation period, we require information regarding when an individual was infected and when they expressed symptoms. observing exact time of infection is unlikely, but it can be possible to find potential exposure windows. we consider three different data sets. the first two consist of individuals who travelled from wuhan before expressing symptoms. we can assume these individuals were infected in wuhan, since at the time of this data, the force of infection was significantly higher in wuhan than elsewhere. the length of time spent in wuhan therefore provides a window during which each individual became infected, and for many of these individuals we also have the date of symptom onset. in the early stages, the growth rate in reported cases was constant, and dependent on the epidemic growth rate in wuhan and the rate at which people left wuhan. by using travel to estimate the true number of cases, we estimate the exponential growth rate in wuhan as 0.25 r = (see section 2.3). therefore, the force of infection on day i, ( ) g i , is proportional to 0.25 e i . after 23 january when significant travel bans were introduced, the rate at which individuals left wuhan diminished significantly, causing the reporting rate for our sample dataset to suddenly drop. this occurs since cases are only included if we have a fixed window of time spent in wuhan prior to developing symptoms. therefore, if the data is truncated after 23 january, the reporting rate must be appropriately adjusted. this is illustrated in figure 1a . the difference between these two datasets is the truncation date, with the first truncated at 20 january and the second at 9 february. the third dataset contains cases that were infected through a discrete infection event, such as spending time with a known infected case. in this ''non-wuhan" dataset, the reporting rate is constant and the force of infection can be assumed constant over each exposure window. the source we use for these three data sets is a publicly available line-list [74] . incubation periods, and many other delay distributions, are generally observed to have right skewed distributions. we therefore choose to use a gamma distribution, though other distributions can also be applied using the proposed methods, such as weibull and log-normal. to fit the data, we use maximum likelihood estimation. to adjust for the biases we use a ''forwards'' approach [55, 69, 73, 75] , where we condition on the time of the first event, time of exposure, and find the distribution looking forward to the second event, time of symptom onset. for a data point { } , , infection occurs between i a and i b , and i y is the symptom onset date, the likelihood function is given by where ( ) g â�� is the density function of the infection date and ( ) f î¸ â�� is the density function of the incubation period parameterised by î¸. from this, the likelihood function for our dataset x is given by this approach is independent of the reporting rate bias, since the reporting rate depends on the date an individual leaves wuhan ( i b ), which is conditioned against (see appendix 5) . we use the mean and standard deviation to characterise the mle. since the tail of the incubation period is important when designing quarantine strategies, we then calculate the probability that the incubation period is longer than 14 days and find the minimum day by which 99% of cases will have expressed symptoms (excluding true asymptomatic cases). we also investigate the reporting date uncertainty mentioned in section 2.1 by considering the different extremes that the data could represent. this is achieved through adding or subtracting a day to all recorded data. methods accounting for truncation and growth biases in epidemic data have been discussed widely in the literature [36, 55, 72, 76] , however there are fewer applications to outbreaks [24] . in the context of covid-19, estimates have considered growing force of infection, for example [44] , and some approaches have considered truncation, for example [47] . however, these attempts do not adjust for the reporting rate in the data or use the correct force of infection, causing the incubation period to be overestimated. although the method presented here is independent of the reporting rate, other approaches for estimating the incubation period are not. here we demonstrate the importance of truncation (table 1) . we use the data truncated at 20 january, which has exposure windows between 1 december and 19 january. this data set is chosen since it is most sensitive to truncation due to the exponentially growing force of infection and high reporting rate. without accounting for truncation, the length of the incubation period is significantly underestimated, which could have a large impact on the success of intervention strategies. to demonstrate the effectiveness of the bias correction method, we compare three different data sets ( table 2) . the similar distributions predicted across these datasets suggests a robust method. figure 1b compares the full distributions for these three estimates. here we investigate the effect that uncertainty in the reporting date can have on the results, using the data truncated at 9 february (table 3) . the standard interval is the recorded data, wide intervals are obtained by removing a day from the exposure window lower bound and adding a day to the upper bound, and the narrow interval vice versa. the uncertainty in the reporting date can impact the estimated incubation period, showing that it is important to consider this risk when designing interventions. when constructing intervention strategies for an epidemic, the incubation period is an important parameter. for example, consider the quarantine strategy deployed in many countries during the early stages of the epidemic, aimed at preventing cases being imported from wuhan. this strategy quarantined individuals upon their return from wuhan for 14 days. for such a strategy to be effective, we require most incubation periods to be less than 14 days, so that the majority of infected people would develop symptoms before quarantine ended, enabling them to be further isolated. in this analysis, we show that in the worst-case scenario we would expect 1 in 62 cases to slip through this quarantine, with the best fit predicting 1 in 101 cases. therefore, the 14 day quarantine period would capture the majority of cases. throughout the epidemic, this seems to have been reasonably successful and prevented early seeding of cases in many countries. however, potentially due to complicated travel patterns or asymptomatic transmission, cases have slipped through detection and not been quarantined, which unfortunately has led to the situation observed today. in addition to the incubation period, there are many other delay distributions that must be estimated while an epidemic is growing, which can be estimated using the same technique. these include the generation time, the time between two infection events in a transmission chain; the serial interval, the time between symptom onset of an infector to their infectee; and the onset-to-death delay, the time from symptom onset to death. transportation modelling plays a crucial role in the early stages of an outbreak; an infected individual may travel outside of the region in which they were originally infected and seed further infections across geographical scales which are impossible to contain. furthermore, as the rate of travelling increases, the number of observed cases within the known ''origin" region decreases, and if exportation is not taken into account this results in an underestimation of the number of cases. these underestimates can be improved by looking at the total number of cases across all known affected regions, but doing so introduces further complications. for example, if an individual has less severe symptoms they may not seek medical assistance, thereby not being recorded as a case at their destination. this underestimation of cases can have significant effects if the traveller is able to infect more people. a new transmission chain can thus be started which remains undetected for some time due to a lacking known connection to the ''origin" region. in the ''origin" region an individual with mild symptoms may still be tested for an infection due to a higher level of alertness in the local health care system. however, this level of active case-finding may not be present elsewhere, or may not have been allocated a comparable level of resources. further complications to this model arise from the incubation period of individuals wherein detection is unlikely, and the variations in movement and mixing between people when preventative measures are put in place. we consider a metapopulation model seeded with an infection in one of the regions, o, and investigate how exportation from this region combined with variability in case-finding can alter estimates for the doubling time and the expected portion of the population we expect to identify. this accordingly bounds the proportion of the infected population one would be able to target for personal intervention (e.g. quarantine or treatment). note that the proportion of identified cases need not necessarily correlate with the proportion of the infected population who exhibit symptoms. let us assume that movement from o begins at time where ï� is the mean case-finding ability across all destinations. in the presence of real-time transition probabilities ij p of moving between two regions, these estimates can be further elaborated. we assume that detection occurs immediately following the end of the incubation period, i.e. . similarly, we assume a gamma-distributed incubation period with shape and scale parameters k and î¸, respectively. we can parametrise this distribution using the ''non-wuhan" estimate of the incubation period in table 2 , which yields a gamma-distribution with mean 4.84 and standard deviation 3. 22 . in contrast to other values in the table, this estimate is obtained from discrete infection events, e.g. contact with a known infected case, and therefore has a constant reporting rate, and a constant force of infection over each exposure window. therefore, this estimate of the incubation period does not rely on the exponential growth rate unlike other estimates from section 2. when accounting for ï�. this difference may seem small, but it reduces the doubling time by approximately 12 hours. the expected value of r grows linearly with the exportation rate, which has also been observed with real-time travel models [42] . further models have also been developed which consider travel and exportation of cases in greater detail [20, 30] . the relationship between the observed cases in our origin and destinations can be used to determine the case-finding ability, though it should be noted that ï� likely varies with time as burdens are increased on public services and the number of cases grow. early estimates using data from [1] indicate at most an 80% case-finding ability, suggesting thousands of undetected cases exported to other regions of china, a sufficient quantity to sustain further transmission post-exportation independently of the number of asymptomatic cases present. the intention of these estimates is not to provide specific values for the doubling time of the spread of covid-19 in china (as the estimates above use historic travel data and are limited by the availability of data), but to bring attention to the unusual circumstances surrounding changes in contact patterns, and mobility during the chinese spring festival, the largest human migration on earth [38] . failing to account for the significant level of dispersion or exportation of cases during these circumstances will significantly skew our estimates. in a scenario where a single individual exposes a group to infection, it can be unclear how many people have been infected since they do not immediately develop symptoms. however, knowing the true prevalence in the population is essential to determine the most effective interventions to put in place, and to estimate future burdens on public services. using the probability density function of the incubation period, we consider the efficacy of using the time it takes for people to present with symptoms as a predictor for the size of the infected group. this analysis is an effective ready reckoner at early stages of a novel infection, or in close contact environments, and is useful for predicting generation size when a complete data set is not yet available. in this analysis we focus on a scenario where infection time is known. in reality, we may only know an exposure window. for short exposure windows this method can still be valid, but for longer exposure windows it will need extending to account for this added uncertainty. we assume that the number of individuals who have been exposed to potential infection is known, in which case the number of people who are infected can be assumed to be binomially distributed with an unknown probability p that each individual has been infected. to determine the distribution of infected individuals, we use the available information regarding the number of individuals who have expressed symptoms. this yields two cases. in the first case, we assume that the true number of symptomatic individuals are observed. in the second case, we take the number of observed symptomatic individuals as a lower bound on the true value. we wish to determine the probability that the first generation has 0 e individuals, 0 0 e e = , given that i ï� symptomatic individuals are observed on day ï�, i i ï� ï� = . this is given by (see appendix 6) this gives a distribution of the generation-size based on the number of observed symptomatic individuals by time ï�. we can extend it to investigate a scenario where no symptomatic individuals have been observed by time ï� by using a value of 0 for i ï� : this can be used to illustrate worst and best case scenarios given ï� time has passed without symptomatic individuals. additionally, if we consider the probability that 0 e = 0, we can find the value of ï� where we can have a 95% confidence that there will not be a second generation: this analysis considers the case when the number of observed symptomatic individuals to date is the true number. in practice however, we do not generally observe every symptomatic individual, so the number of observations is only a lower bound on the true number. to address this, rather than considering i ï� as the total number of people who have developed symptoms by time ï�, we can define i ï� as the minimum number of people who have developed symptoms by time ï�. we assume that the probability that i ï� is equal to i ï� for a given value of i ï� is uniform at 1 1 i ï� + . we can then use the same methods as above to infer a distribution for p. details are provided in appendix 7. e , in an infection event in which 20 people were exposed. a, b and c show the density when the number of observed symptomatics is taken to be the true number of symptomatics, d, e and f consider the case where the observed symptomatics is a lower bound on the true symptomatics. a and d consider the case when zero symptomatics are observed after 5 days, b and e when 5 are observed after 5 days, and c and f when 5 are observed after 10 days. the incubation period for the disease has been modelled as a gamma distribution with a mean of 4.84 and standard deviation of 2.79 ( table 2) . as we can see from figure 2 , this method can be used to predict the number of infected individuals in the original exposed group. however, we have also demonstrated the importance of caution when interpreting this data. if there is uncertainty surrounding the presentation of symptomatic patients, using i ï� as a lower bound is a robust method to ensure the size of the generation is not underestimated. 3 . modelling intervention strategies 3 when designing intervention strategies, we need to consider how adherence may alter their effectiveness. this is important, since highly effective interventions may not be adhered to if they present great individual cost to a population. in this case, a theoretically less effective intervention may perform better, if it has sufficient reduction in individual-level cost. in this section, we illustrate the potential impacts of adherence on the effectiveness of interventions using a toy model. consider a standard sir model, and denote by ( ) s t and ( ) r t , respectively, the susceptible and recovered/immune fractions of the population at time t. we can write s in terms of r such that if an intervention is put in place that reduces (with full adherence) 0 1 r < then the outbreak will be controlled. indeed, let us assume that 0 r is reduced to zero by the intervention: for example, assume that social distancing is perfect and the number of contacts of a fully-adherent individual is zero. if only 50% of people adhere to the intervention then the average number of contacts is effectively reduced by a half and logically â�  0 0 / 2 1.5 r r = = (the â�  representing quantities post intervention) and ( ) â�  0.58 r â�� = in this case. however, this assumes that adherence is an independent random process at each contact. this suggests that for each contact an individual would ordinarily make, they ''toss a coin" to decide whether to isolate or not. in reality, individuals are more likely to show polarity, where some individuals reduce all their contacts and follow the measures and a proportion of individuals choose to not adhere to the intervention. if there was distinct polarity in the population such that 50% adhered perfectly and 50% ignored policy, then a toy model can be created with two infectious groups, a i and b i , that behave differently. in this case where a dot over a variable represents its time derivative. such an epidemic model, where the two groups have the same susceptibility but different infectivity, has the same final size as an epidemic in a single-type model with the same 0 r (e.g. see [5] ). however, they have different durations as can be seen in figure 3 , where this shows that the assumptions about the nature of adherence predict the same growth rate and final size, but that the more polarised adherence has faster early growth and therefore an earlier peak. more complicated model structures could be constructed by incorporating adherence with intervention by susceptible states, which would lead to core group dynamics (see for example [37] ). this issue of independent versus polarised adherence is related to the idea of all-or-nothing versus leaky vaccination [29, 49] , where you either vaccinate a fraction of the population with 100% efficacy or vaccinate 100% of the population with reduced efficacy [34] . note however that vaccination reduces your susceptibility (whether only or also), rather than only your infectivity as in the model discussed above, and variation in susceptibility does reduce the final size, with imperfect coverage with a perfect vaccine (all-or-nothing) leading to a lower final size than full coverage with a leaky vaccine (all individuals having the same mean susceptibility). the ongoing covid-19 outbreak is known to have higher mortality rates amongst the elderly, the immunocompromised and those with respiratory and health complications [31, 82, 83, 84, 85] . in this section, we model the introduction of an infectious disease into care homes, in order to obtain estimates of the final size of the epidemic in the vulnerable population as well as predictions for the number of hospitalisations and fatalities. modelling of care homes in the uk is conducted against the backdrop of a wider epidemic in the general population, which we here assume to be following seir dynamics with a basic reproduction number 0 r that might be different from the within-care home reproduction number c r . care homes are assumed to be closed populations, with the infection entering each of them independently with a certain probability. infection is seeded only once, and within-care home outbreaks then evolve independently from, and do not contribute to, other care home outbreaks and the epidemic in the background population. to keep track of hospitalisations, we model the withincare home infection dynamics using a compartmental model that, in addition to seir model, has compartments for mildly symptomatic prodromal cases (p), who show no symptoms but are capable of transmitting the virus, those who recover from the disease after mild symptoms that did not require hospitalisation (m), those who have severe symptoms and are admitted to hospital (h), those who recover after hospitalisation (r), and those that die (d). this is illustrated in figure 4 . the infection pressure up to time t for a median sized care home is the integral from 0 to t of the force-of-infection (foi) applied to the care home coming from all infectious sources, multiplied by a probability p. this probability represents the probability of the infection being introduced to a median-sized care home. for other care homes, we allow this probability to be proportional to its size, under the assumption that larger care homes employ more staff and are therefore at higher risk of introduction. when the infection pressure becomes higher than an individual care home's resilience threshold, that care home begins its own deterministic infection dynamics with a single initial infected case. the equations describing the background epidemic and the within-care home epidemic are given in appendix 8. figure 4 : compartmental model for disease dynamics within a care-home. we extend a deterministic seir model to include compartments for prodromal (infectious) cases (p), mildly symptomatic cases that recover without requiring hospitalisation (m), cases that do require hospitalisation and are removed from the care home (h), cases that die in hospital (d) and cases that recover in hospital (r). we run this model on data for the entire care home population in the uk, so that there are approximately 15,000 care homes with a total population of approximately 450,000 residents [21] . care home sizes range from 1 to 215, with a mean size of 29.4 . in this model we only consider the vulnerable population within care homes. we assume 0 1.5 r = in the background epidemic, a relatively low value that somehow accounts for a certain degree of control, and an 3 c r = to allow relatively explosive epidemics in care homes due to potentially more frail individuals, difficulty in isolation and staff inadvertently passing the infection from one case to the next. the other parameters in the baseline scenario are reported in table 4 . apart from the reproductive number, the background epidemic uses the same parameters as the care home epidemic. however, in the background model there are only rates from e to i and i to r, which are taken to be the rates from e to p and i to m, respectively. there are a variety of assumptions underpinning this model. firstly, the background epidemic ignores structure and assumes homogeneous mixing. this is likely to make the peak more pronounced, so presents a worst case scenario for the demand on hospital beds. the assumption of 0 r for the background epidemic only affects the shape and duration of the background epidemic, since the tuneable parameter p controls the risk of introduction to the care home. that is, if 0 r is small, a large p still presents a high force of infection into the care homes. therefore, for a fixed p, we expect that changing 0 r does not affect the total number of deaths, but it changes the peak hospitalisation incidence because a faster and more explosive background epidemic makes epidemics in care homes more synchronised. in fact, when testing the impact of a longer, flatter background epidemic, for example obtained by simulating three slightly desynchronised background seir epidemics, results have lower peaks and a much more variable timing (not shown). assuming each care home is independent might not be realistic, since it is likely that staff are shared between multiple homes, in which case they can act as vectors of transmission between homes. however, in the model current outbreaks are already quite synchronised (the within care home outbreaks occur at similar times), so the effect of this assumption is likely to be minimal. the final major assumption is that the epidemic within the care homes is deterministic. this removes the probability of random extinction and random delays, and should obviously be relaxed with a stochastic model, given half of care homes have size smaller than 25. however, the extinction probability is very low with 3 c r = , so this stochastic effect is unlikely to have a large impact. random delays, instead, may change the shape and timing of the epidemic, which could potentially reduce the peak burden. therefore, this model represents a worst case scenario. in the absence of cure or vaccine for covid-19, governments worldwide must rely on nonpharmaceutical interventions (npis) to control the outbreak [32] . a natural such intervention is to ask individuals who express symptoms similar to covid-19 to isolate themselves, but variants to such individual isolation might include policies sometimes referred to as household isolation, household quarantine and mixed isolation. in this section, we investigate how such strategies affect the spread of the epidemic when bearing in mind that adherence to each intervention may differ. individual isolation relies on individuals staying in isolation when they express symptoms, thereby stopping transmission. however, there is potential asymptomatic or prodromal transmission before they go into isolation. additionally, isolation strategies generally ask infected individuals to remain at home, which presents an infection risk to the other members of their household, who may go on to spread the infection. the term 'household isolation' refers to a policy where, upon first detection of symptoms within a household, all individuals within the household go into isolation for a fixed duration of time. this strategy reduces the risk that other household members, if they are infected within the household, transmit in the community when pre-symptomatic (and hence before they self-isolate themselves) or if asymptomatic but still infectious. a blanket policy invoking a fixed duration of household isolation might cover the full epidemic in a small household. however, a larger household might present multiple generations of infection, potentially extending the within-household outbreak beyond the fixed duration of the household isolation policy. to address this issue, 'household quarantine' is another potential strategy. upon detection of symptoms, the entire household is isolated until a fixed duration of time after the last symptomatic case within the household expresses symptoms. this ensures that there are no symptomatic cases evading intervention but applies quite drastic measures to the household. a fourth strategy, that reduces the cost relative to household quarantine, is mixed isolation. here, upon detection of symptoms the entire household is isolated for a fixed length of time. any subsequent cases within the household then undergo individual isolation as described above. this reduces the risk of cases not being isolated whilst allowing recovered individuals to return to work. there is however still some remaining risk that infected individuals may not yet express symptoms after the end of the isolation period, but this risk can be controlled through the duration of each isolation. although there is now a rich theoretical literature on households models [7, 8, 9] , the mainstream methodological tools in this research area present important limitations that make them not directly applicable to studying these control policies. first, exact theoretical or asymptotic results in these models are mostly restricted to time-integrated quantities, i.e. those quantities that do not depend on the detailed temporal shape at which the infectivity is spread by an individual: these are 0 r (or any other reproduction number [10, 60] , e.g. the household reproduction number * r ), the probability of a large epidemic, and the epidemic final size [4] . for this reason, the vast majority of the literature relies on the standard stochastic sir model [4] , despite its unrealistic infectivity profile. even if more recent work has expanded beyond time integrated quantities, for example considering the real-time growth rate [10, 62] , if the interest is on tracking the dynamics of infection spread, a model based on full temporal representation of between-and within-household dynamics [33] appears necessary. a second limitation of standard household models is the key assumption of constant parameter values. this appears essential for any form of analytical progress. however, in the context of the interventions discussed above, a reduction in transmission between households, as well as a potential increase in within the household, require parameters to change over time. to overcome these limitations, we consider two approaches. the first approach fully captures both within and between-household dynamics with a master-equation formalism, i.e. by relying on a markovian within-household dynamics and keeping track of the expected number of households in each possible state of their internal dynamics. the second approach has a greater emphasis on withinhousehold dynamics, and is fundamentally an independent-households, individual-based, stochastic simulation. the more limited mathematical tractability is the price to pay for an increased flexibility, as the within-household markov assumption is relaxed and exact distributions for delays between events, typically informed by the data, can be explicitly inputted. although both approaches can account for increased within-household transmission as isolation and quarantine are imposed, we only consider this for the second method here. this aspect allows us to study the increased risk of infection a vulnerable individual in the household would experience following the implementation of a control policy. to model the households in the uk, we construct a realistic distribution of household sizes (which is given in the supplied code). we take this demographic data from the 2001 census [58] . more recent information, though less specific on large household sizes, shows that sizes of smaller households are largely unchanged over time [57] . 3 . 3 in this section, we investigate the above intervention strategies under the assumption that a fraction of households adhere 100% with an intervention and the remaining households ignore the intervention. to model the interventions, we implement a dynamical household model that explicitly represents the small sizes of households. the dynamics of the outbreak are simulated using an sepir model. this model assumes that there are five possible states in which an individual can be. these are, susceptible, latent, mildly symptomatic prodrome, symptomatic infectious and removed. individuals are infectious during the mildly symptomatic prodrome state and the symptomatic infectious state. following [17] , we assume that within-household transmission scales with the inverse of the household size to a specified power î·. such a model can be used to investigate how the pathogen spreads through and between households. the methodology involved is the use of self-consistent differential equations, first written down by ball [6] . more recent developments, including numerical methods for these equations, include [13, 33, 41, 66] . important features of this approach include allowing for a small, finite size of each household in which random effects are important and each pair can only participate in one infection event. here î� represents infections imported from outside the population of households, and the other terms represent between-household transmissions. in our code, we assume î� is a step function. results are largely insensitive to the precise choice of î� , but compared to, for example, random seeding of infections in households, starting the whole population susceptible and exposing to a small amount of external infection for a fixed time period has less room for the precise initial condition chosen to influence results, and is more realistic for the situation observed in countries apart from china. we take a 'global' intervention as part of the baseline, in particular, we can model phenomena such a school closures that hold during a set of times t as we call îµ the global reduction. we will generally drop this t-indexing for simplicity, and will also consider only a household isolation strategy (though the other strategies can be considered similarly, with an example of how other strategies could be captured in this model framework given in appendix 9). instead of isolating for a fixed duration, we assume that a fraction w î± of households isolates when there is at least one symptomatic case in the household, and isolating households leave isolation when no symptomatic cases remain. we make this assumption since it may potentially capture the behaviour of real households, who are more likely to remain isolated based on presence of symptoms rather than for a fixed duration. in the non-markovian household model in section 3. 3 using the methods in [13, 66] , it is possible to fit household models of this kind to the overall growth rate, r, which we take to correspond to a doubling time of three days. natural history parameters can then be set directly based on reasonable estimates: e p r â�� to the inverse of the latent period; p i r â�� to the inverse of the prodromal period; i r â�� â�� to the inverse of the symptomatic period. shaw [71] analyses various household datasets for respiratory pathogens and estimates values for î· close to 1, so this is taken to be 0. 8 . the remaining degrees of freedom are relative infectiousness of the prodrome (taken as a third) and the probability of transmitting within a pair, which we can take as a typical value given by shaw [71] . for the numerical results in figures 6 and 7 using the given parameter values for our baseline scenario (table 5) , we consider a combination of household isolation (which follows all-or-nothing adherence) with global reduction in transmission (which follows leaky adherence) for three weeks and show the results in figure 6 . the distribution of infectious individuals varies with household size, which is shown in figure 7 for different durations of global intervention. applying household isolation at 65% adherence ( 0.65 w î± = ) manages to reduce the spread of infection, but appears insufficient in this model and with baseline parameters for controlling the outbreak in the long-term, unless other intervention strategies that reduce the global transmission (increasing îµ) are adopted at the same time. alternatively, different levels of adherence can be considered to determine if and when control may be achieved purely through household-based interventions. for the model proposed in the next section, we look into the effectiveness of increasing adherence. parameters are in the main text. the model described above has the advantage of being able to track the dynamics within the household as well as the overall epidemic in the population in a relatively efficient manner. we now discuss a different framework that loses part of the capability in keeping track of the overall epidemic, but offers further flexibility both in the impact of policies on the within-household dynamics and in the distributions between events in the infectious life of an individual. we use this model to investigate the relative effectiveness of the different control policies. we also consider allowing recovered individuals to leave the household, even in the context of household isolation or household quarantine. this has no impact on the transmission dynamics, but reduces the individuals' life disruption and potential economic cost of any policy implemented. this model assumes that there is no reintroduction within households so each household can only be isolated or quarantined once. the assumption that only one household member is infected from outside is approximately satisfied if we assume homogeneous mixing between households and a large number of households, which are all fully susceptible at the start of the epidemic. however, the reality of heterogeneous mixing makes reintroduction a likely possibility even early on in the epidemic. this model, therefore, lacks an explicit description of the social network structure beyond the household. for simplicity, we assume that within households all individuals are identical in terms of their disease dynamics, although the method might be extended to allow for different age/risk groups with different disease dynamics. we assume that the level of within-household transmission in a household of size n scales proportionally to ( ) 1/ 1 n â�� , though we acknowledge that true transmission is slightly more complex [18] . we consider independent households of size each individual is given an indicator function of whether they are symptomatic or not (individuals show symptoms independently of each other with probability s p ) and a resilience threshold. this last quantity is drawn from an exponential distribution with mean 1, and represents the overall infection pressure this individual is able to withstand before they get infected. the infection pressure up to time ï� is the integral from 0 to ï� of the force-of-infection (foi) applied to this individual coming from all infectious sources. at the beginning of the within-household epidemic, a single initial case is assumed. time is discretised with a predefined time step d 0.1 t = days. at any time step, the current infectivity of all infectives in that time step is summed over, keeping track differently of the infectivity spread outside and inside the household. an overall measure of the accumulated infectivity within the household is updated at each time step and when this crosses the resilience threshold of a susceptible individual, they acquire the infection. we assume an individual spends half of their time outside and half inside the household. when selfisolation starts, the assumed adherence i a represents the fraction of the time spent outside that is shifted from outside to within the household. therefore, for perfect adherence, from the moment symptoms occur, the individual stops transmitting outside but their infectivity within the household grows by 100%. we also explore variations in this compensatory behaviour, so that the time of an individual is split in a more flexible proportion than 1:1. the same argument applies to other control policies, with adherence levels h a for household isolation and q a for household quarantine. when multiple control policies are in place at the same time, their effect is assumed to be multiplicative: if an individual has symptoms and the household isolates, the outside transmission rate from that individual is reduced from baseline by a multiplicative factor ( ) ( ) (1) and the area under this curve is known in the literature as the household reproduction number, and is typically denoted by * r . if enough transmission is prevented, so that * 1 r < , the epidemic is controlled. the basic reproduction number 0 r and * r share the same threshold at one, so they are simultaneously larger, equal or smaller than unity. however, in a growing epidemic 0 * r r < [10, 60] . the real-time growth rate r is related to * r by the lotka-euler equation asymptomatic cases, which are assumed to be half as infectious as symptomatic ones. the total number of cases under isolation (possibly compounded, e.g. both household and individual isolation) is shown in red (right axis). all random numbers involved in the realisation of the stochastic epidemic are drawn at the start, before the impact of each control policy is implemented. row 1 shows no isolation and individual and isolation. rows 2, 3 and 4 show, respectively, household isolation, mixed isolation and household quarantine. the difference between the columns is that the basic policy on the left is ''upgraded'' to the more cost-effective version on the right that allows recovered individuals to leave the house as they cannot transmit outside anymore. when no control is implemented, the primary case (individual a, infected at time 0) infects another individual (b) around time 11 . after a long latent period (i.e. incubation minus prodromal), b becomes infectious and infects a further individual (c). the last individual (d) escapes infection. when different intervention strategies are in place, within-household infectivity is increased. this can result in individual c becoming infected earlier in the outbreak and individual d no longer escaping infection, both due to the increased force of infection. in this simulation, the dynamics for individual b do not change since they are infected before a becomes symptomatic. individual d is infected earliest under mixed isolation, because within-household transmission is higher than household isolation alone, due to increased adherence from individual isolation also being in place. adherence levels to household quarantine are lower than those of household isolation, due to the higher demand of full quarantine, thus leading to less enhanced within-household transmission. we assume that adherence to individual isolation is 90%, household isolation is 80% and household quarantine is 60%. the more severe the intervention, the better it captures the infectious periods of infected individuals within the household. the lower x-axis gives the adherence to household quarantine, and the upper x-axis adherence to household isolation. we assume that household isolation is less demanding, and therefore adherence is assumed to be ''twice as high'', meaning it is at the midpoint between that of household quarantine and 1 (e.g. 0.6 for an x value of 0.2, 0.9 for an x value of 0.8, etc.). the black dash-dotted line in (a) gives the amount needed to control the spread by achieving * 1 r = . notice how: the effect of individual isolation is independent of adherence to household quarantine (dotted lines); the effect of household isolation is independent of adherence to individual isolation (overlapping dash-dotted lines); mixed isolation is always superior to household isolation; household quarantine is only optimal at really high levels of adherence (for these baseline parameters, generally, beyond the level needed to achieve control), but quickly becomes suboptimal to mixed isolation as adherence is reduced. when a sufficiently large reduction in * ); similarly, in all households, individual isolation would total exactly 7 days if all cases were symptomatic and all individuals in the household were ultimately infected. in (d), we assume that adherence is 100% to each intervention. under the baseline parameter values (table 6) , control can in principle be achieved via certain interventions, but only for high levels of adherence, which might be difficult to enforce for a prolonged length of time (figure 9a ). more importantly, the model's conclusions are highly sensitive to variations in parameter choices, which are uncertain. parameters that present problems here are the delay from symptom onset to isolation (with control failing for 1 day detection delay unless adherence is essentially perfect), proportion of asymptomatic infections (any chance of control lost at 50%) and the strength of asymptomatic transmission. the short delay before symptomatic individuals isolate may be unrealistic unless the susceptible population is very well-informed about symptoms that call for isolation, and so likely does not apply in very early stages of an outbreak. overall, in the face of the many uncertainties, household-based interventions triggered purely by symptoms appear useful to slow the spread but need to be complemented by other policies. comparing the different strategies (figure 9b , household quarantine can be optimal (as one might expect), but this requires high adherence levels. as adherence drops, this strategy becomes suboptimal to mixed isolation. mixed isolation is significantly better than household isolation on its own and requires little extra social cost, so should not cause adherence to drop (relative to household isolation adherence levels). the difference between the two strategies comes down to the transmission slipping through after the 14 day household isolation. the cheapest strategy, when considering working age adults, is individual isolation (figure 9d ), but the effect is limited compared to the other models and cannot achieve control in the baseline scenario even with 100% adherence. overall, the mixed isolation strategy appears to be most cost-effective. however, this is dependent on the assumption that adherence is better for 14 day isolation rather than a very long quarantine. it can be observed that household-based interventions are more effective than individual isolations, demonstrating the importance of these strategies in designing intervention policy. figure 8 shows how the different isolation strategies contain the infectious periods of individuals within the household and also indicates the number of individuals being isolated within the household. to study the impact such an increased within-household transmission has on the chance that a vulnerable individual is infected in the household, we randomly choose one non-primary case in the household as the vulnerable one and count how many of the e n epidemics result in this individual being infected under the different control policies (figure 9c ). under these interventions, the risk of a vulnerable individual getting infected within-household, conditional on the infection entering it in the first place, is in the range 5 15% â�� . since this model relies on the sellke construction, we calculate the infection pressure that accumulates (within a household) during the outbreak. in relation to figure 8 , we report in figure 10 the infection pressure that accumulates for the different control policies, showing the different impact each intervention can have on the within household dynamics. figure 10 : accumulated infection pressure in the simulation presented in figure 8 for different control policies. horizontal dotted lines represent individuals' resilience thresholds. as time progresses, the accumulated infection pressures (coloured lines) increase and when they cross the resilience thresholds, the corresponding individual acquires infection. notice that: in the absence of control, one individual escapes infection; with household isolation only, the infection pressure reaches a relatively low endpoint because of the last symptomatic individual slipping through and not transmitting much in the household; with mixed isolation, infection pressure is higher due to combined adherence; and with household quarantine, the infection pressure builds up more slowly at the beginning due to lower adherence. we assume that adherence to individual isolation is 90%, household isolation is 80% and household quarantine is 60%. social distancing, isolation and lockdowns act to mitigate the spread of an infectious disease and reduce the number of cases. however, such interventions, particularly widespread lockdowns, cannot be maintained indefinitely and must be lifted at some point. for the disease to be controlled, these interventions can be implemented until pharmaceutical interventions are developed, such as a vaccine, or until the case numbers are low enough that the disease may go extinct. here, we consider the situation where interventions are lifted just before extinction, when the number of cases has reached a low but non-zero initial value 0 n : at this point, the number of cases might rebound or might go extinct by random chance despite an 0 1 r > . we use a time-inhomogeneous birth-death chain model [39] to , q t s satisfies the differential equation subject to the initial condition ( ) 0, . q s s = solving for q and setting 0 s = gives the probability that, at time t, the number of cases has reached zero and the disease has become extinct. we denote this probability by ( ) q t [3] , which is given by the corresponding generating function, ( ) , r t s , for this random variable satisfies again, solving for ( ) we simulate data based on one initial case 0 1 n = , though this may easily be extended to any number of initial cases. we run simulations both with and without immigration, choosing w is the initial (constant) rate of importation of cases before any controls on immigration are put into effect. we set 0 5 w = imported cases per day. with these choices of parameters, the resulting extinction probabilities are given in figure 11 . note that we are assuming the immigration rate is decreasing to 0, so if the infection is controlled internally for long enough, an overall ultimate extinction is possible in this model. for these parameter choices, the final probability of extinction, defined as n q t . these probabilities suggest that, without widespread immunity, stochastic extinction might be aided by social distancing but is heavily compromised by immigration. border controls, therefore, if of limited use when transmission is self-sustaining, become key when the number of cases is low. note that we have assumed an importation function ( ) t î· that goes to 0 for large t, in line with a pandemic that goes extinct in other geographical regions. however, the presence of an animal reservoir might lead to an importation function that is non-zero over longer time scales, thus effectively making ultimate extinction impossible unless the effective reproduction number is kept below one by a systematic and permanent intervention (e.g. technology-based change in behaviour) or herd immunity. contact tracing is a complementary control policy to isolation or quarantine. when a case is discovered, attempts are made to identify and isolate individuals who may have been infected. in doing so, some of the secondary cases will be discovered and isolated early in their infection, decreasing their effective infectious period. if contact tracing is successful, it can greatly reduce the effective reproduction number of the infection, and in combination with other interventions may drive an epidemic extinct, as was seen in the case of sars [81] . contact tracing in itself presents numerous challenges, which are exacerbated by its success relying not only on the effectiveness of the tracing process but also the underlying transmission characteristics. for covid-19, some of these challenges include mild symptoms which cause infections not to be reported, pre-symptomatic transmission which occurs before a case is reported, and short generation times [28] which can cause the epidemic to outrun contact tracing. additionally, contact tracing is only feasible for smaller case numbers, because each case generates multiple contacts to follow up, so the tracing workload expands dramatically, and an increasing number of chains remain unobserved. this makes it a viable strategy in the early days of an outbreak, or, if containment has failed, following a period of severe interventions, such as a lockdown. combining contact tracing with isolation is being considered by many countries as part of a test, trace and isolate strategy to be implemented once lockdowns or comparable measures are lifted, provided these lockdowns succeed at driving case numbers sufficiently low. in this section, we develop a householdlevel contact tracing model for an emerging outbreak, since we do not wish to make assumptions about immunity or depletion of susceptibles. these assumptions can be added to the model as the availability of data into immunity improves. we are interested in the likelihood that the contact tracing process is overwhelmed by large case numbers and the likelihood that, combined with isolation, it can drive the disease to extinction. the early days of an outbreak can be modelled using a branching process, where generations of infections produce infectious offspring. contact tracing processes can be incorporated as a superinfection along the tree generated by the branching process [11] . when a node is 'superinfected' by the contact tracing process, it is isolated. we model the infection spreading through a fully susceptible population of individuals, segmented into households of different sizes according to the 2019 ons survey [57] , and progress through discrete time steps of 1 day. as such, our branching process is at the household level, coupled with localised within-household epidemics. this allows us to model contact tracing strategies that isolate whole households, which may contain several undetected infections. it also enables a wider range of contact tracing strategies to be modelled, each with different intervention scope and costs. each day, individuals (or nodes) make contacts to a random set of individuals; divided into local contacts to members of the same household, and global contacts to members of other households. the number of individuals contacted in a day is distributed using an overdispersed negative binomial distribution and parameterised using estimates from the polymod social contact survey [54] , stratified by household size. since the probability that a contact causes infection cannot be directly observed, we use improper hazard rates that give rise to the 5 day covid-19 generation time [26] and 0 3 r = . for contact tracing to begin, an infection must be diagnosed, which we assume occurs 70% of the time among infected individuals due to flaws in reporting or very mild symptoms in those infected. we assume a gamma distributed incubation period with mean 4.84 (table 2 ) and a geometric reporting delay from symptom onset with mean 4.8 days [42] . intuition suggests that if 0 3 r = then tracing two thirds of contacts will control the epidemic. however, in practice transmission may occur before tracing, so this will not reduce the number of infectious contacts by two thirds. to demonstrate this, we assume that contact tracing successfully traces two thirds of contacts. trained professionals have to trace all reported contacts from the last 14 days, so we assume that the contact tracing delay follows a geometric distribution with a mean of 2 days. individuals are considered recovered 21 days after infection, as the chances that they are still transmitting then are negligible. though our general framework can be modified extensively, we assume the following contact tracing strategy. when an individual reports infection, their household is immediately isolated. contact tracing attempts are then made for all households connected to one of the individuals in this household, whether symptomatic or not. when a connected household is identified (after the contact tracing delay), all individuals within the household are immediately placed under observation. if any of the individuals in the observed households develop symptoms, then the household becomes isolated and the contact tracing process continues to connected households. when a household is isolated, we assume all individuals are isolated with 100% adherence, and cannot transmit the virus within or outside the household. the assumption that isolation prevents local infections is unrealistic, but does not change the overall behaviour of the process as there are no more global infections. this strategy imposes high individual-level cost, since by isolating all individuals within a household, it isolates individuals who have not had direct contact with an infected individual. in practice, such a strategy may have poor adherence. figure 13a shows an example contact tracing network. 3 . 5 when choosing contact tracing strategies, a balance must be struck between the effectiveness of a strategy and the resources that it requires. some strategies are only feasible when there are few infections, since the resources required can grow rapidly depending on the dynamics of the outbreak and the contact tracing process. to define the capacity of the contact tracing process, we consider the ability of a public health agency to observe the condition of those asked to self-isolate, due to their recent exposure to an infected individual. the health agency must remain in contact for the duration of the 14 day self-isolation period, so that if any individual under isolation develops symptoms and then tests positive, the contact tracing process can be initiated on this node. we will define the capacity of the contact tracing process to be the number of people that can be placed under observation and assume two possible capacities: 800 and 8000. we assume that when a node is contact traced, they are asked to report their global contacts for the last 14 days. all global contacts are assumed to be to a new person since we are in the early stages of an outbreak. parameters are given in table 8 . hitting probability (8000) 76 .8% we carried out 6507 simulations of the contact tracing process for 150 days. contact tracing capacity was reached in 5000 simulations, and in 180 the epidemic neither went extinct nor was the 8000 capacity reached. in the remaining simulations, the epidemic went extinct. figure 12a and table 8 show that increasing the contact tracing capacity tenfold less than doubles the time until that capacity is reached. however, it does increase the odds of driving the epidemic to extinction without hitting the capacity by about 10% (table 8) . different contact tracing strategies will strain different aspects of the health agency. a strategy that generates large amounts of work is only feasible if there are few active infections. the optimal strategy will need to compromise and may need to change depending on the number of active infections, which cannot be directly observed. figure 12 : capacity hitting times for the contact tracing model. when there is a small number of cases in a single country, it may be possible to drive the pathogen to extinction. this small case number could correspond to the start of an outbreak or removing of severe interventions. we consider the latter case, but conservatively assume a fully susceptible population. we assume that social distancing is enforced on day 0 and reduces global contacts by 70%. full parameters are given in table 8 . since we are interested in extinction, we will no longer consider the contact tracing capacity. under these baseline parameter assumptions and 10000 simulations, the combined force of this contact tracing strategy and isolation is enough to drive the epidemic extinct ( figure 13b ), but measures will need to be in place for months in some cases. if the infection is ever re-imported, then the process would begin again, since herd immunity is not achieved. note that the minimum extinction time is 21 days due to this being the time after which an infected individual is labelled recovered. additionally, this model only considers extinction under the assumption that no cases are imported. in section 3.4, we have shown that importation of cases significantly reduces the extinction probability. this suggests that extinction may no longer be guaranteed, and the time to extinction will be significantly increased. this analysis has focused on a single contact tracing strategy using indicative parameters for covid-19. the proposed model can be extended to more strategies and region specific parameters to inform the design of control policies. also, as is shown in table 8 , contact tracing capacity is likely to be reached, which may prevent extinction from being achieved. this complication is compounded by the issues of loss of immunity or the presence of an animal reservoir discussed in section 3.4. figure 13 : example of the contact tracing process (a) and the extinction times distribution (b) for the contact tracing model. 4. discussion in this manuscript we have presented a range of mathematical tools to tackle infectious disease outbreaks. in particular, these tools address various technical questions posed by the authors to support the ongoing public health response to covid19 . this toolkit considers both estimation efforts for key parameters, and investigative efforts (often numerical simulations) in gauging the effectiveness of various intervention or control measures. joint consideration of estimation and simulation efforts is critical. parameter estimates are obtained using a certain set of assumptions regarding the data, and investigations or simulations utilising these estimates should ensure that their underlying assumptions are consistent. these challenges in model construction and applicability of statistical methods are compounded by the limitations of the data with which decisions must be made. some of the biases present in the data can be addressed with an improved data collection methodology -often challenging in the context of a fast-moving outbreak -but many are also inherent to the nature of early outbreak data [15, 45] . the consequent lack of intuitive insight from this data underscores the need for careful parametric estimates, especially considering the large variability in predicted outcomes resulting from small differences in parameters. even with robust estimates for some parameters, many other parameters are challenging to estimate using the available data. therefore, models need to address this variability and uncertainty in order to inform public health policy. we have presented methods to address biases arising from a growing force of infection, changes in the reporting rate, truncated data samples and a varying travel rate. we use these methods to account for these biases when estimating delay distributions, such as the incubation period, and the growth rate/doubling time. these biases can have significant impact when estimating key parameters: the mean incubation period estimates for covid-19 range from 3.48 days without correcting for truncation to 4.84 days with the correction, and the doubling time in hubei province decreases from 3.15 days without correcting for travel to 2.77 days. these differences can significantly alter our understanding of the outbreak, and could have a large impact on policy and public health. for instance, underestimating the incubation period may lead to quarantine strategies failing to identify infected individuals if the quarantine length is too short. overestimating the doubling time (or underestimating the growth rate) will underestimate the risk posed to the host population -both in terms of final size of the epidemic and the rate at which it spreads, which can have significant public health impacts as discussed in [63] . it is important to note that the above-mentioned biases, and consequent impact of implementing the methods correcting for their presence, may vary across different settings. as an example, the potential underestimation of the covid-19 growth rate is exacerbated by an overlap in early outbreaks with a period of significant travel and movement in china, and would be less detrimental if first observed in other populations such as italy. also, for the incubation period, we have shown two different types of data; one from wuhan and one from discrete infection events. in the wuhan data set, truncation and force of infection biases are very important, whereas in the other data set, there is no force of infection bias since the infection events are observed. when an outbreak occurs in an enclosed group, such as a large gathering, we may wish to know how many individuals are likely to be infected. we developed a statistical method to estimate the first generation size based on the number of symptomatic individuals, taking care to account for the uncertainty in this quantity. this ready reckoner can inform testing of large groups to help control the disease spread, but does not apply to later generations or the possible interventions enacted on the population. building on these enclosed population scenarios, we have developed a set of models that investigate public control measures or interventions on enclosed populations, such as households and care homes. these structured descriptions improve the population risk profiles relative to assumptions of homogeneous mixing. a complementary aspect to a structured population when modelling interventions is adherence. motivated by vaccination modelling, we consider leaky adherence, where every household chooses to adhere or not whenever an event occurs, and all-or-nothing adherence, where some households adhere every time and some never adhere. we observed that in a homogeneous population, although the two types of adherence predict the same growth rate and final size, the timing of the peak and the early growth can be faster under all-or-nothing adherence. this insight, combined with lessons from the vaccination literature, suggests that efforts should focus on ensuring complete adherence in individuals or households with some level of pre-existing adherence, rather than pushing non-adherent individuals or households to change behaviour. dedicated modelling of disease spread in care homes is essential due to the documented history of comorbidity of their residents during pandemics [31, 82, 83, 84, 85] . we do so by regarding care homes as closed populations that are subjected to a force of infection from an external epidemic. we develop a tool for analysing the risk posed to this population by determining the peak size of the epidemic within the care homes and the number of deaths. applying this model to covid-19, we find that by ''cocooning" the care homes, i.e. shielding them to reduce the chance of introduction from the external outbreak, we can significantly reduce the size of the peak and therefore reduce the number of deaths. however, assessing the necessary level of shielding requires accurate characterisation of the external force of infection, and underestimating this may invalidate shielding efforts. a limitation to the proposed model is the deterministic within care home epidemic. however, since the average size of care homes is relatively large and we assume a high 0 r within care homes, the deterministic assumption is unlikely to significantly alter the conclusions. when modelling households however, we are concerned with much smaller population sizes. therefore, it is important to consider stochastic effects within each household, combined with between-household dynamics. we consider two different household models: one which contains features of both within-and between-household transmission, where small-scale transmission can be linked to the epidemic on a population level, and another which facilitates more detail in the withinhousehold transmission and delay distributions, but with reduced correspondence to the populationwide transmission. with the first model, a 65% adherence to household isolation appears insufficient to control the epidemic without severe global reductions in transmission. coupled with a short term global reduction, the epidemic can be controlled, but upon lifting the global intervention, which could take the form of a lockdown, household isolation is insufficient to maintain control. for the second model, we look into changing the strength of adherence, and the impact this can have on achieving control. indicative but reasonable parameter values suggest that the covid-19 outbreak can potentially be controlled using household isolation strategies, provided the level of adherence is sufficiently high. however, such a high level of adherence may be difficult to maintain in the long-term and this modicum of control is anyway highly sensitive to the chosen parameters. we further investigated the efficacy of various isolation or quarantine measures. a policy of individual isolation struggles to curtail the epidemic for any adherence. instead, mixed isolation, whereby first the whole household isolates and any individual infected during isolation goes on to self isolate after household isolation is lifted, appears to be the most cost-effective strategy. countries have put into place strict social distancing and lockdown intervention to suppress or regain control of epidemics that threaten to overwhelm the health system and cause massive mortality, but they cannot be sustained in the long term without growing social and economic costs. we have shown however, that the probability of the epidemic becoming extinct once these policies are lifted, even when very few cases remain, is very small. we therefore consider a contact tracing intervention as a potential strategy for managing the covid-19 outbreak, once severe lockdown interventions are lifted. we developed a household-level contact tracing model to explore the feasibility of combining these strategies to control the epidemic. firstly, we noted that by using knowledge of household structure, we can reduce the burden on the contact tracing process by isolating household and removing them from the contact tracing process once an infected member has been identified. secondly, we investigated how contact tracing combined with household isolation may drive the disease to extinction, finding that aggressive contact tracing coupled with household isolation can drive the epidemic to extinction under the indicative parameters assumed, when starting with a single infection. however, the time until extinction can be impractically long, which risks the contact tracing capacity being overwhelmed, suggesting such a strategy may be infeasible in practice. a less aggressive strategy could be implemented that would be less likely to overwhelm local health agencies. whilst it may not lead to extinction, this can still be beneficial at mitigating and controlling the spread of an outbreak as part of a test, trace and isolate strategy. there are many complexities when modelling an outbreak of a novel infectious disease. to address some of these, we have described a variety of techniques to serve as part of a generally applicable toolkit. however, our proposed models, and many other models, are subject to important limitations which must be considered prior to their application. key among these is the lack of heterogeneous population mixing, such as through age-stratification [61] and different risk-groups [77] , and spatiotemporal variations [43] , all of which influence modelling estimates and predictions. nevertheless, the relative simplicity of the presented models allows for the development of qualitative intuition regarding the efficacy of various intervention methods, whilst providing tractable theoretical frameworks which can be further developed and better inform policy-makers. 5 . independence of the incubation period likelihood function and the reporting rate to estimate the incubation period distribution, we need to find the distribution that maximises the probability of observing the sampled data. however, the sampled data does not directly record incubation period, and instead contains infection exposure window and the symptom onset date. additionally, the sample does not contain all individuals, and therefore there is a reporting rate that must be incorporated into the likelihood function. if the reporting rate is constant, it can be ignored. however, in the data coming out the wuhan, the reporting rate varies significantly, since individuals are no longer exported from wuhan after travel restrictions. since the reporting rate depends on individuals leaving wuhan, the main factor effecting the probability that a case is included in the data set is the date an individual leaves wuhan. therefore, the reporting rate depends on the days an individual spends in wuhan and is independent of their symptom onset date. we need the likelihood function that an individual was infected between days a and b, had symptom onset on day y, and was included in the data set. we will condition against the infection window, a i b < < , the case being included in the data set, x d â�� , and symptom onset occurring before the truncation date, y t < , and determine the probability that for such an individual we observe the given symptom onset date, y y = . where f î¸ is the probability density function of the incubation period distribution. therefore, the likelihood function ( | , ) p y y a i b y t = < < â�¤ is independent of the reporting rate for the data coming out of wuhan in the early days of the outbreak. 6 . generation-size derivation to solve this, we need to determine the distribution of the infection probability p given the number of observed symptomatics. assuming that p is uniformly distributed, we have f represents the hypergeometric function [2] . substituting this into equation (9) gives ( ) ( 7 . estimating the generation size using a lower bound on the number of symptomatic individuals in the analysis in section 2.4, it is assumed that every person who has developed symptoms by time ï� is known to the observer. however, depending on the disease, symptoms can be subjective. one person may not notice something another person may visit hospital for. additionally, one person may not want to come forward with symptoms if they are worried about the repercussions of coming forward (for example being isolated against their own will). to address this, rather than considering i ï� as the total number of people who have developed symptoms by time ï�, we can consider i ï� as the number of people who have presented with symptoms by time ï�. we do no know the true value of i ï� , but we know that it cannot be below i ï� . we assume that the probability of i ï� being i ï� for a given value of i ï� is uniform at 1 1 i ï� + , di e i dt ï� î³ = â�� (12) . dr i dt î³ = (13) this provides a force of infection that is used to model seeding within each care home via the sellke construction, with the details provided in the main text. once infection has been seeded within a care home, the epidemic progresses using the following ordinary differential equations handbook of mathematical functions with formulas, graphs, and mathematical tables pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics stochastic epidemics in dynamic populations: quasi-stationarity and extinction the final size of an epidemic and its relation to the basic reproduction number stochastic and deterministic models for sis 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incubation period distribution of human infections with mers-cov in south korea and saudi arabia can we contain the covid-19 outbreak with the same measures as for sars? estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the chinese center for disease control and prevention prevalence of comorbidities in the novel wuhan coronavirus (covid-19) infection: a systematic review and meta-analysis clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan author contributions co and hs compiled the manuscript. all authors were involved in the research and revising of the manuscript. the authors declare no competing interests. all data and code used in this analysis is provided in the github repository https://github.com/thomasallanh ouse/covid19-stochastics and https://github.com/thomasallanhouse/covid19-growth, with the exception of uk specific data. this data is provided by public health england under a data sharing agreement and we are unable to share this data. where c is a normalising constant such that we add further compartments to the within care home model since we are interested in the different pathways that these individuals may take. for the background epidemic this is not important, since all we need is a force of infection provided by individuals in the infectious class. 9 . population and household transmission: individual isolation and household quarantine individual isolation does not intimately involve the household and so we assume that a fraction i î± of symptomatic cases self-isolates and ceases transmission outside the household, meaning that we take the baseline but with to capture the essential features of household quarantine, we need to add states to the dynamical variables. let we now suppose that a fraction s in this model, we assume that the duration of isolation after the absence of symptoms is exponentially distributed with mean equal to the fixed isolation period, given by 1/ ï� . this assumption aids the modelling and is justifiable because, in reality, although a household may choose to isolate, they may not strictly follow the fixed period. it is likely that within-household isolation will increase transmission to other members of the household. we do not incorporate this property into the model, but this limitation is worth bearing in mind when drawing conclusions about the effectiveness of different strategies. key: cord-315598-qwh72inx authors: mendoza, jose luis accini; estrada, victor hugo nieto; lópez, nelly beltrán; bolaños, elisabeth ramos; franco, daniel molano; castell, carmelo dueñas; moreno, albert alexander valencia; amaya, iván camilo alarcón; flórez, john serna; valencia, bladimir alejandro gil; camilo pizarro, g; polo, yulieth maría zabaleta; meza, carmen lucia chica title: actualizacion de la declaración de consenso en medicina critica para la atención multidisciplinaria del paciente con sospecha o confirmación diagnóstica de covid-19 date: 2020-10-06 journal: nan doi: 10.1016/j.acci.2020.09.004 sha: doc_id: 315598 cord_uid: qwh72inx antecedentes y objetivos: la enfermedad por coronavirus de 2019 (covid-19) es una enfermedad ocasionada por el nuevo coronavirus del síndrome respiratorio agudo grave (sars-cov-2). se identificó por primera vez en diciembre de 2019 en la ciudad de wuhan, en los meses siguientes se expandió rápidamente a todos los continentes y la organización mundial de la salud (oms), la reconoció como una pandemia global el 11 de marzo de 2020. la mayoría de los individuos son asintomáticos pero una baja proporción ingresan a cuidados intensivos con una alta morbilidad y mortalidad. este consenso tiene como objetivo actualizar la declaratoria inicial emitida por la asociación colombiana de medicina crítica (amci) para el manejo del paciente críticamente enfermo con covid-19 dentro de las áreas críticas de las instituciones de salud. métodos: este estudio utilizó dos técnicas de consenso formal para construir las recomendaciones finales: delphi modificada y grupos nominales. se construyeron preguntas por la estrategia pico. 10 grupos nominales desarrollaron recomendaciones para cada unidad temática. el producto del consenso fue evaluado y calificado en una ronda delphi y se discutió de forma virtual por los relatores de cada núcleo y los representantes de sociedades médicas científicas afines al manejo del paciente con coid-19. resultados: 80 expertos nacionales participaron en la actualización del consenso amci, especialistas en medicina critica y cuidados intensivos, nefrología, neurología, neumología, bioeticistas, medicina interna, anestesia, cirugía general, cirugía de cabeza y cuello, cuidados paliativos, enfermeras especialistas en medicina crítica, terapeutas respiratorias especialistas en medicina crítica y fisioterapia, con experiencia clínica en la atención del paciente críticamente enfermo. la declaratoria emite recomendaciones en los ámbitos más relevantes para la atención en salud de los casos de covid-19 al interior de las unidades de cuidados intensivos en el contexto nacional de colombia. conclusiones: un grupo significativo multidisciplinario de profesionales expertos en medicina crítica emiten mediante técnicas de consenso formal recomendaciones sobre la mejor práctica para la atención del paciente críticamente enfermo con covid-19. las recomendaciones deben ser adaptadas a las condiciones específicas, administrativas y estructurales de las distintas unidades de cuidados intensivos del país. background and objectives: the 2019 coronavirus disease (covid-19) is caused by the new severe acute respiratory syndrome coronavirus (sars-cov-2). it was first identified in december 2019 in wuhan, china. in the following months it spread quickly to all continents and was recognised as a global pandemic by the world health organization (who) on march 11th, 2020. most cases of infection remain asymptomatic, while a low proportion require intensive care, experiencing high morbidity and mortality. this consensus aims to update the initial statement issued by the colombian association of critical medicine (amci) for the management of the critically ill patient with covid-19 within the critical areas of health institutions. methods: this study used two formal consensus techniques to construct the final recommendations: modified delphi and nominal groups. questions were constructed using the pico strategy. recommendations for each thematic unit were developed by 10 nominal groups. the consensus product was evaluated and qualified in a delphi round, and was discussed virtually by the speaker of each nucleus, as well as the representatives of scientific medical societies related to the management of the patient with covid-19. results: a total of 80 national experts participated in the update of the amci consensus, all specialists in critical and intensive care medicine, nephrologists, neurologists, chest physician, bioethicists, internal medicine specialists, anaesthetists, general surgeons, head and neck surgery, palliative care, nurses specialised in critical medicine, respiratory therapists specialised in critical medicine and physiotherapy, with clinical experience in the care of critically ill patients. this update issues recommendations in the most relevant areas for health care of covid-19 patients within the intensive care units, contextualised for colombia. conclusions: a significant multidisciplinary group of professionals, who are experts in critical medicine, reviewed and issued recommendations on best practice for the care of critically ill patients with covid-19 through formal consensus techniques. recommendations must be adapted to the specific, administrative, and structural conditions of the different intensive care units in the country. para la actualización de la declaratoria se utilizaron dos técnicas para el desarrollo de consensos de tipo formal, técnica delphi modificada y grupos nominales. un consenso formal permite integrar las opiniones de un colectivo de expertos que están expuestos a un tema específico (experto afectado) con la mejor evidencia científica disponible, utilizando técnicas que permitan reducir los sesgos de subjetividad. la técnica delphi es una metodología que plantea enviar cuestionarios a un grupo de expertos, para que califiquen una serie de recomendaciones en rondas reiteradas con retroalimentación de los resultados y respuestas anónimas, la técnica delphi empleada fue modificada, variante a la versión original propuesta por la corporación rand en 1948, pero se mantuvo las ventajas de la técnica, la iteración y retroalimentación para reflexión de las propias opiniones. los grupos nominales es una técnica que reúne a un grupo de expertos bajo la coordinación de un facilitador para evaluar y calificar información o preguntas (1, 2) . para la actualización se convocó 10 grupos nominales con 50 expertos multidisciplinarios cada uno con un líder o jefe de núcleo. los grupos construyeron las preguntas por metodología pico y desarrollaron progresivamente las recomendaciones hasta las versiones finales. el proyecto se desarrolló en 3 fases, fase 1: formulación del problema y socialización; fase 2: elaboración de las preguntas, fase 3: formulación de las recomendaciones y ronda de calificación. las estrategias de búsqueda se desarrollaron en bases de datos especializadas (medline, embase, lilacs, central), en las circunstancias donde no se encontró evidencia directa, se utilizó y se adaptó evidencia indirecta del tópico relevante en el paciente críticamente enfermo general. 80 expertos con un promedio de 15 años de experiencia en la atención del paciente crítico evaluaron y calificación las recomendaciones en la metodología delphi mediante un cuestionario distribuido por medio de correo electrónico, respetando la política de privacidad de datos vigente. recomendación se recomienda que los prestadores de servicios de acuerdo con su infraestructura física y la disponibilidad de recursos (tecnológico, humano, de interdependencia y apoyo) definan su modelo de atención para pacientes con covid-19 en estado crítico basado en principios de factibilidad, efectividad, seguridad y la relación entre la demanda (momento epidemiológico) y capacidad/capacidades de respuesta:  modelo 1. atención de pacientes con sospecha o confirmación diagnóstica covid19 . este enfoque permite concentrar, optimizar y racionalizar recursos y reducir el riesgo potencial de contagio al equipo de atención, de apoyo y de pacientes.  modelo 2. atención mixta, de pacientes con y sin diagnóstico de covid-19, en escenarios que cuentan con unidades de aislamiento normatizados (presión negativa y >12-renovaciones completas de aire por hora) soportado en el documento institucional de gestión organizacional y operativo del servicio de cuidados intensivos, descrito en los procesos prioritarios. amci ® menos accidentalidad y violencia). la reducción de procedimientos quirúrgicos complejos electivos es una opción razonable condicionado a las posibilidades del paciente. sin embargo, situaciones como la progresión y descompensación de las patologías crónicas asociadas a las medidas de restricción social puede plantear un efecto bumerang con mayor demanda de camas de uci. con base en las predicciones simuladas de las tasas esperadas de ingreso a uci de pacientes con covid-19 contrastado con el déficit de servicios y camas de cuidados críticos en el país a partir de la capacidad instalada se han planteado 4 fases de desarrollo cuyas características en términos de servicios, recursos y cronología se aprecian en la ilustración 1 y 2.  fase 1 (para el gobierno nacional: ampliación de la capacidad instalada*). parte de la liberación de camas de cuidados intensivos destinadas para atención covid-19 bajo el modelo 1 y/o 2. la liberación de camas y servicios con mínima adaptación es la fase más inmediata y resolutiva que debe acogerse a la exigencia normativa (resolución 3100 de 2019), en la que se espera menos mortalidad, morbilidad y tasa de complicaciones asociados con la atención de pacientes con covid-19 en estado crítico.  fase 2 (optimización para el gobierno nacional*) representan el reordenamiento de las camas de cuidados intermedios adultos en camas de cuidados intensivos y de hospitalización en intermedio. de adultos. el gobierno nacional toma en cuenta la ampliación de la capacidad instalada hospitalaria descrita en el plan territorial. para esta fase se necesitan equipos de ventilación mecánica (excluidos por la norma de estos servicios), monitoreo básico y avanzado y un número mayor de talento humano multidisciplinario competente. amci ® acuerdo con las etapas (1-3) y los perfiles requeridos priorizados como primera, segunda y tercera línea de respuesta*. en la ilustración 1 podemos observar que avanzar de las fases 1 a 4 se va a necesitar mayor intervención en términos de organización, planeación operativa, formación por competencias y apoyo por telesalud (teleapoyo o teleexperticia). el personal no especializado o especializado de servicios hospitalarios diferente a urgencia, quirófano o uci pueden constituir grupos de apoyo para la gestión administrativa y de índole humanitaria (líneas de respuesta) la integración de estos requerimientos adaptativos se ha puesto de manifiesto en la experiencia del centro médico new york -presbyterian weill en la ciudad de nueva york, en donde la demanda de camas de unidades de cuidados intensivos (uci) y ventilación mecánica excedió su capacidad.(3) se recurrió a los quirófanos y de recuperación las cuales no estaban en uso porque los procedimientos electivos habían sido pospuestos. se hicieron adecuaciones físicas para garantizar la vigilancia continua de los pacientes y la seguridad del equipo de atención. se capacito a todo el personal de cuidado perioperatorio disponible y fueron distribuidos en las áreas recién configuradas. las enfermeras familiarizadas con las máquinas de anestesia asumieron como terapeutas respiratorios y los intensivistas de anestesia supervisaban estas unidades. recomendación se recomienda la adopción de un modelo simulado de predicción (basado en el cociente de fatalidad, tasa de ingreso a uci y el número de reproducción ro) para proyectar, de manera anticipada las necesidades de recurso físico, tecnológico y humano de cuidados críticos en fase de preparación de la pandemia por covid-19. las tomas de decisiones relacionadas con el fortalecimiento de la capacidad/capacidades de la oferta de cuidados críticos (habilitadas o adaptadas) pueden deducirse mediante la aplicación de modelos matemáticos que intentan, desde la dinámica epidemiológica, establecer el efecto simulado de las medidas de mitigación o supresión adoptadas sobre la tasa de contagio a través del tiempo. con ello se busca planear el uso de recursos e implementar acciones de prevención y de distanciamiento social más eficientes, así como establecer las necesidades en materia de cama de cuidados críticos (intensivos e intermedios) habilitadas o adaptadas en áreas de expansión y con ello los recursos resolutivos como tecnologías, interdependencias y talento humano capacitado. la capacidad predictiva del modelo resulta de establecer: la información en términos de casos proyectados (población susceptible), el modelo de transmisión, el impacto de las amci ® intervenciones no farmacológicas (mitigación y supresión) para lograr disminuir el número de reproducción r (tasa de contagio), la distribución de la gravedad de la enfermedad y con ello el porcentaje esperado de casos críticos el decreto 417 del 17.03.20 (4) , por el cual se declara un estado de emergencia económica, social y ecológica en todo el territorio nacional proyectó para una tasa de contagio de 2.68 y cerca de 4 millones de casos, la ocurrencia de 187 mil casos de pacientes con covid-19 en estado crítico (4.7%) y la necesidad de incrementar las camas de cuidados intensivos en un 10% que con una estancia promedio de 14 días tendría un costo de 200 mil millones de pesos. colombia cuenta con cerca de 8500 camas de cuidados intensivos (1/3 parte son intermedio) de las cuales el 60% podría ser utilizada para la atención de pacientes covid-19 (5100). con base en el modelo matemático ha proyectado la necesidad de 9500 camas de uci indicando por deducción la necesidad de 4400 camas a partir de un plan adaptativo de expansión y extensión. colombia reporta a la fecha actual 113,389 casos confirmados y 3984 nuevos casos de covid-19 confirmados y cerca del 4% ocupan una cama de cuidados intensivos (esta cifra es mayor si se tomaran en cuenta los casos sospechosos). de este modo, los modelos matemáticos permiten predecir el comportamiento epidemiológico de la enfermedad y con esto anticiparse a proyectar el plan de fortalecimiento hospitalario (incluyendo camas, tecnologías, talento humano) y los recursos financieros para respaldar la expansión del cuidado críticos. estos modelos deben ser predictivos y no reactivos al comportamiento epidemiológico de la enfermedad y solo debe des escalarse hasta después de reducirse a menos de 1.0 el índice ro. (5-10) recomendación se sugiere la implementación de una estrategia de telesalud (teleapoyo o teleexperticia) en el marco de la pandemia covid-19, cuando no se cuente con un intensivista presencial, que, mediante una tecnología adecuada complemente la atención en las áreas de cuidados críticos realizado por personal capacitado. aún cuando es considerada ventajosa sus implicaciones en términos de resultados clínicos, económicos y de riesgos legales no se ha demostrado. en situaciones donde se declara una pandemia los sistemas de salud pueden tener dificultades para hacer frente a una demanda exponencial y fuera de control. esto puede ser así en el marco pandemia covid-19 que prevé un 5% de pacientes en condición crítica y que amerita reorganización y/o adaptación de su capacidad de respuesta. incrementar la disponibilidad de camas y servicios de cuidados críticos mediante una estrategia de expansión supone retos asociados a la insuficiencia que se puede presentar en talento humano especializado específicamente de especialistas en medicina crítica y cuidado amci ® intensivo, escenario que se puede complicar en la medida que intensivistas sean separados o aislados en el curso de la epidemia. en este contexto se hace necesaria la implementación de modelos ágiles de telesalud (ts) para el acompañamiento de las unidades de cuidado crítico en expansión y de instituciones prestadoras de servicios de salud de baja y mediana complejidad para la regulación con los equipos de referencia y contrarreferencia de pacientes que pueden necesitar atención en cuidados intensivos. (11) (12) (13) (14) (15) (16) el decreto ley 538 de 2020 (17) plantea la adopción de medidas en el sector salud para garantizar la prestación de los servicios de salud y para facilitar la implementación de modelos de atención que incluyan la telesalud y la prestación de los servicios en la modalidad de telemedicina se determinan algunas medidas temporales para: i) adecuar temporalmente un lugar no destinado a la prestación de servicios de salud, intra o extra mural. ii) prestar servicios en modalidades o complejidades diferentes a las habilitadas dentro de las cuales puede estar la telemedicina iii) prestar servicios de salud no habilitados. en este decreto también se establecen condiciones temporales para la implementación de plataformas tecnológicas para la telesalud. en complemento, la resolución 3100 de 2019(18) (estándares de habilitación) plantea la modalidad de la telemedicina (prestador remisor-prestador de referencia) para las unidades de cuidado intermedio e intensivo. la telesalud se puede prestar de dos maneras: teleapoyo y teleexperticia. tabla 2. teleapoyo (ta) soporte solicitado por un profesional de la salud a otro profesional de la salud a través de tic siendo responsable de la conducta quién solicita el apoyo. no requiere habilitación y por tanto no requiere autorización transitoria relación a distancia con comunicación sincrónica o asincrónica utilizando tic entre dos profesionales de la salud, uno de los cuales atiende presencialmente al usuario y otro atiende a distancia. el primero es responsable de las decisiones/recomendaciones entregadas al paciente y el segundo es responsable de la calidad de la opinión que entrega y debe especificar las condiciones en las que se da dicha opinión, lo cual debe consignarse en la historia clínica. requiere autorización transitoria (decreto 358 2020) (17) la telesalud y la prestación de servicios de salud en esta modalidad son estrategias seguras y efectivas para guiar, a distancia, el diagnóstico y el tratamiento del paciente hospitalizado y en estado crítico. sus ventajas generales se presentan en la tabla 3. 14 asociación colombiana de medicina crítica y cuidados intensivos. amci ® tabla 2. ventajas generales de la telesalud decreto legislativo 538 de 2020.  facilita la viabilidad de aplicación modelos organizativos que favorecen la continuidad y la integridad asistencial y la atención centrada al entorno del paciente, aplicando conceptos de globalidad e interoperabilidad a las organizaciones sanitarias, dando lugar a nuevas formas de organización y trabajo en red.  mejora de la calidad asistencial, ya que facilitan el acceso y la disponibilidad de servicios asistenciales en condiciones de calidad.  mejora calidad de vida del paciente por la disminución de desplazamientos para la atención ya que permite la atención o monitorización remota con tic en su domicilio.  mejora la oportunidad y la resolutividad de la atención.  facilita la equidad en el acceso a los servicios de salud independientemente de la localización geográfica (acerca la atención especializada a toda la población).  mejora la atención integral y seguimiento tanto de los pacientes crónicos, como los de las enfermedades de baja prevalencia.  reduce los tiempos de espera (tanto en la realización del diagnóstico como en el tratamiento), evitando complicaciones por no atención oportuna.  posibilita realizar atención remota de mediana y alta complejidad en la baja complejidad, reduciendo el número de remisiones.  disminuye la posibilidad de infección cruzada entre usuarios de los servicios de salud y el personal de salud.  incide en la formación y competencia del talento humano en salud.  facilita la educación de pacientes en medicina preventiva y salud pública.  descongestiona servicios de urgencias y consulta externa.  contribuye a la reducción de movilidad de personas en la ciudad.  responde a las necesidades inmediatas en salud de la comunidad.  es un medio de racionalización de costos en salud. puede abarcar otros servicios de gestión administrativa como entrega de fórmulas o facturación. amci ® se recomienda la implementación de un modelo de cuidados críticos covid-19 liderado por intensivistas, en áreas habilitadas o adaptadas, con el beneficio preponderante de disminuir la mortalidad, tiempo de estancia y optimización de recursos. se recomienda una cobertura por intensivistas de al menos 12 horas diarias y un cociente intensivista/paciente cercano a 1 intensivista por cada 8-10 pacientes, basado en la alta complejidad de la enfermedad critica covid-19 con un alto porcentaje de pacientes en ventilación mecánica, largos tiempos de estancia y alto riesgo de mortalidad. fuerte a favor fundamento un intensivista es un profesional médico capacitado en medicina crítica y de cuidados intensivos conforme a los estándares establecidos por una institución de educación superior debidamente reconocida ante el ministerio de salud. este especialista debe liderar y tomar todas las decisiones con respecto al cuidado de los pacientes críticos, incluyendo admisiones y egresos, qué médicos consultar, estándares de atención, gestión de la calidad y seguridad, gestión humana y ética, interacción con la familia e implementación de un programa de investigación y de formación continua para mejorar capacidades y competencias del equipo de atención, control de conflictos, entre otras.(20) existe una enorme validez conceptual y una preponderancia de evidencia que sugiere que ser atendido por un especialista en cuidados críticos (intensivista) es "bueno" para los pacientes de la uci. la mayoría de los estudios demuestran el impacto positivo de un uci dirigida por intensivistas los modelos de personal médico de la uci más ampliamente estudiados difieren en el nivel al cual los intensivistas están involucrados en el manejo de los pacientes. las uci de alta intensidad son aquellas donde un intensivista de tiempo completo u obligatorio maneja a la mayoría de los pacientes diariamente. las uci de baja intensidad no tienen participación intensivista u ofrecen consultas intensivistas electivas. un metaanálisis mostró que un modelo de alta intensidad en comparación con uno de baja intensidad estuvo asociado con una menor mortalidad en la uci, menor mortalidad hospitalaria, y una reducción significativa en la duración de la estancia hospitalaria. un modelo de alta intensidad por la noche se asoció con menor mortalidad solo cuando durante el día era de baja intensidad. (21) (22) (23) (24) (25) (26) (27) (28) (29) (30) (31) (32) (33) (34) (35) (36) 17 asociación amci ® forzosa" por condición de riesgo siempre en consonancia con los términos establecidos en el decreto ley 588 de 2020 (39). según la normatividad vigente todo miembro del equipo de atención, especialista no intensivista o no especialista (enfermeras, fisioterapeutas/terapeutas respiratorias) y auxiliares de enfermería deben tener constancia de asistencia a acciones de formación continua y/o capacitación en atención covid-19 en cuidados críticos las cual puede ser parte de un programa institucional de capacitación liderado por el intensivista coordinador o titular del servicio o a partir de cursos respaldados por instituciones académicas acreditadas o los ofrecidos por la asociación colombiana de medicina crítica y cuidados intensivos (amci). las tablas 5 y 6 nos muestra como dentro de este proceso adaptativo por estado de emergencia y atribuido a un desequilibrio entre la oferta y la demanda, otras especialidades, profesionales de la salud y personal en formación pueden hacer parte de los equipos de atención bajo las siguientes premisas: 1. la supervisión, coordinación y liderazgo del intensivista es necesaria y 2. el intensivista establece los roles y competencias del th no intensivista y no normatizado, de acuerdo a sus perfiles, y delegada acciones asistenciales (vía aérea, accesos vasculares, reanimación cardiopulmonar, pronación), administrativas (ordenes médicas, notas clínicas) o de naturaleza humanitaria (comunicación con la familia, apoyo emocional al th, etc.). es necesario considerar los roles de las especialidades que formarán parte de la gestión asistencial y/o administrativa de pacientes con covid-19 en áreas críticas habilitadas o adaptadas de manera transitoria en colombia tabla 7. integridad de interdependencia (norma3100/10) integralidad e interdependencia (adaptiva) gfa integridad de interdependencia (norma3100/10) integralidad e interdependencia (norma 3100/10) integridad de interdependencia (norma3100/10) obligatorio en gestión asistencial integralidad e interdependencia(norma 3100/10) obligatorio gestión asistencial apoyo a tomas de decisiones(gfa) apoyo a tomas de decisiones (gfa) a:formacion continua + covid-19 (curso virtual); b: requiere capacitación covid-19 (curso virtual); c: gfa: grupo focal asistencial, sistema alerta-acción, rcp, pronación, accesos vasculares, ingreso a uci. d: gfad: grupo focal administrativo: consentimiento, notas de evolución. ts: telesalud. se recomienda la aplicación de la escala news-2 por parte de un equipo de respuesta rápida, para establecer el lugar de atención de pacientes con diagnóstico definitivo o sospecha de infección por covid-19 que encuentran en los servicios de urgencias o de hospitalización. se recomiendan escalas como el qsofa y el curb-65 para apoyar la decisión tomada con base en la escala news-2. sin embargo, un qsofa mayor o igual a 2 puntos (mínimo 2/3) y un crb-65 mayor o igual 2 puntos tienen baja sensibilidad (alta incidencia de falsos negativos) para identificar pacientes que puedan requerir ingreso a uci. se recomienda el score de riesgo covid-19-gram para identificar el riesgo de desarrollar un estado de la enfermedad crítico en pacientes con covid-19 y como herramienta complementaria a la escala news-2 en escenarios de alta demanda y escasez de recursos, de manera que la decisión de ingreso a uci se haga sobre aquellos pacientes que realmente se beneficiarán de la misma en términos de vidas salvadas y número de años salvados. la escala news fue construida y validada en paciente con infección por el virus de la influenza a/h7n9 y se recomienda como una herramienta objetiva para decidir nivel de atención, incluyendo ingreso a uci o situaciones terminales que requieren acompañamiento familiar y medidas de cuidado paliativo. esta escala incluye 6 variables fisiológicas que son: frecuencia respiratoria, saturación arterial de oxígeno (spo2), uso de oxígeno suplementario, presión arterial sistólica, frecuencia cardiaca (pulso), temperatura y nivel de conciencia. es de mencionar que esta escala no contempla la edad del paciente. en 2007 un reporte del acute medicine task force of the royal college, london, uk, recomendó la utilización de la escala news en los servicios de urgencias (41) . un estudio que evaluó una base de datos con 198.755 signos vitales obtenidos de 35.585 pacientes demostró que esta escala tiene una buena capacidad para discriminar pacientes en riesgo para un desenlace combinado de paro cardiaco, ingreso no anticipado a uci o muerte dentro de las primeras 24 horas de atención; de esta manera genera una gran oportunidad para el establecimiento temprano de una intervención clínica que cambie el pronóstico del paciente (42) . la escala news-2 tampoco contempla la edad, pero sí incluye la presencia de hipercapnia bajo diferentes niveles de spo2 y oxígeno suplementario. esta escala es la que ha sido estudiada como herramienta para identificar pacientes en riesgo de desarrollar un estado de enfermedad crítica por covid-19 con un valor ≥ 5 puntos (5/20) (43) . con base en la escala news-2 se establece el grado de riesgo, el tipo de alerta, y la intensidad de monitoreo requerido; y de acuerdo con el puntaje arrojado, se define claramente el nivel de atención que requiere el paciente con diagnóstico de infección por covid-19, incluso ingreso a uci (tabla 7). esto se establece a través de una escala de puntuación así: -score 0 puntos: manejo domiciliario bajo aislamiento y signos de alarma. -score 1 punto: manejo domiciliario y seguimiento clínico en casa. -score 2-4 puntos: manejo en salas de hospitalización. -score 5-7 puntos: manejo en uci, área covid-19. -score ≥ 7 puntos sin condición extremadamente grave o irreversible y con alta posibilidad de recuperación: traslado a uci, área covid-19. amci ® -score ≥ 7 puntos con condición extremadamente grave y con datos de irreversibilidad o enfermedad terminal: no ingresa a uci y se traslada a salas de hospitalización con acompañamiento familiar y consulta a experto en bioética y cuidados paliativos. la ilustración 4 establece un flujograma de conductas basado en el puntaje del news-2. tabla 6. news-2 score. el qsofa con un valor ≥ 2 puntos es otra herramienta recomendada para decidir qué pacientes que ingresan a uci. esta herramienta fue recomendada por la tercera definición de consenso (sepsis-3) para identificar pacientes con alto riesgo de muerte o estadía prolongada en uci entre aquellos con sospecha de infección (44) . en este score, un punto es asignado para 3 variables así: frecuencia respiratoria ≥ 22/min, presión arterial sistólica ≤ 100 mmhg y escala de coma de glasgow (ecg) < 15. el score curb-65 y su versión simplificada, el crb-65 se utilizan para evaluar la severidad de enfermedad en personas hospitalizadas con neumonía adquirida en comunidad (nac). ambos scores han sido adoptados por la sociedad británica de tórax para predecir la necesidad de soporte respiratorio o vasopresor intensivo (srvi) en pacientes con covid-19 (40) . el score crb-65 asigna un punto para 4 variables así: confusión de reciente inicio, frecuencia respiratoria ≥ 30/min, presión arterial sistólica < 90 mmhg o presión arterial diastólica ≤ 60 mmhg y edad ≥ 65 años. pacientes con un score ≥ 2 puntos necesitan hospitalización (43) . en un estudio clínico observacional realizado sobre los primeros 42 pacientes ingresados en un hospital de noruega con diagnóstico confirmado de covid-19, se evaluó la utilización de 4 sistemas de score clínicos al momento del ingreso: news-2, qsofa, crb-65 y sirs, con los puntos de corte previamente mencionados (43) . la enfermedad se clasificó como enfermedad severa y enfermedad crítica. solo 9 pacientes (21%) se clasificaron como enfermedad crítica. al evaluar los scores con sus puntos de corte, 2 pacientes presentaron un qsofa ≥ 2 [1 con enfermedad severa (3%) y 1 con enfermedad crítica (11%)], solo 7 pacientes presentaron un crb-65 ≥ 2 [6 con enfermedad severa (18%) y 1 con enfermedad crítica (11%)] y 19 pacientes presentaron un news-2 ≥ 5 [(11 con enfermedad severa (33%) y 8 con enfermedad crítica (89%)]. la mediana del score news-2 para pacientes con enfermedad severa fue de 3.3 [riq: 3-9] vs 7.6 [riq: 8.4 -10] para pacientes con enfermedad crítica. los autores concluyen que el qsofa y el crb-65 se comportan similar y con una baja capacidad para la identificación de enfermedad crónica en pacientes con covid-19; por otro lado, los datos indican que el news-2 podría ser una herramienta más útil para identificar pacientes con riesgo de un curso más agresivo de la enfermedad (33% vs. 89%) (43) . amci ® un estudio de cohorte retrospectivo realizado en un hospital en liverpool (uk), el puntaje qsofa se comportó como el más específico (79%; 95% ic: 77% -81%) pero el menos sensible (37%; 95% ic: 31% -43%) en comparación al puntaje sirs y la escala news como predictor de mortalidad hospitalaria en un grupo de 1818 paciente admitidos por sepsis al servicio de emergencias (45) . otro estudio retrospectivo de un único centro comparó el rendimiento de 3 sistemas de score, qsofa, curb-65 y crb-65 para predecir la necesidad de soporte vasopresor o respiratorio intensivo (svri) en 116 pacientes ingresados con diagnóstico confirmado de covid-19 a un hospital de wuhan (china) (40) . un total de 25 pacientes (21.6%) necesitaron svri durante su estadía en el hospital. la tasa de mortalidad hospitalaria en esta cohorte fue de 9 pacientes (7.8%). se evalúo el rendimiento de las escalas con análisis de curva roc (auc), puntos de corte óptimo, sensibilidad, especificidad y valores predictivos. el punto de corte óptimo del crb-65 para predicción de srvi fue de 2 puntos, con una sensibilidad del 64% y una especificidad del 93.4%. el valor auc del score crb-65 para predecir la necesidad de svri fue significativamente más alto que el del qsofa (0.81 ± 0.05 vs. 0.70 ± 0.06, p= 0.02). los valores de auc fueron similares entre crb-65 y curb-65 para predecir svri (0.81 ± 0.05 vs. 0.85 ± 0.05, p= 0.08). los autores concluyen que el crb-65 podría ser mejor que el qsofa para identificar paciente con covid-19 en riesgo de necesitar svri. su et al consideran que fue la inclusión de la edad ≥ 65 años dentro del score crb-65 lo que le dio un mayor grado de superioridad sobre el qsofa (40) . el crb-65 puede ser una herramienta de puntuación útil para covid-19 debido a su simplicidad en la aplicación, especialmente en emergencias y condiciones de escasez de recursos. finalmente, el score de riesgo covid-19-gram fue descrito por un grupo de investigadores en covid-19 quienes reunieron datos de 1590 pacientes en 575 hospitales en china (46) . esta fue una cohorte retrospectiva multicéntrico en la que se recogieron un total de 72 variables entre demográficas, médicas, clínicas (signos y síntomas), imagenológicas y de resultados de laboratorios. utilizando la metodología de regresión lasso (least absolute shrinkage and selection operator) construyen un modelo de regresión multivariable resultando en un score de riesgo predictivo para desarrollar enfermedad critica en pacientes con covid-19 confirmado al momento de la admisión. de las 72 variables iniciales 10 fueron predictores independientes estadísticamente significativos para el desarrollo de enfermedad crítica. estas variables fueron: anormalidad en los rx tx (or: 3.39; 95%ic: 2. 14 -5.38 recomendación se recomienda la aplicación de un algoritmo basado en una evaluación dinámica del score news 2 que involucre una escala de evaluación funcional, para priorizar el ingreso a uci con transparencia científica y ética con equidad social, y de ser posible respaldado por un comité de priorización clínica (cpc) integrado por expertos de cuidado intensivo y un representante del comité de ética hospitalaria durante la pandemia por covid-19. se recomienda un modelo determinado por 4 prioridades para definir criterios de ingreso a uci, permite establecer rápidamente qué pacientes se benefician de ingreso uci y qué pacientes deben permanecer en servicios de hospitalización, o con acompañamiento familiar y cuales con medidas de cuidado paliativo. fuerte a favor page amci ® fundamento la pandemia covid-19 nos ha enseñado que la disponibilidad de camas de uci puede ser insuficiente y el plan estratégico diseñado para ampliar la capacidad de respuesta debe ir de la mano con la implementación rigurosa de un protocolo de triaje y de priorización de ingreso a cuidados intensivos, como medida extraordinaria para optimizar los recursos, mitigar y controlar los efectos de la pandemia sobre el balance oferta (efectiva y resolutiva) y la demanda. los protocolos de triaje y priorización están diseñados para asignar los limitados recursos de una manera justa y transparente donde, por definición, algunas personas serán excluidas del acceso a la atención orientado a aumentar la disponibilidad de camas de cuidados intensivos. sin embargo, es necesario enfatizar que la disponibilidad de camas no es un fin en sí mismo. la intención implícita y explícita de los protocolos de clasificación debiera ser el «bien público» de maximizar la supervivencia de la población. pero es incorrecto suponer que este bien público se logra al maximizar la supervivencia entre los que reciben cuidados intensivos. si bien muchos protocolos de triaje reconocen esto al tratar de excluir a los pacientes que no lo necesitan absolutamente (el «demasiado sanos») y los que tienen menos probabilidades de beneficiarse (él «demasiado enfermo»), no prestan suficiente atención a las diferencias entre grupos en términos de la duración de los cuidados intensivos necesarios para lograr resultados. si el objetivo del triage es mejorar la supervivencia de la población con un recurso escaso, entonces el recurso escaso no son camas, sino días de cama; no son ventiladores, sino tiempo de ventilación. de ello se deduce que el triaje no será efectivo si en la valoración, no se discrimina adecuadamente y se considera de manera equívoca que la gran mayoría de las personas que requieren cuidados intensivos tienen una probabilidad similar de supervivencia y una duración de estadía anticipada similar. (47) de este modo, el ingreso a uci debe acogerse a los criterios habituales, científicos y éticos, bajo el rigor de "idoneidad clínica" tomando en cuenta parámetros como la gravedad de la enfermedad, la presencia de comorbilidades (severidad, clase funcional), potencial de recuperabilidad, deseo del paciente (o la familia), de equidad distributiva y el uso de las escalas validadas de severidad y de predicción de ingreso a cuidados intensivos. los pacientes con covid-19 tienden a progresar después del inicio de los síntomas dentro de los 7 a 12 días a una forma grave con síndrome de dificultad respiratoria aguda (sdra) o falla multiorgánica órgano. la identificación temprana y simple de pacientes que requieren respiración intensiva o el soporte vasopresor sería de gran valor durante el brote covid-19. (48) (49) (50) (51) la implementación de un algoritmo "dinámico" que vincule uno o más de las escalas fisiológicas (news con o sin qsofa y/o crb-65 ≥2), una escala de predicción de ingreso a uci (covid-19-gram) y un puntaje de fragilidad (vipi) puede informarnos sobre el estado actual y evolutivo de la enfermedad y a priorizar el ingreso de pacientes a uci permitiendo un uso óptimo de los recursos y tomar decisiones éticas, transparentes y centradas en la dignidad de los pacientes y el bien público ilustración 4-5. se recomienda no usar escalas de severidad de enfermedad (criterios objetivos) para definir el traslado de pacientes de uci hacia un nivel de menos complejidad de atención, ya que estas escalas no han sido validadas para este uso. se recomienda en la atención por covid-19 en cuidados intensivos utilizar los mismos criterios de egreso que se emplean para el traslado desde uci hacia una unidad de menor complejidad de pacientes sin infección por covid-19. se recomienda contar con áreas de bajo nivel de complejidad asignadas solo a la atención de paciente con infección por covid-19, las cuales serán las áreas hacia donde se realiza el de-escalamiento gradual de los pacientes basado en su evolución clínica. cuando se habla de criterios objetivos, se hace referencia a escalas de severidad de enfermedad que ayuden a tomar decisiones más racionales y no basadas en consideraciones tradicionales de resolución de cuadros clínicos. no hay una recomendación definida sobre el uso de escalas de severidad de enfermedad para definir el de-escalamiento de la atención para pacientes críticos. los sistemas de evaluación de severidad de enfermedad generales y específicos pueden identificar una población específica de pacientes en alto riesgo de deterioro clínico luego del traslado fuera de la uci(53); sin embargo, su valor para evaluar que tan preparado está un paciente individual para ser trasladado a un nivel inferior de cuidado no ha sido evaluado(53). los criterios que recomienda el colegio americano de cuidado intensivo(53) para definir el traslado desde uci a un nivel de menor complejidad (unidad de cuidados intermedios o sala de hospitalización) se basan en 3 principios:  cuando el estado fisiológico del paciente se ha estabilizado y ya no es necesario monitoreo y tratamiento en uci.  cuando el paciente cumpla con los criterios de admisión del nivel de menor complejidad, teniendo en cuenta la disponibilidad actual del recurso, el pronóstico del paciente y la presencia de intervenciones activas en curso. específicamente para los pacientes con alto riesgo de muerte y reingreso a uci en quienes se decide no hacer intervenciones adicionales (alta severidad de enfermedad, inestabilidad fisiológica, soporte orgánico), el colegio americano de cuidado intensivo(53) siguiere pasarlos a una unidad de menor nivel de atención o a un hospital de cuidado agudo de largo plazo; siempre con un formato escrito donde se deje claro la decisión para reducir la tasa de reingreso a uci(53). específicamente en situaciones de pandemia y escasez de recursos, la sociedad española de medicina intensiva, crítica y unidades coronarias (semicyuc) recomienda la realización de la escala sofa al menos cada 48 horas para identificar pacientes con evolución tórpida y progresiva a un fallo multiorgánico luego de la iniciación de tratamientos de soporte vital. esto permitirá la adecuación y reorientación de medidas terapéuticas a un objetivo más paliativo, incluyendo la transferencia del paciente a un nivel más bajo de complejidad y la consulta al servicio de cuidado paliativo para que brinde la atención respectiva(52). finalmente, se debe mencionar que no se ha establecido una diferencia en los criterios de egreso de pacientes con covid-19 para su traslado desde uci hacia una unidad de menos complejidad, con respecto a los utilizados para pacientes sin infección por covid-19(54). todo paciente hospitalizado en uci sea covid-19 o no, debe ser valorado diariamente para establecer en qué momento su condición clínica permite que sea trasladado fuera de la uci hacia una unidad de menor complejidad. en caso de tratarse de pacientes con sospecha o diagnóstico de covid-19, este traslado puede hacerse a una unidad de cuidados intermedios dispuesta como área covid-19 o una sala de hospitalización con igual asignación(54); esto es lo que se conoce como de-escalamiento gradual de la atención hasta el final egreso del paciente a casa. se recomienda para pacientes con covid-19 que evolucionan hacia la mejoría, utilizar los criterios clásicos de de-escalamiento del nivel de atención (unidad de cuidados intermedios o sala de hospitalización) que propone el colegio americano de cuidado intensivo(53) . se recomienda aplicar la escala sofa al menos cada 48 horas sumado al criterio de fragilidad y años de vida saludables salvados estos criterios podrían ser válidos en pacientes con fallo terapéutico a las medidas óptimas y orientar decisiones de deescalamiento de medidas y de nivel de complejidad de atención cuando la demanda potencial supera la oferta (capacidad y capacidades), estas decisiones deben ser tomadas idealmente en junta médica. amci ® se recomienda generar procesos administrativos más eficientes para el traslado de pacientes fuera de la uci hacia niveles de menor complejidad, estos ayudarán a liberar recursos para otros pacientes. se recomienda no utilizar el resultado de la rt-pcr positiva para decidir el egreso de la unidad de cuidados intensivos. la literatura no ha definido unos criterios de flexibilidad en uci para el traslado de pacientes con sospecha o diagnóstico confirmado de covid-19; y los criterios que definen la posibilidad de egreso de uci y que aplican a todos los pacientes, incluso aquellos ingresados por una condición crítica en relación con infección por covid-19, están claramente definidos por el colegio americano de cuidado intensivo en su documento-guía del 2016.(53). los principios fundamentales han sido revisados en los fundamentos de la pregunta 8. es importante implementar una estrategia de identificación temprana para aquellos pacientes con soporte vital avanzado que evolucionan progresivamente a fallo multiorgánico y pocas probabilidades de recuperación; el de-escalamiento de medidas y su posterior traslado fuera de la uci, liberará espacio para otros pacientes en situaciones de desborde de la demanda. la sociedad española de medicina intensiva, crítica y unidades coronarias (semicyuc) recomienda que en caso de complicaciones o que se prevea una mala evolución tanto clínica como funcional, se plantee el retiro terapéutico por futilidad y se inicie un manejo con medidas de soporte paliativo, tal como ha sido considerado en los fundamentos de la pregunta 8 (55) . para el grupo español es claro que, adecuar procesos administrativos más eficientes para traslado de pacientes fuera de la uci a los usualmente utilizados en condiciones normales de práctica clínica, ayudaría a ser más eficientes en la gestión de la demanda (55) . finalmente, la persistencia de una rt-pcr positiva no es una contraindicación para el traslado del paciente fuera de la uci siempre y cuando se aseguren condiciones de aislamiento por contacto y aerosol en aquellas áreas de menor complejidad de atención; estas incluyen zonas de expansión o área del hospital específicamente acondicionadas para el manejo de pacientes estables o pacientes con limitación de esfuerzo y manejo paliativo de su condición (55). recomendación se recomienda que la disposición final de cadáveres de personas con sospecha o diagnóstico de covid-19 se haga preferiblemente por cremación. en tal caso, las cenizas pueden ser objeto de manipulación sin que suponga ningún riesgo. amci ® se recomienda que la disposición final del cadáver se haga por inhumación en sepultura o bóveda individualizada cuando no se cuente con instalaciones para cremación en el territorio donde ocurrió el deceso o la disponibilidad de esta tecnología desborda la capacidad económica de las personas. se recomienda realizar siempre el aislamiento del cadáver en el lugar del deceso, siguiendo las recomendaciones del ministerio de salud y la protección social (msps). se recomienda que en los casos que se requiera necropsia médico legal y estuviese indicada la cremación, esta deberá contar con la orden del fiscal del caso. se recomienda que la institución establezca en sus procesos prioritarios un protocolo humanizado de despedida bajo estrictos criterios de bioseguridad. no existe una evidencia fuerte que recomiende hacer una disposición de cadáveres de pacientes fallecidos con sospecha o diagnóstico confirmado de covid-19 con un acto de cremación o con inhumación y sepultura en féretro; sin embargo, siempre y cuando la manipulación y manejo del cadáver hasta su disposición final se haga manteniendo todas las medidas de precaución para evitar la diseminación del virus y siguiendo la normatividad legal vigente, ambas formas son aceptadas. la infección por covid-19 es una enfermedad con gran variabilidad en presentación clínica, alta tasa de contagio y para la cual no existe en el momento un tratamiento definido. el riesgo de contagio al personal que ejecuta autopsias o procedimientos de tanatopraxia y la probabilidad de diseminación de la enfermedad por la manipulación de cadáveres no se conoce, pero se considera que puede ser alto, teniendo en cuenta que, en ausencia de la aplicación de un método de diagnóstico masivo, todo caso debe considerarse potencialmente positivo. por tanto, el manejo de cuerpos de personas fallecidas con diagnóstico confirmado, sospechoso o probable de sars-cov-2 (covid-19), debe realizarse con la mínima manipulación posible(56). el cadáver debe ser transferido lo antes posible al depósito y entregado al servicio funerario antes de 24 horas luego del fallecimiento(57). el transporte, la cremación o inhumación, según sea el caso, se efectuará en el menor tiempo posible, con el fin de prevenir la exposición de los trabajadores y comunidad general al virus sars-cov-2 (covid-19). se debe evitar la realización de rituales fúnebres que conlleven reuniones o aglomeraciones de personas(56). el alistamiento del cadáver será realizado en el ámbito hospitalario del mismo sitio del deceso. las personas que accedan a la habitación donde se encuentre el cadáver, deben tomar las precauciones de transmisión por contacto y gotas, y para ello deben contar con todos los elementos de protección personal (epp) y seguir los procedimientos de amci ® bioseguridad de acuerdo con lo establecido en el protocolo del msps.(58) para hacer el alistamiento del cadáver, se debe cubrir todos los orificios naturales con algodón impregnado de solución desinfectante y se deberá envolver en su totalidad sin retirar catéteres, sondas o tubos que puedan contener los fluidos del cadáver, en tela antifluido o sábana; luego se deberá envolver en dos bolsas plásticas biodegradables que cumplan con las características técnico-sanitarias de impermeabilidad y resistencia a la presión de gases en su interior(57). se debe rociar el interior y el exterior de ambas bolsas con solución desinfectante de hipoclorito sódico que contenga 5.000 ppm de cloro activo(57) (exceptuando los casos asociados de covid-19 y muerte violenta). una vez el cadáver esté adecuadamente dispuesto en las bolsas, se podrá movilizar sin riesgo hacia el depósito de cadáveres siguiendo la ruta intrahospitalaria dispuesta para este traslado. luego el cadáver podrá será entregado al personal del servicio funerario para su depósito en ataúd o contenedor de cremación o inhumación y posterior traslado al sitio de destino final (horno crematorio y/o cementerio), luego de completar toda la documentación necesaria. cuando deba practicarse necropsia médico legal, el cuerpo será entregado a los servidores del sistema judicial quienes asumirán la custodia(56). si se han seguido correctamente todas estas indicaciones, se asume que no hay ninguna diferencia entre disponer del cuerpo enviándolo al crematorio o colocarlo en ataúd para llevarlo al tanatorio y realizar el entierro. si se opta por lo primero, las cenizas pueden ser objeto de manipulación sin que supongan ningún riesgo.(57) se recomienda que el trabajador de la salud conozca a través de la institución donde labora, los riesgos éticos, de salud y seguridad a que se expone por la atención en el paciente covid-19, evitando así conflictos e incertidumbres que afecten la atención. se recomienda que las instituciones prestadoras de salud a través de los líderes de atención médica, guíen y orienten a los trabajadores, para ofrecer una mejor atención médica y menor daño emocional durante la pandemia. se recomienda dar a conocer las directrices institucionales sobre el nivel de atención (uci vs. sala médica); inicio del tratamiento de soporte vital (incluyendo rcp y soporte de ventilación); retirada del tratamiento de soporte vital; y derivación a cuidados paliativos (centrados en la comodidad) en la atención médica de los pacientes durante la pandemia, esto genera una atención caracterizada por alivio del sufrimiento, no abandono, respeto a amci ® los derechos y preferencias de los pacientes, igualdad moral de las personas y la equidad en la distribución de riesgos y beneficios en la sociedad. el apoyo de la práctica ética es necesario integrarlo al cuidado de la salud y al bienestar de la fuerza laboral del cuidado en salud. reconociendo los desafíos especiales a que se enfrentan al responder al covid-19. esto forma parte del liderazgo en la atención médica y del servicio del deber cívico. berlinger n. el 29 de abril del 2020. en su artículo "respondiendo a covid-19 como un desafío regional de salud pública pautas preliminares para la colaboración regional que involucra hospitales". refiere que los trabajadores del equipo médico tienen el deber de conocer la gestión asistencial de los "desafíos éticos" previsibles durante la emergencia de salud pública (pandemia covid-19). que los desafíos éticos surgen cuando existe incertidumbre acerca de cómo "hacer lo correcto" es cuando los deberes o valores en los trabajadores entran en conflicto. estos desafíos afectan a la fuerza laboral (carga moral y emocional ante una decisión no prevista) en la atención médica. así como la operatividad en la atención médica (falta de epp y recursos que pueden limitar el buen desempeño por temor a infectarse).(59) los líderes de atención médica tienen el deber de guiar a los trabajadores de atención médica que experimentan condiciones laborales exigentes, mayor riesgo de daños ocupacionales, incertidumbre ética y angustia moral durante una emergencia de salud pública.(60) chih chen a, t. el 6 de abril del 2020. en su editorial ¿cómo deben prepararse los sistemas de salud para la evolución de la pandemia de covid-19? sugiere un apoyo emocional adecuado para el personal y horas razonables de exposición al riesgo para evitar el agotamiento, ya que los profesionales de la salud luchan por cuidar a los pacientes y proteger sus vidas y sus familias. se refiere que a medida que aumenta el número de casos, los médicos y los trabajadores de la salud en la primera línea deben reducir al mínimo su carga de trabajo clínico. las instituciones de atención médica deben reasignar al personal realizar tareas no clínicas, incluidos el papeleo y la recopilación de datos, tanto como sea posible. los hospitales deben tomarse su tiempo para capacitar al personal para implementar eficazmente las precauciones de contacto y los procesos de flujo. (61) jick j.l. el 5 de marzo del 2020. en relación con la obligación de planificar la atención médica, considera que: los líderes de atención médica tienen el deber de planificar la gestión de los desafíos éticos previsibles durante una emergencia de salud pública. la planificación de los desafíos éticos previsibles incluye la identificación de posibles decisiones de triage, herramientas y procesos. en una emergencia de salud pública que presenta una enfermedad respiratoria grave, es posible que se deban tomar decisiones de clasificación sobre el nivel de atención (uci vs. sala médica); inicio del tratamiento de soporte vital (incluyendo rcp y soporte de ventilación); retirada del tratamiento de soporte vital; y derivación a cuidados paliativos (centrados en la comodidad) si el tratamiento de soporte vital no se iniciará o se suspenderá. es posible que también se deban tomar decisiones de clasificación en relación con la escasez de personal, espacio y suministros. el deber de cuidado fundamental requiere fidelidad al paciente (no abandono como una obligación ética y legal), alivio del sufrimiento y respeto a los derechos y preferencias de los amci ® pacientes. el deber de cuidado y sus ramificaciones son el enfoque principal de la ética clínica, a través de los servicios de consulta de ética clínica a pie de cama, el desarrollo de políticas institucionales y la educación y capacitación en ética para los médicos. deberes de promover la igualdad moral de las personas y la equidad (justicia en relación con la necesidad) en la distribución de riesgos y beneficios en la sociedad. estos deberes generan deberes subsidiarios para promover la seguridad pública, proteger la salud de la comunidad y asignar de manera justa recursos limitados, entre otras actividades. estos deberes y sus ramificaciones son el foco principal de la ética de la salud pública. no se puede emitir una recomendación a favor o en contra acerca del uso de los medicamentos y dispositivos "prototipos" utilizados en el manejo del covid-19 denominados de uso compasivo o fuera de etiqueta, se considera sin embargo que no pueden ser utilizados por fuera de ensayos clínicos o protocolos institucionales estandarizados de evaluación del perfil de riesgo/beneficio y bajo la aplicación de consentimiento informado. se entiende como uso compasivo la utilización, en pacientes aislados y al margen de un ensayo clínico. dichos medicamentos experimentales no han sido aprobados aún por la fda, (64) y no se ha demostrado su seguridad y eficacia. es importante recordar que el medicamento médico puede tener efectos secundarios inesperados y graves, y que los pacientes deben considerar los posibles riesgos cuando procuran acceder a un producto médico experimental. hay que tener en cuenta que, para utilizar un medicamento bajo las condiciones de uso compasivo, se requerirá el consentimiento informado por escrito del paciente o de su representante legal, un informe clínico en el que el médico justifique la necesidad de dicho tratamiento. la regulación de la utilización de medicamentos por la vía del uso compasivo se ha realizado dentro de un texto legal sobre la realización de ensayos clínicos. una interpretación común del uso no indicado en la etiqueta y el uso compasivo de medicamentos es que, si el paciente murió, murió de la enfermedad, pero si el paciente sobrevivió, sobrevivió debido al medicamento administrado. recomendación se recomienda en la comunicación inicial con los familiares del paciente adulto con sospecha o diagnóstico de covid-19 críticamente enfermo incluir de forma clara y transparente los aspectos relacionados con el derecho al final de la vida que incluye: proporcionalidad en el tratamiento, adecuación del esfuerzo terapéutico, documento de voluntad anticipada, adecuación del esfuerzo terapéutico y la atención paliativa. situaciones estas que se pueden presentar durante la evolución hospitalaria y que requieren de una decisión conjunta entre el médico y el familiar del paciente. se recomienda dar una información específica, y adecuada a los familiares del paciente con sospecha o diagnóstico de covid-19, para que firmen el consentimiento informado, generando esta información confianza y comprensión en el familiar. la información del consentimiento que recibe el familiar debe constar dentro de la historia clínica. fundamento el ministerio de salud y protección social del 23 de marzo del 2020 a través del documento de "recomendaciones generales para la toma de decisiones éticas en los servicios de salud durante la pandemia covid-19". ante la posible circunstancia de pacientes sin capacidad para la toma de decisiones, por deterioro del estado general o requerimiento de aislamiento, en el cual no se puede contactar a su representante, conduzca la toma de decisiones teniendo en cuenta la prioridad de no hacer daño y la modificación en las condiciones de disponibilidad de los recursos en caso de presentarse deterioro. recuerde que esta situación debe preverse y debe ser informada a los representantes desde la admisión del paciente". durante toda la atención debe darse información sobre la posibilidad de que se presenten limitaciones de acceso a los soportes necesarios incluido al personal de salud , lo anterior puede limitar los derechos individuales o preferencias, esto debe ser informado al paciente y su familia, para que les permita entender que bajo la emergencia, puede presentarse una circunstancia que en condiciones habituales pudiera ser reversible de ser tratada pero en el contexto actual los recursos pueden verse trágicamente limitados, sin que esto implique abandono en el cuidado. el documento se refiere a la información que debe recibir el paciente o su familiar sustituto durante su evolución o fallecimiento. (65)la información durante la evolución también debe incluir: la información sobre el ejercicio de derechos al final de la vida incluyendo la adecuación de los esfuerzos terapéuticos y la suscripción de documentos de voluntad anticipada la consulta y revisión de existencia de este en todos los casos. se recomienda tener un consentimiento informado al ingreso hospitalario del paciente covid-19, se deben tener en cuenta las circunstancias del paciente al ingreso hospitalario, si la capacidad para la toma de decisiones está limitada por su estado clínico o incapacidad mental. de ser estas las circunstancias se dará la información al familiar en primera línea de consanguinidad quien asume por el paciente el consentimiento de la información (consentimiento sustituto). se recomienda tener el consentimiento informado en situaciones de excepción o urgencia ante la pandemia por covid-19, debe ser universal, en el que se informe el ingreso a la uci, o a cualquier otra área hospitalaria, realización de procedimientos, administración de tratamientos, posibles riesgos, beneficios durante su hospitalización. con esto se respeta el derecho a la autonomía personal en el paciente competente. en caso contrario el familiar tomará la información y asume el consentimiento a la información dada. es importante que el familiar esté informado de las decisiones que se vayan tomando durante la evolución hospitalaria (realización de procedimientos, inicios o cambios de tratamientos, movilización dentro del área hospitalaria. etc.) fuerte a favor fundamento el ministerio de salud y protección social, el 25 de marzo del 2020 ha elaborado un formato de "consentimiento informado para acompañante de casos probable/confirmado de covid-19". en que se expresa: "que de manera detallada se me ha suministrado información completa, suficiente, con un lenguaje sencillo y claro. el profesional de la salud me ha explicado la naturaleza de la enfermedad, acerca del significado de caso sospechoso o confirmado del coronavirus covid-19 en cuanto a su presentación clínica, modo de contagio, medidas para contenerla, posibilidad de sufrir la enfermedad, complicaciones o muerte, mientras permanezca como acompañante del paciente". este documento se firma al ingreso por el acompañante o familiar quien asume las decisiones durante su estancia hospitalaria. (67) el consentimiento informado en los pacientes covid-19 será un consentimiento sustituto para su ingreso a la uci y para los procedimientos que en la uci se realicen (colocación de tubo orotraqueal, diálisis, colocación de catéteres, reanimación cardiopulmonar, ecmo, etc.). previa información y autorización del familiar. en circunstancias normales el consentimiento debe ser firmado por el paciente quien en su autonomía acepta la información sobre su manejo y tratamiento. feld ad. recomendación se sugiere ante la pandemia del covid-19, si es posible, que el grupo de expertos en bioética y/o comité de ética institucional sean consultados y estén informados por el médico responsable para la orientación o consejo en la toma de directrices ante decisiones difíciles. se sugiere en lo posible que el médico tratante no asuma solo la responsabilidad moral de la decisión y que la decisión sea institucional y documentada en la historia clínica e informada a los familiares. en caso de no contar con un comité de bioética y/o ética hospitalaria el médico responsable podrá tomar la decisión fundamentada en principios éticos y derechos del paciente o convocar a una junta médica u otro comité relacionado con su dilema o consultar un apoyo externo en bioética. débil a favor fundamento el ministerio de salud y protección social. (65) el 23 de marzo del 2020 en el documento "recomendaciones generales para la toma de decisiones éticas en los servicios de salud durante la pandemia covid-19 establece: "que en caso de que la institución cuente con un comité de bioética y/o ética, con el servicio de bioética o ética clínica, o consultoría clínico-ética, se debe definir una ruta de consulta para los casos que de forma concreta puedan superar las recomendaciones generales. de igual forma establece que en las circunstancias actuales que se viven el actuar ético es parte integral del profesionalismo del cuidado. teniendo en cuenta que los profesionales de la medicina serán los llamados a tomar decisiones de alto estrés moral, al tener que adherirse y promover conductas concretas basados en las circunstancias que les rodean para dar o retirar tratamientos de las personas infectadas, quienes esperan confirmación del diagnóstico y de las personas que acuden a la atención en salud por razones diferentes a la infección por covid-19. partiendo de lo antes referenciado, se recomienda que las acciones emprendidas, busquen siempre poder responder a: a. no hacer daño b. beneficiar c. actuar con justicia sobre la persona en el contexto de la emergencia frente a la justicia sanitaria de la población d. mantener la integridad profesional" el comité de bioética y/o comité de ética institucional en tiempos normales o en tiempos de pandemia deberá mantener actualizadas las directrices de toma de decisiones. que apoyaran al médico responsable en la decisión. de no contar el médico con dicho comité o directrices institucionales y deba tomar una decisión que no permite interconsultar, deberá justificar en la historia clínica fundamentado en los principios éticos y derechos del paciente las razones que lo llevaron a tomar la decisión e informar y dialogar con los familiares del hecho. esto es importante que siempre quede documentado en la historia clínica la acción moral y ética de la decisión y el diálogo con la familia. en caso de que el médico responsable no cuente con un comité de bioética y/o comité de ética institucional, ni con el apoyo externo de expertos en bioética. y no quiera tomar la amci ® decisión a título personal podrá consultar a otro médico de la institución su decisión y entre ambos definir la acción a seguir. esta decisión conjunta debe ser documentada en la historia clínica e informada al grupo de trabajo y a los familiares como junta médica. si los familiares después de recibir la información no quedan satisfechos ellos tienen el derecho a la segunda opinión. los comités de bioética y/o comités de ética hospitalaria son entes administrativos, consultores, orientadores, asesores y consejeros de las situaciones que tienen que ver con el respeto y cumplimiento de los principios éticos, deberes y derechos de los pacientes, sus recomendaciones no son vinculantes, apoyan y orientan la decisión médica. aconsejando la mejor decisión ante una situación que genera un dilema moral o ético en el médico responsable. las decisiones médicas son tomadas por el consultor en bioética, quien es médico. los comités institucionales fuera de un comité de bioética y/o ética que podría dar apoyo al médico responsable y que serían otras instancias consultivas serian el comité de humanización, comité de historias clínicas, comité de bioseguridad, comité de infectología, comité de mortalidad hospitalaria, comité de paliativos o un comité de gerencia. pues todos los mencionados tiene que ver con el bienestar del paciente y la seguridad del médico ante una decisión. las decisiones especiales deben ser tomadas inicialmente a través de la realización de un comité (pueden ser los mencionados), en su defecto una junta médica. una vez se tenga la decisión esta debe ser consultada a la familia como una decisión institucional respaldada por el comité o junta médica realizada. se recomienda que todo ensayo clínico que se realice en la institución debe ser presentado, revisado y aceptado por un comité de investigación local o un comité de investigación externo nacional o internacional. se recomienda que todo paciente que se incluya en un ensayo clínico debe contar con un consentimiento informado el cual garantiza la aceptación voluntaria a participar y la comprensión de los objetivos, riesgos, beneficios, derechos y responsabilidades que tiene dentro de la investigación. se recomienda el consentimiento informado en todo ensayo clínico, el cual debe ser debe ser individual en tiempos de normalidad como en tiempos de pandemia por covid-19. solo el comité de ética en investigación podrá establecer en tiempos de normalidad o de pandemia las condiciones de dispensa o excepción al requisito de obtener el consentimiento informado. refiere que el consentimiento informado tiene sus raíces en el código de núremberg de 1947 y la declaración de helsinki de 1964 y ahora es un principio rector para la conducta en la investigación médica. en el consentimiento informado para investigaciones clínicas es claro que los participantes deben entender ampliamente los componentes del consentimiento. (69) thanh tam, n. et al. el 22 de enero 2015. mediante una revisión sistemática de pubmed, scopus y google scholar y revisando manualmente las listas de referencias para publicaciones hasta octubre de 2013. realizó un metaanálisis de los resultados del estudio utilizando un modelo de efectos aleatorios para tener en cuenta la heterogeneidad. evaluó la proporción de participantes en ensayos clínicos que entienden los diferentes componentes del consentimiento informado. encontrando que los participantes en ensayos clínicos deben comprender los componentes fundamentales del consentimiento informado como: la naturaleza y los beneficios del estudio, la libertad de retirarse en cualquier momento y la naturaleza voluntaria de la participación, así como la comprensión de otros componentes, como la aleatorización y el placebo. la proporción de participantes en ensayos clínicos que comprendieron diferentes componentes del consentimiento informado varió de 52.1% a 75.8%. esto asegura que la toma de decisiones de los participantes es significativa y que sus intereses están protegidos. (70) la red de américa latina y el caribe de cnb-unesco, (26 de marzo de 2020) que agrupa a las comisiones y consejos nacionales de bioética cuya finalidad es la de asesorar sobre los problemas éticos relativos a las ciencias de la vida y la salud humana expresa su preocupación ante la realización de investigaciones biomédicas en relación con la pandemia de enfermedad infecciosa por coronavirus covid-19. reconociendo lo siguiente en relación con el consentimiento informado: que la investigación con seres humanos durante las emergencias debe contar con garantías éticas mayores, no menores, que en las situaciones ordinarias. que en situación de excepción o emergencia los participantes deben seleccionarse en forma justa y proporcionar una justificación adecuada cuando se escogen o excluyen determinadas poblaciones, distribuyendo en forma equitativa las posibles cargas y beneficios de participar en esa investigación. "que se debe obtener el consentimiento informado individual de los participantes incluso en una situación de excepción o alarma, a menos que se cumplan las condiciones para la dispensa del consentimiento informado. las cuales el comité de revisión ética solo puede decidir dar la dispensa al requisito de obtener consentimiento informado: a) si no es factible obtenerlo; y si además los estudios: b) tienen un importante valor social y científico, c) solo suponen riesgos mínimos para los participantes, d) no implican agravio comparativo con otros grupos en situación o no de vulnerabilidad; y si e) se garantiza que no se privará a la población investigada de acceder en forma preferencial al beneficio derivado. de otorgarse un consentimiento informado amplio, éste debería ser única y exclusivamente para los procesos asociados con covid-19".(71) amci ® se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de covid-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( manejo de secreciones -tratamiento del dolor -tratamiento de la disnea -sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. fuerte a favor fundamento la sociedad española de anestesiología, reanimación y terapéutica del dolor en su documento: "marco ético pandemia covid-19" madrid, 20 de marzo de 2020 refiere: la sedación paliativa en pacientes hipóxicos con progresión de la enfermedad no subsidiaria de tratamiento debe considerarse como una expresión de buena práctica clínica y debe seguir las recomendaciones existentes. si se prevé un período agónico no corto, se debe proporcionar una transferencia a un entorno no intensivo.(71) se recomienda la utilización de guías establecidas previamente a la pandemia por el ministerio de salud y sociedades científicas para orientar las decisiones que se tomen al final de la vida en pacientes con sospecha o diagnóstico de covid-19. estas guías deben ser divulgadas al equipo de atención y aplicadas en los pacientes en casos de: adecuación del esfuerzo terapéutico (aet), orden de no reanimar (onr), consentimiento sustituto, voluntades anticipadas, cuidados paliativos. se recomienda fundamentar las decisiones del final de la vida individualizadas a cada paciente y a cada situación sin llegar a tomar decisiones apresuradas sin fundamento científico o ético, solicitando de ser posible una valoración por medicina paliativa para el manejo de síntomas. se recomienda indagar durante la hospitalización de todo paciente con sospecha o diagnóstico de covid-19, si en tiempos de salud hizo válida su autonomía y realizó un documento de voluntad anticipada, teniendo en cuenta que esta será equivalente al consentimiento informado. amci ® terapéuticos y la suscripción de documentos de voluntad anticipada.(72) el inicio de sedación paliativa con reubicación del pacientede ser necesario el des escalonamiento por deterioro clínico. en situación de pandemia covid-19 cuando se refiere a situaciones del final de la vida se relaciona a la adecuación del esfuerzo terapéutico, la sedación paliativa la cual será la maniobra terapéutica que se utilizará en pacientes no recuperables y que no son candidatos a cuidados intensivos por covid-19,(73) que evolucionan desfavorablemente y tienen mal pronóstico a corto plazo, así como la disnea refractaria y la limitación del esfuerzo terapéutico. el delirium o síndrome confusional por fallo cerebral agudo, es un problema habitual en situaciones de alteración orgánica severa, y ha sido descrito como uno de los síntomas neurológicos presente en los pacientes que sufren infección por el covid-19(74). wilson c. 24 de abril del 2020. en su artículo "la crisis golpea al final de la vida" se refiere a que el brote de coronavirus está obligando a las personas a enfrentar dilemas en torno a la cantidad de atención médica que se debe brindar al final de la vida y apresurar decisiones controvertidas sobre rechazar ciertos tratamientos. dicen los expertos que esto ha alentado a más personas a tomar decisiones de tratamiento anticipadas relacionadas con la rcp y la ventilación,(75) haesen s. el 16 de mayo de 2018. en su artículo "dirigir a los ciudadanos a crear directivas anticipadas" las voluntades o directrices anticipadas son para las personas que quieran asumir plenamente su papel de ciudadanos responsables tomando decisiones proactivas. la decisión de redactar directivas anticipadas marca un cambio del enfoque actual de "aceptación" a un escenario de "exclusión voluntaria".(76)al emitir una directiva de tratamiento anticipado, una persona autónoma puede expresar formalmente qué tipo de tratamiento desea y no desea recibir en caso de que se enferme o se lastime y no pueda decidir de manera autónoma sobre su tratamiento. (77) ministerio de salud y protección social en su documento de voluntades anticipadas que es el documento en el que toda persona capaz, sana o en estado de enfermedad, en pleno uso de sus facultades legales y mentales y como previsión de no poder tomar decisiones en el futuro, declara, de forma libre, consciente e informada su voluntad sobre las preferencias al final de la vida que sean relevantes para su marco de valores personales.(72) se recomienda que el paciente crítico con covid-19 que no es candidato para ingresar o continuar recibiendo cuidados intensivos y que presente deterioro rápido con mal pronóstico a corto plazo, se le brinde una adecuación del esfuerzo terapéutico orientada a acompañamiento al final de la vida, alivio del sufrimiento y control de síntomas. dependiendo de la disponibilidad de recursos se sugiere dentro del plan de atención hospitalaria contar con un área destinada a la atención del final de vida con el recurso físico, humano y de procesos necesario. marzo 13 del 2020. refiere: en situación de adecuación terapéutica, retirada de medidas y/o mala evolución es adecuado derivar al paciente a un área de menor complejidad para establecer el plan de cuidados paliativos. consultar al servicio de cuidados paliativos para procurar la continuidad de cuidados de los pacientes en los que se haya acordado la limitación de tratamientos y aliviar su sufrimiento, incluyendo la sedación paliativa en los casos en los que sea precisa.(71) schmidhauser tf. el 8 de abril 2020. considera en su publicación que: los cuidados paliativos durante la pandemia de covid-19 deben adaptarse a un estilo de" cuidados paliativos de emergencia" ya que los pacientes pueden deteriorarse rápidamente y requieren decisiones rápidas y planes de tratamiento claros. estos deben ser seguidos fácilmente por los miembros del personal de salud que atienden a estos pacientes. además, los cuidados paliativos deben estar a la vanguardia para ayudar a tomar las mejores decisiones, atender a las familias y ofrecer apoyo espiritual.(71) se recomienda como estrategia de protección personal en las unidades de cuidado intensivo sin presión negativa y cubículos abiertos utilizar de forma continua el respirador n95 o fpp2, adicional a otros elementos de protección para prevención del contagio por covid-19. la atención segura en áreas crítica para todas las modalidades de atención se fortalece a través de las medidas de precauciones estándar en el manejo de todos los pacientes, establecidos en el "manual de medidas básicas para control de infecciones en prestador servicios de salud" ley 9 de 1979, por la cual se dictan medidas sanitarias. resolución 4445 de 1996, numeral 3 y numeral 4.3 epp. el respirador, n95 o fpp2, puede utilizarse de manera continua por 8 a 12 horas, o desecharlo antes si está visiblemente contaminada o si está húmeda. luego de colocar la n95 se debe verificar prueba de ajuste antes de ingresar a la unidad para atención de pacientes con covid-19 de la siguiente manera: mascarillas sin válvula de exhalación: cubra la totalidad de la mascarilla con ambas manos y exhale con fuerza. si nota fugas de aire por sus bordes, reajuste la posición del respirador. mascarillas con válvula de exhalación: cubra el respirador con ambas manos e inhale con energía. deberá sentir una presión negativa dentro de la mascarilla. si detecta alguna pérdida de presión o entrada de aire, reajuste la posición del respirador. no se puede emitir una recomendación a favor o en contra acerca de la efectividad de bioseguridad del uso extendido, continuo o intermitente de los respiradores n95 ó ffp2. sin embargo, se considera que puede ser una alternativa, bajo la adopción de un protocolo riguroso, cuando se debe optimizar el uso de los epp en el contexto de un acceso limitado. el reúso no está permitido en colombia. la duración máxima del uso continuo de la n95 es de 8 a 12 horas, siguiendo las recomendaciones del manual de medidas básicas para control de infecciones en ips de minsalud. pero en la vida real, ningún trabajador tolera 8 a 12 horas continuas con un respirador. por esto, su uso continuo en el sitio de trabajo dependerá de la necesidad de pausar para comer, para ir al baño, etc. en este caso, se guardará en una bolsa de papel para su nueva colocación, si tiene menos de 12 horas, o desechará si está visiblemente contaminada o se torna húmeda. el reúso de la n95 dependerá de la casa del fabricante, de si contiene o no celulosa en su estructura del respirador. por ejemplo, la recomendación de desinfección para los respiradores sin celulosa es con peróxido de hidrógeno vaporizado al 58% por 28 minutos (tabla 9 y 10). los respiradores n95 de uso industrial tienen mayor contenido de celulosa que los de uso médico por lo tanto para procesos de esterilización, solo los n95 de uso médico podrán ser esterilizados mediante de peróxido de hidrógeno vaporizado (sterrad®) (84-88) 22. ¿existe superioridad en términos de protección personal para el personal sanitario y de apoyo dentro de las unidades de cuidados intensivos con la utilización del overol frente a la bata manga larga con antifluido durante la atención del paciente con covid-19? no se puede emitir una recomendación a favor o en contra si los overoles ofrecen mayor protección por cobertura corporal frente a otros elementos como vestidos largos, batas y delantales. resulta intuitivo que su uso genera una mayor protección en especial en servicios cohortizados. sin embargo, su uso está asociado con una mayor dificultad para su colocación y retiro, lo que puede potencializar el contagio del usuario, la utilización debe hacerse bajo un protocolo supervisado y chequeado. las batas modificadas para ajustarse firmemente en el cuello pueden reducir la contaminación. en estudios ya descritos el uso de un respirador eléctrico purificador de aire con overol puede proteger contra el riesgo de contaminación mejor que una máscara n95 y una bata con un rr: 0.27, intervalo de confianza (ic) del 95%: 0.17 a 0.43 pero fue más difícil su retiro con rr 7.5, ic del 95% 1.81 a 31.1. en un eca (59 participantes), las personas con una bata larga tenían menos contaminación que aquellas con un overol. las batas pueden proteger mejor contra la contaminación que los delantales.(89-92) los epp como batas y overoles deberían estar hechos de un material que cumpla con los requisitos mínimos de la asociación americana de químicos textiles:  tipo a: buena repelencia al agua, resistente a la penetración, pero mala permeabilidad al aire.  tipo b: buena repelencia al agua, buena permeabilidad al aire, pero poca resistencia a la penetración del agua.  tipo c: bata quirúrgica que tiene poca repelencia al agua y resistencia a la penetración de agua.  tipo d: hecho de fibras de polietileno de alta densidad, tela no tejida (tyvek®), tiene buena repelencia y resistencia al agua, mala permeabilidad al aire. no se puede emitir una recomendación a favor o en contra para el uso de respiradores elastoméricos como elementos de protección personal dentro de las unidades de cuidados amci ® intensivos. no hay evidencia que soporte la superioridad de los respiradores elastoméricos frente a los n95, son más costosos, difíciles de utilizar y pueden implicar algún riesgo para el paciente. por tanto, su uso sólo debería considerarse frente a un desabastecimiento de los n95 y bajo la adopción de un protocolo institucional riguroso y bajo chequeo. los respiradores elastoméricos son respiradores ajustados a media cara o cara completa, esta última otorga protección ocular. su filtración está determinada por el filtro que se utilice, estos van desde partículas de nivel n95 a p100. están hechos de material sintético o de goma que les permite desinfectarse, limpiarse y reutilizarse repetidamente. están equipados con cartuchos de filtro reemplazables. al igual que los respiradores n95, los respiradores elastoméricos requiere entrenamiento adecuado para su correcta colocación y retiro. por eso es muy importante revisar el manual del usuario antes de su uso. los respiradores elastoméricos no deberían utilizarse en entornos quirúrgicos, debido al riesgo potencial de contaminación del campo quirúrgico, con el aire que sale de la válvula de exhalación. como recomendación de buena práctica, aprobado por la fda, debe colocarse una máscara quirúrgica encima de la válvula de exhalación para evitar este riesgo. solo se debe permitir el uso del respirador elastoméricos por clínica para evitar infecciones cruzadas, esto permitirá una protección esencial contra agentes infecciosos y la auto contaminación. aunque los cartuchos de filtro son finalmente desechables, están destinados a ser reutilizados hasta que ya no se puede respirar o se vuelven visiblemente sucio. generalmente se recomienda, en la mayoría de los casos, hacer recambios cada 30 días. deben tener procedimientos de limpieza/desinfección actualizados y aprobados por su manufacturador.(78, 93-110) recomendación se recomienda realizar la limpieza y desinfección de equipos biomédicos y de superficies las veces que sean necesarias y en el momento de egreso del paciente siguiendo los protocolos de cada institución. el desinfectante para este proceso debe ser de nivel intermedio o alto para superficies y equipos biomédicos y cumplir con las recomendaciones del fabricante según lo aprobado en el registro sanitario. fuerte a favor fundamento para la desinfección de las superficies ambientales hospitalarias y domiciliarias, la oms recomienda emplear un desinfectante que sea efectivo contra virus cubiertos (el coronavirus pertenece a esta categoría), específicamente, recomienda emplear alcohol etílico para la desinfección de algunos equipos biomédicos reusables (p. ej.: termómetros) y para las superficies, el hipoclorito de sodio o precursores de sodio como el dicloroisocianurato de sodio (nadcc) que tiene la ventaja de la estabilidad, la facilidad en la dilución y que no es corrosivo.(87) (tabla 11). page se recomienda que el ingreso de un paciente a uci debe hacerse bajo un procedimiento estandarizado que incluya la coordinación y comunicación de los servicios vinculados, adecuación de la unidad de atención a las necesidades del paciente y la garantía de la bioseguridad del equipo multidisciplinario. se recomienda que cada institución establezca en sus procesos prioritarios el circuito del traslado que incluye el itinerario del traslado, el uso de ascensor, el número y la organización de los intervinientes sanitarios y no sanitarios (celadores, seguridad, limpieza), las medidas de protección empleadas por los mismos (epp, limpieza) y los recursos materiales necesarios durante el traslado. el traslado de pacientes con casos sospechosos o confirmados de covid-19 se puede presentar entre servicios a nivel hospitalario o entre instituciones con diferentes niveles de atención y deben tenerse las precauciones universales de un traslado seguro. una posición responsable es evitar el traslado de estos pacientes el máximo posible, a menos que sea imprescindible, teniendo en cuenta el riesgo/beneficio. considerar evitar traslados interinstitucionales solo por temas administrativos. el personal sanitario que realice el traslado debe contar con todos los epp, considerando este traslado como de alto riesgo de transmisión vírica. se debe utilizar mascarilla quirúrgica o n-95, de acuerdo con el riesgo amci ® de aerosolización. hasta que la rt-pcr para sars-cov-2 este negativo se podrían retomar las prácticas habituales de traslado de los pacientes . (111) (112) (113) capítulo 2. abordaje diagnóstico y covid-19 se recomienda en pacientes con diagnóstico o sospecha de infección por sars-cov-2 clasificar la enfermedad en leve, severo o paciente crítico, teniendo en cuenta los criterios de la clasificación por las fases y estadios de la enfermedad. se recomienda en pacientes con diagnóstico o sospecha de infección por sars-cov-2, clasificados como críticos y que requieren de intubación orotraqueal realizar la clasificación por fenotipos (1 o 2), con el fin de proyectar una estrategia de ventilación mecánica. el covid-19, es una enfermedad con una presentación clínica diversa, desde formas leves hasta presentaciones graves que incluyen el sdra, la mediana del período de incubación desde la exposición hasta el inicio de los síntomas es de aproximadamente 4 a 5 días, y el 97.5% de los pacientes sintomáticos tendrán síntomas dentro de los 11.5 días después de la infección (114) , que incluye fiebre, tos, disfagia, malestar general, mialgias, anorexia, náuseas, diarrea, anosmia y ageusia; la disnea se presentó entre los 5 y 13 días (115) y puede representar progresión a covid-19 severo, que se manifiesta con hipoxemia, disfunción orgánica múltiple, documentación de arritmias cardíacas, rabdomiólisis, coagulopatía y choque (116) . dentro del espectro de enfermedad, siddiki et al, proponen un enfoque estructurado por fases expresados en tres estadios (historia natural de la enfermedad), siendo el primero donde la patogenicidad viral es dominante, se incluye el periodo de incubación, síntomas leves, con multiplicación del sars-cov-2 centrándose principalmente en el sistema respiratorio gracias a la unión del virus con el receptor de la enzima convertidora de angiotensina 2 (ace2), el hemograma puede revelar linfopenia y neutrofilia sin otras anormalidades significativas. el estadio 2 es la enfermedad pulmonar establecida, neumonía viral, tos, fiebre con progresión en algunos casos a hipoxia con trastorno de los índices de oxigenación (pao2/fio2 menor 300 mmhg), hallazgos en imágenes de tórax (radiografía y/o tomografía) de infiltrados alveolares o vidrio esmerilado, mayor linfopenia y elevación de transaminasas (2a: sin hipoxemia, 2b: con hipoxemia). el estadio 3 o fase de híper inflamación sistémica extrapulmonar se caracteriza por elevación de biomarcadores inflamatorios y estado protrombótico (il -2, il-6, il-7, ftn -α, proteína c reactiva, ferritina y el dímero d), con presencia en las formas más graves de disfunción orgánica múltiple, lesión miocárdica (troponina y péptido natriurético de tipo b elevados), con fenómenos trombóticos, progresión a sdra y choque (117) . amci ® la neumonía por sars-cov-2, se característica por disociación entre la severidad de la hipoxemia y el mantenimiento relativamente bueno de la mecánica respiratoria, con compliance del sistema respiratorio en promedio de 50 ml / cmh2o; gattinoni, marini et al, proponen dos fenotipos de presentación de la insuficiencia respiratoria; el primero (tipo 1) con una mecánica pulmonar adecuada, con baja probabilidad de reclutabilidad y con hipoxemia, relacionado al desbalance entre la perfusión y la ventilación; el segundo (tipo 2) más acorde a las definiciones de sdra (csdra "covid-19 patient with sdra"), con una compliance pulmonar baja y reclutabilidad potencial(118, 119) (120). se propone la siguiente clasificación clínica del covid-19. (121, 122 , y pacientes críticos de 5%, con tasa global de mortalidad de 2,3%, siendo mayor entre los pacientes de 70 a 79 años con 8% y entre los mayores de 80 años con 14.8%, dentro del grupo de pacientes clasificado como crítico la mortalidad descrita fue del 49%(121). recomendación se recomienda en cuidado intensivo, realizar el diagnóstico de covid-19 del paciente sospechoso por medio de rt-pcr conociendo su alta especificidad, su variabilidad en relación con el tiempo y pérdida de rendimiento diagnóstico luego de la primera semana de inicio de los síntomas. se recomienda tomar la primera muestra para rt-pcr de hisopo nasofaríngeo o de cornete medio sobre hisopado oro faríngeo o de saliva, de ser negativo se puede repetir la prueba de 24 a 48 horas preferiblemente de tracto respiratorio inferior, esputo no inducido o en aspirado traqueal en paciente intubado. se recomienda el uso conjunto de rt-pcr e igm por elisa en pacientes con sospecha de covid-19, primera rt-pcr negativa, que se encuentren entre la segunda y tercera semana desde el inicio de los síntomas, con el objetivo de mejorar la sensibilidad en la identificación de infección por sars-cov-2. en cuidado intensivo, el diagnóstico de covid-19 se fundamenta con base en la presentación clínica compatible y factores epidemiológicos asociados con probabilidad de infección; el diagnóstico definitivo se realiza con pruebas de amplificación de ácido nucleico del virus (naat), la detección del genoma viral del sars-cov-2 se realiza por medio de reacción en cadena de la polimerasa por transcriptasa reversa (rt-pcr) dado a su especificidad del 100% (123, 124) ; por lo cual todo paciente que cumple con la definición de caso sospechoso se le debe realizar rt-pcr, sars-cov-2 independientemente de si se encuentra otro patógeno respiratorio (124) . las muestras para el diagnóstico por rt pcr se recolecta de las vías respiratorias superiores, nasofaringe, cornete medio u orofaringe; todos con alta especificidad. sin embargo, se sugiere recolectar los hisopos nasofaríngeos o de cornete medio por tener mayor sensibilidad (125 (17/34) . en pacientes con neumonía severa a quienes se le realizó lavado broncoalveolar (bal) y rt-pcr entre los días 8 y 14 el 100% de las muestras fueron positivos, en pacientes no intubados con esputo no inducido el 83% de las muestras fueron positivas (126, 127). wang et al, en un estudio de 205 pacientes con covid-19, las rt-pcr con tasas positivas más altas fue en muestras extraídas por bal (95%; 14 de 15 muestras) y esputo 72% (72 de 104 muestras) (128) . para la detección del sars-cov-2 por rt-pcr en pacientes en cuidado intensivo, teniendo en cuenta la rigurosidad de aspectos de bioseguridad y aerosolización, se debe tomar la primera muestras en nasofaringe o cornete medio, si esta prueba es negativa se puede repetir en 24 a 48 horas, si este es el caso o existe más de 8 días desde el inicio de los síntomas se prefiere una muestra del tracto respiratorio inferior, por esputo no inducido por personal de salud o por aspirado traqueal en pacientes intubados (126, 129), aunque el rendimiento diagnóstico del bal es alto por lo general, se debe evitar la broncoscopia para minimizar la exposición de los trabajadores de la salud (130) . la probabilidad de detección del arn de sars-cov-2 puede variar según la fase de la enfermedad, si bien una rt-pcr positiva confirma el diagnóstico de covid-19, los reportes falsos negativos y la sensibilidad se ve influenciado por el tiempo desde la exposición e inicio de síntomas. kucirka et al, en un análisis de siete estudios evaluaron el rendimiento diagnóstico de la rt-pcr en relación con el tiempo desde el inicio de los síntomas o la exposición, con resultados expresados en tasa estimada de falsos negativos, siendo del 100% el día de la exposición, del 38% el día 5 (estimado como primer día de síntomas, ic: 18% a 65%), 20% en el día 8 (día 3 desde el inicio de síntomas, ic: 12% a 30%) luego comenzó a aumentar nuevamente de 21% en el día 9 (ic: 13 a 31%) a 66% en el día 21 (ic: 54 a 77%) (131) . la precisión y los valores predictivos de rt-pcr para sars-cov-2 no se han evaluado sistemáticamente, la sensibilidad de las pruebas moleculares está influenciada por múltiples factores como sitio y calidad de la muestra, técnica de procesamiento; probablemente las menores tasas de falsos negativos (sensibilidad entre 65 y 80%) está entre el día 3 y 10 luego de inicio de los síntomas (131) . a partir de aquí el rendimiento diagnóstico disminuye, por lo tanto, es importante que el intensivista valore estas consideraciones en el momento de tomar conductas, en cuanto tipo de aislamiento, tratamiento y pronóstico. amci ® las pruebas serológicas detectan anticuerpos contra el sars-cov-2 y ayudan a identificar pacientes que han tenido la enfermedad y algunos con la enfermedad activa, la seroconversión se ha descrito entre el día 13 y 21, sin embargo, hay incertidumbre en la incidencia de la seroconversión (132) . estas pruebas se usan principalmente en tamizaje poblacional y estudios de seroprevalencia; en cuidado intensivo el análisis de la igm por elisa contribuye a la detección de pacientes con infección reciente, además con el análisis conjunto con la igg se clasifica el estado de infección en agudo o convaleciente. las pruebas serológicas se realizan por diferentes técnicas como la inmunocromatográfica de flujo lateral, la inmunofluorescencia indirecta (ifi) y el ensayo de inmunoadsorción ligado a enzima (elisa) (133, 134) . las pruebas serológicas no deben usarse como la única prueba para diagnosticar o excluir la infección activa por sars-cov-2. la sensibilidad y la especificidad de muchas de estas pruebas serológicas son inciertas, así como su valor predictivo positivo. los anticuerpos detectables generalmente tardan varios días en desarrollarse. guo et al, documenta niveles de anticuerpos por elisa, con una mediana de detección de anticuerpos igm e iga de 5 días (iqr, 3-6) y de igg de 14 días (iqr, 10-18) después del inicio de los síntomas, con una probabilidad de resultados positivos de 85.4%, 92.7% y 77.9 % respectivamente; es probable que el rendimiento diagnóstico de igm por elisa sea mayor que la de rt-pcr después del quinto día luego de inicio de síntomas; cuando se combinan estas técnicas (elisa igm con rt-pcr) la tasa de detección positiva es del 98.6% (135) . zaho et al, en un estudio de 173 pacientes con covid-19, donde el 18,5% estaba en condición crítica, la mediana del tiempo desde el inicio de los síntomas hasta la detección de anticuerpos (técnica elisa) fue de 12 días para igm y 14 días para igg; dentro de los primeros 7 días desde el inicio de los síntomas solo el 38.3% tenía anticuerpos detectables, entre los días 8 a 14 la sensibilidad de igm fue 73.3% e igg de 54.1%, luego de los 15 días la sensibilidad igm e igg fue de 94.3% y 79.8% respectivamente; el uso combinado de rt-pcr y elisa igm presentó una sensibilidad del 78% entre los días 1 a 7 y del 97% entre los días 8 a 14. (136) la rt-pcr tiene especificidad del 100%, con adecuado rendimiento diagnóstico entre los días 3 y 10 luego del inicio de los síntomas con sensibilidad que varía entre el 65 y 80%, con presencia ascendente de falsos negativos luego del día 9, por lo cual el diagnóstico debe tener consistencias epidemiológicas y clínicas (síntomas y hallazgos radiológicos compatibles con covid-19) donde una rt pcr negativa no excluye la enfermedad; la precisión y el tiempo para la detección de anticuerpos varían con la técnica utilizada, su uso es limitado en cuidado intensivo, sin embargo su identificación por técnica elisa en conjunto con rt-pcr mejora la sensibilidad y la probabilidad de falsos negativos, especialmente entre los días 3 y 14 desde el inicio de síntomas. faltan estudios que evalúen el rendimiento diagnóstico de las diferentes pruebas. amci ® se recomienda la medición de marcadores de severidad al ingreso a uci del paciente críticamente enfermo por covid-19 (hemograma, transaminasas, ldh, ferritina, troponina, dímero d y pcr) los cuales se han asociado con peor pronóstico en la enfermedad por covid-19, logrando ofrecer intervenciones más tempranas. se recomienda no utilizar una periodicidad de rutina para la medición de seguimiento de biomarcadores de severidad en el paciente con sospecha o diagnóstico de covid-19. en un estudio cohorte retrospectivo que evaluó 140 pacientes diagnosticados con covid-19 desde el 18 de enero de 2020 hasta el 12 de marzo de 2020, fang liu y colaboradores encontraron correlación en la elevación de il-6 y pcr con la gravedad clínica, lo que sugiere podrían usarse como factores independientes para predecir la severidad del cuadro, los pacientes con il-6> 32.1 pg./ml o pcr> 41.8 mg/l tenían más probabilidades de tener complicaciones graves (137) , así mismo en otro estudio multicéntrico retrospectivo de 150 pacientes infectados se identificó resultados de laboratorio con diferencias significativas con elevación de glóbulos blancos, valores absolutos de linfocitos, plaquetas, albúmina, bilirrubinas, función renal, transaminasas, troponina, proteína c reactiva e interleucina (il 6) en el grupo con desenlace de mortalidad contra los dados de alta (138) . entre otros marcadores la troponina como lesión cardiaca (elevación de troponina por encima del percentil 99 límite de referencia superior) se ha reportado en 7% a 23% de los pacientes con covid-19 en wuhan, china, en dos estudios retrospectivos por xiabo yang y colaboradores (37, 139) . en una revisión sistemática de mayo 2020, kermali m. y colaboradores exponen que existe evidencia a favor de los valores bajos de linfocitos y plaquetas y valores elevados de los biomarcadores il-6, pcr, troponina, ldh, ferritina, proteína amiloidea a y dímero d, pueden relacionarse con la gravedad de la infección por covid-19 y su fuerte asociación con la mortalidad (140) . estos resultados pueden usarse como un complemento en la práctica clínica para guiar a los médicos a identificar pacientes con mal pronóstico y la rápida implementación de medidas de soporte, monitorización y reanimación en la evolución de los pacientes críticos en la unidad de cuidados intensivos. solo en 1 estudio, karmali et al, en 2002, determinan en promedio entre 48 a 72 horas, la periodicidad en el seguimiento de estos, sin embargo, no se discrimina entre pacientes críticos y no críticos. consideramos que el seguimiento de estas pruebas debe estar ajustado al juicio clínico del médico intensivista tratante, según la evolución de los pacientes. se muestran el comportamiento de los biomarcadores mas frecuentes en la tabla 12. tabla 11. biomarcadores en pacientes críticos con sospecha o diagnóstico de covid-19. tendencia de biomarcador en relación con la gravedad covid-19 pcr aumentada recomendación se recomienda la no medición de marcadores de inflamación o de severidad de forma rutinaria solo con el objetivo de iniciar un tratamiento específico o algoritmos terapéuticos en la enfermedad por covid-19 en pacientes críticos. el síndrome de liberación de citocinas o denominado "tormenta de citocinas" parece asociarse en pacientes con afecciones graves por covid-19. la citocina proinflamatoria il-6 es la citocina mejor documentada en covid-19 correlacionada con la gravedad, el estado crítico del paciente, la carga viral y el pronóstico (138, 141, 142) . se han descrito mayores niveles de citoquinas proinflamatorias (il-2, il-6, il-7, factor estimulante de colonias de granulocitos, factor de necrosis tumoral e interferón gamma) asociadas a compromiso pulmonar severo en pacientes con infección por coronavirus, determinado por la rápida replicación del virus, infiltración masiva de células inflamatorias y trastorno severo de la inflamación (143, 144) . igualmente, está asociada la presencia de linfopenia como biomarcador de mal pronóstico para covid-19 (145) . hallazgos similares se encontraron en la pandemia de influenza a (h1n1) de 2009 sin ser especificó su valor (146) . las manifestaciones clínicas de la tormenta de citocinas incluyen síndrome de respuesta inflamatoria sistémica, hipotensión, síndrome de fuga capilar, insuficiencia renal, sdra, miocarditis, entre otras (116) , algunos autores han determinado este cuadro como un síndrome de linfohistiocitosis hemofagocitica secundaria. es razonable pensar que, en pacientes con sospecha de tormenta de citocinas basado en los hallazgos de laboratorio, el manejo con inmunomoduladores puede resultar beneficioso, sin embargo, los resultados del manejo de la hiperinflación basado en pruebas diagnósticas han tenido resultados encontrados en pacientes con covid-19. el uso de esteroides, inmunoglobulina endovenosa, inhibidores del receptor de citoquinas (tocilizumab) o inhibidores de janus kinasa, han disminuido los valores de los biomarcadores, días de hospitalización (147) o necesidad de fracciones elevadas de oxígeno (148) , sin embargo no han demostrado beneficio sobre la mortalidad y en algunos casos, si un aumento en la incidencia de infecciones bacterianas o fúngicas sobreagregadas (116) . se recomienda realizar radiografía simple de tórax para todos los pacientes con sospecha o diagnóstico de covid-19 en uci. se recomienda realizar tac de tórax según disponibilidad de tecnología institucional, ante la incertidumbre diagnostica, teniendo en cuenta las condiciones clínicas, la tolerancia del paciente al traslado y los protocolos administrativos de seguridad. fuerte a favor fundamento se reconoce como el gold estándar diagnóstico de infección pulmonar por covid-19 a los estudios moleculares, sin embargo, estos presentan limitaciones: a) contaminación de las muestras b) errores en la técnica de la toma, c) muestra insuficiente para ampliación genética favoreciendo falsos negativos d) demora de reporte de los resultados. por lo anterior, se recomienda imágenes diagnósticas en la aproximación de paciente con sospechas de infección pulmonar por covid-19 (149, 150) .  radiografía simple de tórax: ventajas: mayor accesibilidad que la tac de tórax y realización de la prueba a la cabecera del enfermo desventaja: baja sensibilidad en estadio temprano, después del día 9 de inicio de los síntomas presenta aumento en el rendimiento diagnóstico  tac de tórax: ventaja: es ampliamente recomendada. alta sensibilidad en estadios tempranos. permite describir extensión, distribución, localización, densidades parenquimatosas, aplicables en clasificaciones y puntajes diagnósticos, pronósticos y de seguimiento en permanente evolución y mejoría. algunas asociaciones referentes como asociación china de radiología, en su recomendación de expertos propone clasificación tomografía en 4 estadios 1 temprana 2 avanzada 3 severo 4 disipación desventaja: traslado del paciente hasta el tomógrafo (no todos los enfermos toleran el transporte) y tecnología no disponible en todos los niveles de atención page no se puede emitir una recomendación a favor o en contra para el uso de ecografía pulmonar a la cabecera del paciente crítico como herramienta diagnóstica o de pronóstico en con covid-19. se puede considerar como una alternativa para la valoración imagenológica pulmonar en el paciente crítico con covid-19 cuando las condiciones del paciente no permitan su traslado. no se sugiere la utilización de la ecografía pulmonar para el seguimiento de lesiones pulmonares agudas en el enfoque del paciente crítico con covid-19. puede utilizarse para determinar complicaciones asociadas a la enfermedad o en la inserción de dispositivos invasivos. en general los estudios de imágenes no representan un papel concluyente para el diagnóstico de covid-19. la ultrasonografía en específico requiere estudios de validación, un programa de entrenamiento es operador dependiente, y se le atribuido limitaciones en la capacidad de discriminación en la cronicidad de las lesiones pulmonares. la ultrasonografía pulmonar puede servir como herramienta a la cabecera del paciente para mejorar la evaluación del compromiso pulmonar y reducir el uso de radiografías de tórax y tomografía computarizada (151) , sin embargo no debe usarse para el diagnóstico inicial, pues éste se compone de criterios clínicos, radiográficos y microbiológicos que actualmente son el estándar de oro; la ecografía no los reemplaza debido a la baja especificidad en relación con el virus, se sugiere su uso como complemento en la valoración diaria del paciente, ojalá realizada por el mismo observador. la ecografía pulmonar es altamente sensible y puede revisar de forma rápida y precisa la condición pulmonar, creando un potencial para evaluar los cambios o la resolución con el tiempo, especialmente en la uci, escenario en el que cada vez se usa más para la detección de múltiples patologías pulmonares que se pueden demostrar junto con covid-19, sin embargo, hasta la fecha no hay hallazgos específicos, ni patognomónicos que se relacionen con covid-19 en el examen ecográfico del paciente (152) . la adopción de ultrasonido pulmonar puede reducir la necesidad de exposición a la radiación ionizante y, a su vez, reducir la cantidad de radiografías necesarias para la evaluación rutinaria del paciente, disminuyendo también la exposición de personal asistencial adicional como el uso de elementos de protección personal (153) . es bien conocido el beneficio de la ecografía durante y después de la colocación de accesos venosos centrales para establecer la presencia o no de complicaciones inmediatas como neumotórax. a la fecha no hay publicaciones acerca de la utilidad del ultrasonido como herramienta para establecer pronóstico. se necesitan más estudios para evaluar la utilidad de la ecografía pulmonar en el diagnóstico y manejo de covid-19 (153) . se recomienda no establecer un punto de corte en el valor de dímero d para el inicio rutinario de anticoagulación plena en el contexto de infección por covid-19. se recomienda la administración de profilaxis antitrombótica según protocolo institucional independiente de niveles de dímero d en el paciente críticamente enfermo por covid-19. los fenómenos inflamatorios inherentes a procesos infecciosos son considerados desde décadas previas, factores protrombóticos, no siendo una excepción la infección por covid-19. en algunas publicaciones se hallan asociaciones con desenlaces cardiovasculares negativos (154) y sugieren asociación entre niveles elevados de dímero d ( marcador de estado de trombosis ) y riesgo de embolismo pulmonar con or crecientes or de 1.7 a los 3 días hasta 2.4 a los 9 días de seguimiento (155) . de igual manera, zhou et al, reportan asociación de dímero d mayor a 1 mcg/ml y mortalidad (37) sin embargo los estudios presentan limitaciones en su diseño, a pesar de ello algunos autores proponen anticoagulación como factor de protección en mortalidad sin precisar precisión en la dosis, tipo de heparina y selección de enfermos (156) . finalmente la european heart journal en su entrega de farmacología cardiovascular desarrolla una propuesta en la cual combina un puntaje previo de riesgo de cid en uci a niveles de fibrinógeno; esta pudiera ser una herramienta para selección de pacientes a recibir anticoagulación sin embargo aún está en proceso de validación (157) . por estos motivos, hasta el momento, no se tiene suficiente cuerpo de evidencia que permita hacer una recomendación basado en los niveles de dímero d como variable aislada para administración de anticoagulación terapéutica. se recomienda no utilizar de rutina la procalcitonina en un algoritmo diagnóstico, para diferenciar entre neumonía viral vs bacteriana o confirmar la presencia de una sobreinfección bacteriana en el paciente con sospecha o diagnóstico de covid-19. se recomienda no medir de forma rutinaria la procalcitonina en pacientes con sospecha o diagnóstico de covid-19 como factor pronóstico. la procalcitonina es un biomarcador que ha sido incluido en algoritmos de diagnóstico y pronóstico durante los últimos años. schuetz et al, en 2017, concluyen en una revisión sistemática de 26 estudios, que la procalcitonina es segura dentro de un algoritmo, para guiar a los médicos tratantes entre iniciar o suspender antibióticos en neumonía adquirida en la comunidad; sin embargo en una revisión sistemática más reciente, kamat et al, reportaron una sensibilidad 55% [ic 95% 37%-71%; i2 = 95.5%], especificidad 76% [95% ic, 62%-86%; i2 = 94,1%]) para el inicio de tratamiento antibiótico para neumonía bacteriana, lo cual nos determina que la prueba es inespecífica para diferenciar entre infecciones virales vs bacterianas. en neumonía por sars-cov-2, se han publicado algunos artículos evaluando el uso de la procalcitonina como prueba asociada al pronóstico de los pacientes. liu et al encontraron que la procalcitonina se asoció a mayor severidad de los cuadros de neumonía. hr, 4.908; 95% ci, 1.797-13.402; p=0.002. en este estudio también se tuvo un resultado similar con la proteína c reactiva y la il-6. plebani et al, publican un metaanálisis, donde sugiere que los niveles elevados de procalcitonina se asocian a mayor severidad de la infección. (or, 4.76; 95% ci, 2.74-8.29). es importante mencionar, que en estos estudios se evaluaron otros biomarcadores de inflamación como interleucina 6, proteína c reactiva y ferritina; presentando todos ellos, aumento en sus valores y asociándose a severidad de la enfermedad; por tanto, se considera que, en particular, la procalcitonina elevada, no representa una diferencia en el pronóstico, comparado con otros biomarcadores de inflamación. hasta el momento no se han publicado estudios en infección por sars-cov-2 donde se evalué el papel de prueba diagnóstica para confirmar sobreinfección bacteriana o diferenciar entre neumonía viral vs bacteriana. (137, (158) (159) (160) se recomienda no usar de forma rutinaria el uso de pruebas clínicas de laboratorios clínicos para determinar la resolución de la enfermedad crítica por covid-19. se recomienda considerar la ausencia de dificultad respiratoria y fiebre por más de 72 horas, requerimiento de oxígeno a baja concentración y bajo flujo, como indicadores clínicos de resolución de la fase crítica de la enfermedad por covid-19. se recomienda no utilizar de forma rutinaria el uso de pruebas microbiológicas de erradicación viral, para determinar la resolución de la enfermedad en pacientes en uci con covid-19. amci ® enfermedad está asociado tanto a la carga viral como a la respuesta hiperinflamatoria del huésped a la infección viral. en cuanto a la carga viral, en pacientes que tienen un curso leve de infección, el pico de la carga viral en muestras nasales y orofaríngeas ocurre durante los primeros 5-6 días tras el inicio de síntomas y prácticamente desaparece al día 10, mientras que en los que cursan con neumonía severa en uci, la carga viral es 60 veces mayor y puede persistir la excreción viral hasta el día 21 a 28 (161) . por esta razón, consideramos que en los pacientes en uci no es necesario confirmar la erradicación del virus o su negativización en muestra respiratorias, orina o heces, para determinar la mejoría clínica, curación o para el egreso del paciente crítico (162) . en el contexto clínico, el pronóstico se ha asociado a la presencia de marcadores bioquímicos elevados, sin embargo, no existe evidencia que el seguimiento con estos marcadores iniciales de inflamación determine el momento exacto de la resolución de la enfermedad. varias organizaciones internacionales como el cdc de usa y el european centre for disease prevention and control (10 mar 2020) (162, 163), national centre for infectious diseases (ncid) singapore (164), world health organization (13 de marzo de 2020)(165), han establecido criterios para resolución clínica y egreso hospitalario de los pacientes. estos criterios incluyen: ausencia de fiebre mayor a 72 horas sin antipiréticos, mejoría de los síntomas respiratorios, ausencia de requerimiento de hospitalización por otras patologías, el resultado de dos (2) rt-pcr para sars-cov-2 negativas, con intervalo de muestra mayor a 24 horas. la utilidad de dichos criterios no ha sido evaluada en pacientes en cuidado intensivo. en uci, huang et al (115) , describieron en 28 pacientes a quienes se dio egreso, la ausencia de fiebre por 10 días, mejoría radiológica y evidencia de erradicación viral, como criterios de alta. sin embargo, consideramos que deben primar los criterios clínicos sobre los paraclínicos, en el momento de definir el egreso de un paciente de cuidado intensivo, teniendo como principal indicador la ausencia de dificultad respiratoria y la mejoría en los índices de oxigenación, con requerimiento de oxígeno suplementario a bajos flujos y concentración (166) . se recomienda la cánula de alto flujo, donde esté disponible, en pacientes con covid-19 a nivel del mar con hipoxemia leve (pao2/fio2<300 y >200 o sao2/fio2<300 y>200). en alturas superiores a los 2000 mts por encima del nivel del mar esta terapia se puede considerar en pacientes que no tengan hipoxemia severa (pafi< 100). amci ® se recomienda en pacientes críticos por covid-19 el uso de la cánula de alto flujo en salas de presión negativa, donde estén disponibles, que garanticen la seguridad del recurso humano. si no se dispone de habitación con presión negativa se puede optar por habitación individual cerrada. se debe contar con todo el equipo de protección personal necesario para el personal sanitario y de apoyo. se recomienda colocar mascarilla quirúrgica por encima de la cánula nasal en el paciente con sospecha o diagnóstico de covid-19 y mantener una distancia mínima de 2 metros con otros pacientes. se recomienda la intubación inmediata en pacientes críticamente enfermos con sospecha o diagnóstico covid-19 con índice de rox ([spo2/fio2] / frecuencia respiratoria) < 3 a las 2 horas de iniciada la oxigenación con cánula de alto flujo teniendo en cuenta que el retraso en la intubación aumenta la mortalidad. se recomienda considerar la cánula de alto flujo en caso de agotamiento de ventiladores mecánicos. la cánula de alto flujo ofrece flujos de hasta 60 litros/minuto, que aportan una fracción inspirada de oxígeno (fio2) constante que reduce el espacio muerto y produce una presión positiva que genera reclutamiento alveolar y puede redistribuir el líquido alveolar (167) (168) (169) . se ha reportado que al generar aerosoles, aumenta el riesgo de contagio para el personal de salud (167, (170) (171) (172) . hasta el punto de que se ha recomendado su uso en salas con presión negativa (167) . recientes publicaciones han establecido que la cánula de alto flujo genera una corta distancia de dispersión de aerosoles con lo cual las medidas de distanciamiento, un adecuado equipo de protección personal y donde estén disponibles, realizarla en salas de presión negativa darían seguridad al uso de la cánula de alto flujo (167, 173) . a pesar de que la experiencia en la actual pandemia ha sido escasa, basada en series de casos, estudios retrospectivos y de metodología limitada, ha resultado ser promisoria en cuanto a la mejoría en la oxigenación y la tolerancia por el paciente (37, 121, 139, 166, 167, (174) (175) (176) (177) (178) . sin embargo, hasta el momento no se ha establecido que la cánula de alto flujo evite la intubación. la caf podría convertirse en un alto riesgo de mortalidad al prolongar la decisión de intubación y al favorecer la lesión pulmonar autoinducida (p-sili) por aumento del esfuerzo inspiratorio. por todo ello es necesario un estricto y estrecho monitoreo del paciente durante una o dos horas para definir si ha habido mejoría o no mientras se realizan estudios que demuestren que evita la intubación y genera desenlaces clínicos importantes como menor estancia en uci, menor estancia hospitalaria y menos días de ventilación mecánica. la terapia de oxígeno de caf podría ser considerada para pacientes atendidos en altitudes mayor a 2000 mts, que no tienen hipoxemia severa (pafi < 100), la respuesta debe evaluar dentro de los 30 a 60 minutos posteriores a su inicio y los pacientes que no mejoran amci ® significativamente y progresa la dificultad respiratoria no deben mantenerse con esta terapia. el monitoreo del paciente con caf para la toma de decisión de éxito o fracaso de esta estrategia y considerar la posibilidad de intubación incluye la evaluación gasométrica, la oximetría de pulso, así como considerar los criterios para intubación: frecuencia respiratoria >30 por minuto, deterioro de conciencia, inestabilidad hemodinámica, pao2/fio2<150 (a nivel del mar), sao2/fio2<150, índice de rox<2,85, spo2<93% (119, 166-169, 175-177, 179,180) . se recomienda crear o ajustar protocolos institucionales de sedoanalgesia basado en objetivos con escalas validadas. se recomienda el uso de analgesia multimodal que incluya analgésicos opioides, no opioides y bloqueos regionales en el paciente crítico por sospecha o diagnóstico de covid-19. se recomienda sedación profunda con agentes como midazolam o propofol para mantener rass entre -4 y -5 en pacientes covid-19 con sdra severo, necesidad de uso de relajantes neuromusculares o posición prona. se puede considerar en planos de sedación superficial agentes como propofol o dexmedetomidina (coadyuvante) para mantener rass entre 0 y -3 en pacientes seleccionados con sospecha o diagnóstico de covid-19 con sdra no severo. en la actualidad no se encuentra evidencia de alta calidad proveniente de ensayos clínicos, sino editoriales, series, reportes de casos y artículos de revisión de expertos (180) (181) (182) . la creación y aplicación de protocolos de sedoanalgesia adaptados a cada institución ha mostrado disminución del tiempo en la uci y menores complicaciones (183, 184) . es importante definir objetivos guiados por escalas, recomendándose sedación profunda o completa en situaciones especiales como ventilación mecánica invasiva por sdra severo, disincronía ventilatoria persistente, posición prona y bloqueo neuromuscular (bnm), como puede observarse en pacientes covid-19 con compromiso pulmonar severo. mientras que se debe procurar sedación ligera, cooperativa o no sedación en pacientes en ventilación mecánica invasiva en pacientes con sdra no severo, ventilación no invasiva y en el retiro de la ventilación (185, 186) . los opioides han sido el pilar de la analgesia en dolor moderado a severo. el fentanilo es actualmente el más usado; el remifentanilo reduce el tiempo en ventilación en pacientes amci ® renales, hepáticos, ancianos y neurológicos; la hidromorfona se prefiere en el retiro de la ventilación y en pacientes extubados; y la metadona ha mostrado disminuir la tolerancia a opioides (187) . se propone el uso de estrategias de analgesia multimodal asociando medicamentos no opioides como el paracetamol, ketamina a dosis analgésicas (<0,5 mg/kg) en dolor somático, lidocaína en dolor visceral, y pregabalina en dolor neuropático (188) . la sedación ligera o cooperativa son mejores con propofol en cuanto a tiempo de despertar y con dexmedetomidina para preservar funciones cognitivas y el impulso respiratorio, con menor desacondicionamiento (189) . en sedación profunda, el propofol ha mostrado más fácil titulación y menos acumulación que el midazolam; sin embargo, su uso se ve limitado hasta 48 horas y a dosis < 3,0 mg/kg/h, ante el riesgo de pris (síndrome relacionado con la infusión de propofol). el midazolam, sin dosis techo ni tiempo límite y de bajo costo, ha sido el más utilizado de los sedantes, disminuyendo su uso por su asociación con delirium y de retraso en los tiempos en ventilación; sin embargo, la pandemia covid-19 ha vuelto a aumentar su uso. la dexmedetomidina ha sido utilizada como adyuvante en sedación profunda, disminuyendo el consumo de sedantes, con menos efectos secundarios (190, 191) . se muestran los medicamentos para sedoanalgesia y relajación neuromuscular que se pueden utilizar en los pacientes con covid-19 en la tabla 13. se recomienda iniciar una estrategia individualizada de ventilación mecánica ajustadas a las condiciones específicas de severidad en el paciente crítico con covid-19. amci ® se recomienda la ventilación protectora en modos controlados por volumen o por presión que garanticen un volumen corriente < 8 cc/kg de peso predicho teniendo como metas una presión meseta < 30 cm h2o y una presión de conducción < 15 cm h2o. se recomienda emplear fracciones inspiradas de oxígeno para lograr metas de saturación de acuerdo con la pao2/fio2 entre 88 y 92% en el paciente con sospecha o diagnóstico de covid-19. en la paciente embarazada entre 92 y 95%. se recomienda en el paciente crítico por covid-19 iniciar con peep individualizado a la severidad del compromiso pulmonar y ajustar el nivel de peep de acuerdo con la tabla de fio2/peep. el estudio arma (192) demostró que la ventilación con bajos volúmenes corrientes (vt) se asocia con reducción de: mortalidad (p=0.007), en días libres de ventilación mecánica (p=0.007) y días libres de falla orgánica (p= 0.006). una revisión sistemática posterior confirmó que el uso de bajos volúmenes se asocia con menor progresión a sdra (193) . un metaanálisis que revisó 159 estudios y 29 meta-análisis en uci confirmó que la ventilación protectora era una de las tres intervenciones que mejora la sobrevida en pacientes con sdra (194) . esto fue confirmado por landoni en un análisis de estudios multicéntricos con impacto en mortalidad en uci (195) . recientes publicaciones han sugerido que en covid-19 puede haber dos fenotipos que se diferencian en la distensibilidad (119, 196) . sin embargo, el mismo estudio arma demostró que "el beneficio de ventilación con vt más bajo fue independiente de la distensibilidad de las vías respiratorias, lo que sugiere que el vt más bajo fue ventajoso independientemente de la distensibilidad pulmonar". más aún, el uso de bajos vt se asoció con una reducción en las concentraciones de interleuquina 6 lo cual explicaría el mayor número de días sin falla orgánica múltiple y sugeriría una reducida respuesta inflamatoria asociada a la ventilación protectora (192) . con el tiempo la evidencia ha demostrado que la ventilación protectora, además de vt y presión meseta bajos, debe incluir presiones de conducción menores de 15 cm h2o (197) (198) (199) . existe suficiente evidencia que demuestra que fio2 y pao altas se asocian con aumento en la morbimortalidad (200) (201) (202) . en sdra el estudio arma y una más reciente publicación demostraron que el tener metas conservadoras de pao2 se asocia con mayor sobrevida (192, 203) . hasta el momento, la literatura en ventilación mecánica ha demostrado que la mejor estrategia para ajustar el nivel de peep en sdra es la tabla de fio2/peep (192, 204) . amci ® se recomienda la ventilación mecánica protectora en sdra por covid-19 independiente del fenotipo de presentación. se recomienda la clasificación de fenotipos en sdra para pacientes con covid-19 para ajustar la toma de decisiones de manera individualizada en ventilación mecánica. el manejo ventilatorio en covid-19 tiene los mismos principios generales de los pacientes con sdra (205) . sin embargo, la identificación de fenotipos podría impactar en la evolución y pronóstico (206) . gattinoni ha postulado el desarrollo de un sdra típico (fenotipo h: con alta elastancia, alto cortocircuito, alto peso pulmonar) o una presentación atípica (fenotipo l: caracterizado por baja elastancia, bajo shunt, bajo peso pulmonar). (207) . pelosi et al sugiere clasificar los pacientes con tres fenotipos similares (208) . con base en tales fenotipos se han propuesto estrategias ventilatorias diferenciales para minimizar el daño inducido por el ventilador (vili) (209): 1. el primer paso, en el fenotipo l, es revertir la hipoxemia aumentando la fio2. 2. en el tipo l, hay varias opciones no invasivas: cánula nasal de flujo alto, presión positiva continua en la vía aérea (cpap) o ventilación no invasiva (niv). se debe evaluar el esfuerzo inspiratorio y, de estar disponible, medir la presión esofágica. la peep alta puede disminuir los cambios de presión pleural y detener el ciclo vicioso que exacerba la lesión pulmonar. sin embargo, la peep alta, en pacientes con distensibilidad normal, puede tener efectos hemodinámicos perjudiciales. en cualquier caso, las opciones no invasivas son cuestionables, ya que pueden asociarse con altas tasas de fracaso y retraso de la intubación. 3. la magnitud de las presiones pleurales inspiratorias puede determinar la transición del tipo l al h. la presión esofágica > 15 cmh2o aumenta el riesgo de vili y, por lo tanto, la intubación debe realizarse lo antes posible. los tipo l, si son hipercápnicos, pueden ser ventilados con volúmenes > 6 ml / kg (hasta 8 ml / kg). la posición prona debe ser usada solo en último caso, ya que las condiciones pulmonares son buenas. la peep debe reducirse a 8-10 cm h2o, dado que la capacidad de reclutamiento es baja y el riesgo de falla hemodinámica aumenta. la intubación puede evitar la transición al fenotipo tipo h. 4. los pacientes tipo h deben ser tratados como sdra grave, incluyendo mayor peep, si es compatible con la hemodinamia, posición en pronación y soporte extracorpóreo. en el fenotipo 3 se deben aplicar las estrategias de ventilación protectora convencional (208, 209) . amci ® se recomienda en paciente con covid-19 considerar hipoxemia refractaria cuando no se obtienen las metas de oxígeno propuestas, a pesar de las maniobras ventilatorias recomendadas y cumple con los siguientes parámetros: pafi < 150, fio2 > 0,6 y peep apropiado, considerando la altitud. se recomienda considerar la utilización de ecmo, en sitios donde esté disponible y con alta experiencia para obtener resultados aceptables, en pacientes con hipoxemia refractaria luego de haber implementado ventilación protectora, relajación neuromuscular y posición prona. se recomienda administrar tromboprofilaxis en todos los pacientes con covid-19 con hipoxemia refractaria que no presenten contraindicaciones. la hipoxemia refractaria no es un concepto estático y absoluto, según la definición de berlín del sdra, se clasifica el sdra en leve, moderado y severo de acuerdo con la relación pao2 y fracción inspirada de oxígeno, con peep mayor de 5 cms de h2o. la hipoxemia severa es aquella que cuenta con una pafi menor de 100 (210) (211) (212) . la hipoxemia refractaria hace referencia a un estado de hipoxemia severa que a pesar de las diferentes estrategias ventilatorias no aumenta la pafi y tiene consecuencias en el estado ácido básico y metabolismo celular permitiendo una anaerobiosis (213, 214) . para definir la hipoxemia refractaria deben coincidir varios escenarios , una pafi menor de 150, una fracción inspirada de oxígeno mayor de 0.6, a pesar de un peep apropiado no se tiene en cuenta en la definición el ph ni la paco2 ni el tiempo transcurrido (122) . algunas de las medidas terapéuticas no ventilatorias que se han empleado en sdra y covid-19 con hipoxemia refractarias son la oxigenación con membrana extracorpórea (ecmo) y la tromboprofilaxis o anticoagulación de rutina. la oxigenación extracorpórea a través de una membrana ha sido una estrategia controvertida en pacientes con hipoxemia refractaria de diferentes orígenes, en la epidemia de la influenza por el virus h1n1 fue usada en pacientes con hipoxemia refractaria teniendo resultados aceptables (215) . en el estudio eolia los resultados no mostraron mejoría en la supervivencia, aunque hay diferentes posiciones y estudios post hoc de este ensayo clínico con beneficios, su uso se limita a casos muy restringidos y en sitios de alta experiencia para obtener resultados aceptables (216) . en sdra por covid-19 el ecmo se ha usado en hipoxemia refractaria entre un 4 a 11.5% en diferentes series con resultados variables (205, 217, 218) . un tipo de pacientes hipoxémicos y con ventilación mecánica han presentado cuadros tromboembólicos pulmonares en estos casos la trombólisis de rescate con activador de plasminógeno tisular rtpa (alteplase) se ha recomendado con resultados alentadores en serie de casos, pero su evidencia es muy débil para ser recomendada(219-223). dada la alta frecuencia de enfermedad tromboembólica reportada en covid-19 se ha reportado la utilidad de la tromboprofilaxis, especialmente en casos de dímero d o índice de sic elevado (156) . amci ® se recomienda monitorizar sistemáticamente la oxigenación con los índices: pao2/fio2 y sao2/fio2, y en donde esté disponible el monitoreo continuo con capnografía. se recomienda monitorizar de forma rutinaria la presión meseta y la presión de conducción como estrategia al pie de la cama para verificar la ventilación protectora. el sdra y covid-19, es una condición dinámica que apenas se está caracterizando, hay varias presentaciones que no cumplen con todos los criterios de berlín (209, 211) . gattinoni ha caracterizado en dos presentaciones el sdra en los pacientes con neumonía por coronavirus sars-cov-2, una con alta compliance, mínima reclutabilidad; la otra con baja compliance, pulmones pesados y reclutabilidad, tal vez esta presentación sea el verdadero sdra (118, 224, 225) . los pacientes que requieren ventilación mecánica por falla ventilatoria en covid-19, son los que mayor mortalidad tienen al parecer por la lesión pulmonar inducida por la intubación tardía y el gran esfuerzo respiratorio con presiones transpulmonares oscilantes y muy negativas (212, 213, 226) . la monitoria de estos pacientes soportados con ventilación mecánica tiene dos objetivos: el primero detectar el deterioro clínico para sugerir estrategias más avanzadas como el ecmo, y el segundo es evitar el daño pulmonar inducido por la ventilación mecánica. se debe tener presente la mayor posibilidad de contagio con el número de manipulaciones en el paciente, por esto nunca olvidar el perfecto uso de los elementos de protección personal y disminuir el número de contacto con el paciente. las metas que se buscan con la ventilación mecánica en el paciente con sdra por covid-19 son mantener una oxigenación adecuada teniendo en cuenta la altura sobre el nivel del mar con pao2 entre 70 y 80 mmh20 y metas de saturaciones reportadas entre 89 y 92% a 90 y 95% , mantener una ventilación adecuada evitando el espacio muerto , disminuir el trabajo respiratorio y protegiendo el pulmón del daño ocasionado por la ventilación mecánica y las repercusiones hemodinámicas (214) .  el confort de los pacientes en ventilación mecánica es la principal señal de un uso adecuado del modo ventilatorio y los parámetros ventilatorios apropiados para la patología y demanda del paciente (214) .  las curvas y bucles son herramientas indispensables para valorar la mecánica respiratoria del paciente soportado con ventilación mecánica, se puede diagnosticar amci ® las asincronías del paciente y el ventilador, el origen, tipo y frecuencia además de la respuesta al manejo. también se evalúa la resistencia de la vía aérea (214) . variables fisiológicas:  es importante valorar la oxigenación del paciente, la literatura actual sugiere el monitoreo de la pafi es el más representativo y sencillo test para valorar la oxigenación y representa el shunt pulmonar, se debe hacer mínimo diariamente, o cuando se haga una intervención en el ventilador o paciente; en sdra por covid-19 la hipoxemia se relaciona directamente con mortalidad, debe mejorar con la ventilación mecánica (214, 227) .  la medición de la paco2 indica la de la ventilación, la hipercapnia tiene relación directa con el espacio muerto en el paciente con sdra, y varios estudios la relacionan con la mortalidad. puede evaluarse directamente en los gases arteriales o relacionarla con el pco2 expirado por medios de la capnografía, gattinoni propone una forma de evaluarla al lado de la cama del paciente relacionando el etco2/paco2, cuando es < de 1 sugiere un shunt elevado y mayor espacio muerto; áreas de pulmón ventiladas y no aireadas. otras tecnologías incluidas en el ventilador moderno como la capnografía volumétrica se está validando para evaluar el espacio muerto, la reclutabilidad y la titulación de peep (214, 228) .  la saturación venosa mixta svo2 , refleja de manera subrogada la función ventricular, no todos los pacientes tienen catéter de arteria pulmonar para su medición por lo que se está reemplazando con el ultrasonido en la cabecera del paciente; recordar que el 30% de los pacientes con sdra cursan con falla ventricular derecha (214) . monitoria de mecánica ventilatoria y protección pulmonar:  para evitar el daño pulmonar debe propender por un volumen corriente bajo (4-8 ml/kg de peso predicho) y presión plateau menor de 30 cms h20, para garantizar la ventilación con protección pulmonar (192, 229) .  driving pressure ( presión cambiante de la vía aérea, presión diferencial o presión de conducción) es la presión plateau (presión pico en ventilación controlada por presión) menos peep, debe ser menor de 15 cm h20, está relacionado con aumento en la mortalidad en pacientes ventilados por que representa una medición indirecta del strain pulmonar porque relaciona el volumen corriente con la compliance del sistema respiratorio y este a su vez se relaciona con el volumen espiratorio pulmonar final (198) .  la medición de la compliance del sistema respiratorio es necesaria y nos clasifica el paciente de acuerdo con su fenotipo para trazar el plan de manejo ventilatorio, cuando la compliance es baja, esto se puede hacer al lado de la cama del paciente con los ventiladores modernos (214, 225) .  la construcción de la curva presión/volumen aún es una herramienta útil para ubicar el área de ventilación segura del paciente, evitando el atelectrauma y la sobredistensión pulmonar(estrés) , el peep se calcula dos puntos por encima del punto de inflexión inferior y el punto de inflexión superior nos indica hasta dónde podemos aumentar el volumen corriente este punto debe estar por debajo de 30 cms h20 para evitar la sobre distensión, con los ventiladores modernos se puede construir esta curva (214, 229) . amci ®  las curvas presión tiempo en pacientes ventilados con modos volumétricos pueden monitorizar la resistencia de la vía aérea, la compliance pulmonar, el trabajo respiratorio, las curvas de flujo puede también indicar si se presenta autopeep, resistencia aumentada de la vía aérea entre otras (214) .  presión transpulmonar, en casos más complicados donde es más difícil obtener la meta de oxigenación a pesar del peep en aumento una opción es el catéter esofágico, para medir la presión transpulmonar en la inspiración y espiración y calcular así el stress pulmonar y evitar las presiones oscilatorias y sobre todo negativas para evitar el daño pulmonar. esta herramienta también ayuda a evaluar el trabajo respiratorio, y el diagnóstico de las asincronías que se presenten en el paciente ventilado (214, 230) . se recomienda no utilizar de forma rutinaria la relajación neuromuscular en el paciente crítico con covid-19 con sdra. se recomienda utilizar la relajación neuromuscular en pacientes en posición supino o prono, que están fuera de parámetros de protección pulmonar (presión de conducción mayor 15 y presión plateau mayor a 30) con pafi menor 150 y cuando ya no es posible limitar el volumen corriente. se debe considerar la utilización de protocolos estandarizados con el fin de disminuir la variabilidad, y según disponibilidad seleccionar el cisatracurio como primera opción, en caso de escasez se pueden utilizar otras opciones teniendo en cuenta su farmacodinamia y farmacocinética. el 13 de marzo de 2020, la organización mundial de la salud emite una serie de orientaciones para el manejo de la infección respiratoria aguda grave (irag) en pacientes con sospecha o diagnóstico de covid-19. en el paciente críticamente enfermo con sdra moderado o grave (pao2/fio2 <150) por covid-19 no está indicado de forma sistemática el bloqueo neuromuscular mediante infusión continua debido a que no se cuenta con evidencia suficiente que sustente mejoría en la supervivencia con respecto a una estrategia de sedación ligera sin bloqueo neuromuscular, se debe considerar su uso cuando se evidencia asincronía paciente-ventilador a pesar de la sedación, hasta el punto de que no se pueda limitar el volumen corriente de forma fiable, hipoxemia o hipercapnia que no mejoran con el tratamiento (231) . recomendación se recomienda no utilizar de forma rutinaria oni en pacientes adultos que presenten sdra e infección por sars-cov-2. fuerte en contra fundamento a la fecha (mayo 18 de 2020) no contamos con estudios sobre el uso de óxido nítrico inhalado (oni) como tratamiento de pacientes con infección covid-19. existe evidencia indirecta sobre el uso de oni en el síndrome de dificultad respiratoria aguda (sars-cov), y la infección por coronavirus en el síndrome respiratorio de oriente medio (mers-cov) (233) . en 2016 cochrane realizó una revisión sistemática que incluyó 14 ensayos de calidad moderada con 1275 pacientes adultos con sdra tratados con óxido nítrico inhalado. los resultados no mostraron ningún efecto estadísticamente significativo sobre la mortalidad (rr 1.04, 95% ci 0.9 -1.19). se mostró mejora transitoria en el índice de oxigenación a las 24 horas (md (diferencia media) -2,31, ic del 95% -2,73 a -1,89) y mejoría en pao2/fio2 a las 24 horas (md 15,91, ic del 95% 8,25 a 23,56). no se identificó diferencia significativa en los días libres de ventilación y finalmente se presentó aumento estadísticamente significativo en la incidencia de insuficiencia renal en pacientes con óxido nítrico inhalado (rr 1,59, ic del 95% 1,17)(234). amci ® en 2014 se realizó un estudio observacional que incluyó 14 pacientes tratados de dos hospitales de beijing con oni como tratamiento para sars (235) . en comparación con ningún tratamiento, oni mejoró la saturación arterial de oxígeno (spo2) de 93% a 99% (p<0.05); se asoció a menor necesidad de oxígeno suplementario (p< 0.05) y menor necesidad y retiro de cpap y bial (p < 0.05). los cambios en radiografía de tórax mejoraron en 5 de los 6 pacientes que recibieron oni. sin embargo, debido a problemas graves de validez por pequeño tamaño de la muestra (n= 16, oni=6, control=8), no aleatorización y no enmascaramiento en la asignación, se considera que este estudio cuenta con baja calidad metodológica, lo cual limita la interpretación de los resultados. en un estudio retrospectivo multicéntrico que incluyó 330 pacientes con mers-cov en condición crítica en arabia saudita, se mostró que el manejo con ventilación no invasiva (niv) tenía mayor probabilidad de requerir óxido nítrico en comparación con los pacientes con ventilación mecánica invasiva (20,0% vs 11,7%, p a 0,05) (236) . en una serie de casos en la que participaron 12 pacientes con infección por mers-cov confirmada o probable, 6 pacientes recibieron oni debido a hipoxemia refractaria. en el seguimiento a 90 días, cinco de los pacientes continuaron vivos (237) . los estudios sobre mers-cov se limitaron a una serie de casos y una cohorte retrospectiva con baja calidad de evidencia. en ambos estudios, los pacientes recibieron otras terapias de rescate (relajación neuromuscular, ventilación oscilatoria de alta frecuencia, ecmo y posición en prono), por lo tanto, se desconoce el efecto terapéutico clínico del oni en el tratamiento de la infección por mers-cov. a la fecha (18 de mayo de 2020) tres ensayos clínicos evalúan el papel del óxido nítrico inhalado en pacientes con covid-19 y sdra leve/moderado, y como profilaxis para los trabajadores de la salud covid-19(tabla 14). tabla 13. comparación de ensayos clínicos que evalúan el papel del óxido nítrico inhalado en pacientes con covid-19 y sdra leve/moderado, y como profilaxis para los trabajadores de la salud covid-19. no se cuenta con evidencia por el momento que respalde el uso de óxido nítrico inhalado en pacientes con covid-19. los resultados de los ensayos en curso, así como ensayos clínicos de alta calidad son necesarios para apoyar su uso. sólo evidencia indirecta metodológicamente limitada de óxido nítrico en pacientes con sras mostró una mejor oxigenación, una menor necesidad de oxígeno suplementario y mejoría en la radiografía de tórax. en pacientes con sdra y mers-cov, no mostró un beneficio claro e incluso mostró un mayor riesgo de insuficiencia renal (238) . otros estudios han evaluado el efecto tóxico asociado a su uso documentando metahemoglobinemia(239), inhibición de la agregación plaquetaria y formación de dióxido de nitrógeno (240) . razones por la cuales guías recientemente publicada no recomienda su uso de forma rutinaria(205). recomendación se recomienda el uso temprano de la ventilación en posición prona, por al menos 16 horas continuas, en pacientes con sdra por covid-19 con pao2/fio2<150 mmhg. la ventilación en posición prono como estrategia ventilatoria propuesta desde los años 70 (241), cuenta con evidencia que demuestra resultados positivos en cuanto a mejoría de mortalidad, mejoría en el trastorno de oxigenación y el reclutamiento alveolar en pacientes con sdra. los mecanismos por los cuales la posición prona conduce a la mejoría en el trastorno de oxigenación y del reclutamiento alveolar en los pacientes con sdra, incluyen (242) (243) (244) (245) : amci ®  mejoría de la relación ventilación/perfusión y mayor homogeneidad en la distribución de aire en los pulmones.  aumento del volumen de fin de espiración.  disminución del efecto compresivo del corazón en los pulmones.  mejoría del drenaje de las secreciones.  optimización del reclutamiento alveolar, con mejoría de la distribución del volumen corriente, a su vez, limita el desarrollo del daño alveolar pulmonar. los estudios coinciden en el efecto benéfico que esta terapia tiene en la mejoría de la oxigenación, el objetivo se centrará en evaluar las recomendaciones con respecto a:  beneficio de la terapia con respecto a la mortalidad al día 28, al día 90 y a los 6 meses.  beneficio de la terapia según el grado de severidad de sdra con respecto la relación pao2/fio2.  tiempo de terapia en posición prono con mayor beneficio.  número de sesiones de la terapia en posición prono.  recomendaciones según balance riesgo/beneficio en lo que respecta a los efectos adversos: retiro o desplazamiento no planeado de catéteres, obstrucción de tubo endotraqueal, neumonía asociada a ventilador, lesiones de presión. se eligieron 8 artículos que con las características metodológicas consistentes (246) (247) (248) (249) (250) (251) (252) (253) . de estos ocho artículos se excluyó uno por corresponder a pacientes pediátricos (253) . al evaluar los escritos de forma cronológica, se puede apreciar en los primeros artículos (246, 247) , la dificultad para lograr enrolar (reclutar) el suficiente número de pacientes, de tal manera que algunos estudios fueron detenidos de forma prematura (246, 247, 251, 252) . era entonces esperable que los resultados no fueran concluyentes, y que no lograran ser robustos, al no alcanzar el tamaño de muestra deseado, comprometiéndose la confiabilidad, el poder y corriendo el riesgo de obtener resultados falsamente negativos. sin embargo, se podía percibir en los diferentes estudios, una notoria mejoría en la oxigenación, sin repercusión en la mortalidad (246) (247) (248) (249) (250) (251) . por otro lado, es necesario tener en cuenta que los estudios iniciales (246) (247) (248) (249) no se realizaron con el uso de ventilación protectora asociada a la pronación. esto es un elemento pertinente, pues la ventilación protectora puede per se, brindar un efecto adicional en la mejoría de la oxigenación. otro efecto importante que debe analizarse es el bloqueo neuromuscular, cuya evidencia hoy sugiere su uso en criterios ya mencionados (254) . con el tiempo y según la experiencia de cada centro, se fue utilizando con menor dificultad (255) . sin embargo, no se tenía aún claro qué tipo de pacientes obtenían el mayor beneficio de la terapia, además que el tiempo de la terapia en posición prona, seguía siendo una incógnita. la evidencia reflejaba hasta el momento que los pacientes con sdra más severos y la terapia aplicada por más tiempo se asociaban con una tendencia a la reducción en mortalidad. para dirimir qué tipo de pacientes se beneficiarían más de la terapia, se tomó como base, la severidad del sdra según la relación pao2/fio2 (210) . a pesar de que los estudios iniciales(246-250) enfrentaban el reducido tamaño de muestra, algunos análisis identifican beneficio de la mortalidad (246) en pacientes con sdra más severo, constituyendo un probable umbral de beneficio cercano y por debajo de 140-150 mmhg (256) . amci ® antes del estudio proseva (252) en totalidad 2 estudios reportan mortalidad al día 28 (247, 251) , un estudio mortalidad al día 30 (246) , uno estudio mortalidad al día 60 (250)y uno mortalidad al día 90 (248) . sin embargo, al tomar todos los estudios, aún no se alcanzaba suficiente significancia estadística para reducir la mortalidad a los 28 días y 6 meses. con el estudio proseva -guerin et als -en el año 2013 (252) , se alcanza más poder estadístico, demostrando un beneficio importante en pacientes con pao2/fio2 menor de 150 mmhg, ventilados con bloqueo neuromuscular y ventilación protectora en su totalidad, y logrando una reducción de la mortalidad al día 28 y mantenida hasta el día 90 con respecto al grupo control (16.0% (38 de 237 participantes) versus 32.8% (75 de 229) (p<0.001). de tal manera que, según la evidencia disponible, en lo que al trastorno de oxigenación se refiere (según la relación pao2/fio2), sugiere que el mejor candidato para esta estrategia ventilatoria es el paciente con sdra severo con una pao2/fio2 menor de 150 mmhg. es de primordial importancia detenerse a considerar por otra parte, el número de horas que se implementaría la terapia. el estudio inicial realizado por gattinoni et al. (246) , llevó a los pacientes a un período corto de 6 horas, sin encontrar resultados positivos en mortalidad. (resultados que no se pueden solamente atribuir a la calidad del estudio, sino también, al reducido número de horas de la ventilación en posición prono). mancebo et als (la abreviación latina para "otros "es et al.), y fernández et al. (249, 250) por su parte, optan por ventilar un mayor número de horas (18-20 horas) obteniendo resultados (que sugieren una reducción en mortalidad) con tendencia a disminuir mortalidad. si bien diferentes metaanálisis sugieren no (la ausencia de beneficio) beneficio de la ventilación en prono (256, 257) , los resultados son diferentes cuando se aborda la terapia con períodos mayores a 12 horas (256) . teniendo en cuenta, que el estudio con más poder estadístico (252) postula 16 horas de terapia en posición prono, la recomendación es la pronación por un tiempo mayor a 16 horas, contemplando hasta las 20 horas por sesión. otra pregunta que surge con frecuencia es el número de veces que se puede implementar la terapia. existen diferentes estudios en los cuales se indica el número de veces en promedio en que se llevó el paciente a posición prono (247, 248) , otro protocolo en donde se estipula un número límite de días en los que se llevó a cabo la terapia(249), y otro estudios en los cuales no se precisó el número de sesiones de la terapia (246, 250) . se podría entonces recomendar con respecto a la mayor evidencia disponible (252) , pronar a los pacientes en varias sesiones (4 en promedio) (depende de los criterios para continuar o suspender el prono que deben ser individualizados para cada paciente, en cada zona geográfica y en cada unidad de cuidados intensivos, es difícil saber si 4 es el promedio para todos), y considerarla más veces si es necesario. en lo que respecta a los efectos adversos, tres estudios reportaron barotrauma y neumonía asociada a ventilador (247, 249, 250) ; dos estudios desplazamiento de catéter central (246, 251) y siete estudios reportaron extubación (246) (247) (248) (249) (250) (251) (252) . sin embargo, los efectos adversos no alcanzaron significancia estadística para proscribir la terapia (256) . recientemente fue publicado el consenso colombiano de sdra(204) en el cual se hace referencia a las recomendaciones para realización de ventilación prono. se presenta la lista de chequeo, y medidas que deben ser realizadas en la maniobra para lo cual se cuenta con la participación de terapia respiratoria, enfermería y médico. se recomienda implementar un protocolo de retiro de ventilación mecánica basado en la prueba de respiración espontánea y articulado con un protocolo de sedación y analgesia en el paciente críticamente enfermo por sospecha o diagnóstico de covid-19. desde diciembre de 2019, un número de casos de neumonía por síndrome respiratorio agudo severo sars-cov2/covid-19 en wuhan china se identificaron, como causa de insuficiencia respiratoria aguda(258). el síndrome de dificultad respiratoria aguda (sdra) ocurre en el 20% de los 138 pacientes hospitalizados y en el 61% de los 36 pacientes admitidos a la unidad de cuidados intensivos (uci) en wuhan (174) . mientras la ventilación mecánica es una intervención que potencialmente salva la vida, esta puede llevar a múltiples complicaciones y contribuir a la lesión pulmonar (259) . es por todo esto que el retraso en el retiro de la ventilación mecánica puede aumentar el riesgo de amci ® infecciones, aumenta la sedación innecesaria, el trauma de la vía aérea y aumento en el costo de la atención de estos pacientes (260) . el retiro de la ventilación mecánica es un proceso de tres pasos, el primero es conocido como preparación la cual depende de variables fisiológicas, criterios clínicos y predictores de weaning (destete), el segundo paso es el propio weaning, el cual consiste en la disminución del soporte ventilatorio entregado al paciente, con el objetivo de llevar al último paso que es la extubación(261), ilustración 7. por todo lo anterior, se recomienda realizar un proceso de retiro de ventilación mecánica invasiva adoptando un protocolo, seleccionando adecuadamente a los pacientes, ya que evidencia sugiere que la adecuada selección de los pacientes disminuye los días de ventilación mecánica, disminuye la estancia hospitalaria y la estancia en uci (262) . se recomienda realizar el retiro de la ventilación mecánica siguiendo los pasos antes mencionados, iniciando con la preparación, la cual consiste en: preparación 1. asegurarse que la lesión pulmonar que llevó a la falla respiratoria esté resuelta. 2. adecuado intercambio de gas, definido como adecuados índices de oxigenación con peep (presión positiva al final de la expiración) 5 a 8 cmh2o, y fio2 (fracción inspirada de oxígeno) < 0.5. al igual que el proceso de intubación, es un proceso que genera aerosoles por lo cual se recomienda la aplicación de lidocaína dosis de 0,5 a 1,5 mg por kilogramo de peso, 1 a 5 minutos antes la extubación con el objetivo de disminuir el reflejo de tos (266) y la exposición del personal de salud. se recomienda en el paciente con sospecha o diagnóstico de covid-19 a quien se considera realizar vmni, utilizarla en salas de presión negativa, donde estén disponibles, que garanticen la seguridad del recurso humano, con todo el equipo de protección personal necesario. se recomienda considerar la vmni en pacientes con covid-19 con hipoxemia leve (pao2/fio2<300 y >200 o sao2/fio2<300 y>200) en salas de presión negativas, donde estén disponibles que garanticen la seguridad del recurso humano, con todo el equipo de protección personal necesario. fuerte a favor se recomienda considerar la vmni en pacientes con covid-19 con hipoxemia leve (pao2/fio2<300 y >200 o sao2/fio2<300 y>200) y con historia de epoc o cuadro de edema pulmonar agudo asociado en salas de presión negativas, donde estén disponibles que garanticen la seguridad del recurso humano, con todo el equipo de protección personal necesario. se recomienda colocar doble filtro en el circuito del ventilador para reducir el riesgo de generación de aerosoles en vmni del paciente crítico con sospecha o diagnóstico de covid-19. se recomienda la intubación inmediata en pacientes críticamente enfermos por covid-19 si se evidencia respiración toraco-abdominal, uso de músculos accesorios, frecuencia respiratoria > 30, hipoxemia (pao2/fio2<200 o sao2/fio2 <200), fracaso ventilatorio (ph<7.35 con paco2>45 mmhg), hacor>5. existe suficiente evidencia que demuestra que la vmni es una estrategia que reduce la mortalidad en pacientes críticos (195, 267, 268) . además, reduce la necesidad de intubación. los números de casos necesarios a tratar (nnt) son: ocho para salvar una vida y 5 para evitar una intubación (268) . estos desenlaces son fundamentalmente en pacientes con epoc y edema pulmonar agudo (268) (269) (270) ; también hay evidencia a favor, aunque menos fuerte, en pacientes inmunosuprimidos (259, 271) . se ha planteado mayores tasas de éxito con interfaces faciales totales o con helmet (195, (267) (268) (269) (270) (271) . por el contrario, en falla respiratoria hipoxémica hay evidencia en contra del uso de vmni (272) . la experiencia previa con h1n1, sars y mers no apoya el uso de la vmni en falla respiratoria hipoxémica de origen viral (273) (274) (275) (276) (277) (278) . además, se ha cuestionado el uso de vmni en covid-19 por el riesgo de contagio al generar aerosoles (279) . recientemente se demostró que la distancia de dispersión de aerosoles era menor de un metro (280) . por otro lado, el fracaso de la vmni se ha asociado con alta morbimortalidad (281) (282) (283) . ello obliga a evaluar estrictamente la posibilidad de éxito o fracaso. así, en falla respiratoria amci ® hipoxémica la escala hacor ha sido validada para este fin y un puntaje>5 contraindicaría la vmni (284) . adicionalmente si se emplea la vmni el prolongar la decisión de intubación puede aumentar la mortalidad y es por ello necesario monitorizar estrictamente al paciente y evaluarlo para establecer, ojalá antes de dos horas, si el paciente responde a la vmni (167, 285, 286) . las indicaciones para intubación en este caso son respiración toracoabdominal, uso de músculos accesorios, frecuencia respiratoria mayor de 30, hipoxemia (pao2/fio2<200 o sao2/fio2 <200), fracaso ventilatorio (ph<7.35 con paco2>45 mmhg), hacor>5 o índice de rox (spo2/fio2)/frecuencia respiratoria) < 3 (119, 167, 179, 180, 285, 286) . recomendación se sugiere el uso de posición prono en pacientes no ventilados críticamente enfermos por covid-19 que no responden a la oxigenoterapia convencional de acuerdo con los protocolos institucionales, las condiciones de cada servicio y la tolerancia individual de cada paciente. débil a favor fundamento los pacientes con enfermedad por coronavirus 2019 (covid-19) están en riesgo de desarrollar un síndrome de dificultad respiratoria aguda (sdra) (287) . en pacientes intubados con síndrome de dificultad respiratoria aguda grave, la posición prona (pp) temprana y prolongada (al menos 16 horas diarias) mejora la oxigenación y disminuye la mortalidad (252, 288) .debido a que las unidades de cuidados intensivos (uci) están sobrecargadas con pacientes con covid-19, la pp en paciente despierto con respiración espontánea puede ser útil para mejorar la oxigenación y prevenir las transferencias hacia uci. un estudio describió la viabilidad del uso de la ventilación no invasiva y la cánula de alto flujo asociado a la pp estableciendo su tolerancia y su seguridad en pacientes con sdra moderado y severo(289); la pronación puede reclutar todas las regiones pulmonares y favorecer el drenaje de secreciones de la vía respiratoria, mejorando el intercambio gaseoso y la supervivencia en el síndrome de dificultad respiratoria (sdra) (252) . en una comunicación corta proveniente de italia en el cual se incluyeron 15 pacientes que son sometidos al pp asociada con el uso de ventilación no invasiva, se concluye que proporcionar niv en la posición prona a los pacientes con covid-19 y sdra en salas generales en un hospital en italia era factible. la frecuencia respiratoria disminuyó durante su implementación y la oxigenación mejoró durante una pronación posterior a su línea de base. si la intubación se evitó o se retrasó, queda por determinar (290) . en otro reporte de caso, publicado recientemente por un grupo francés(291) de pacientes con covid-19 e insuficiencia respiratoria hipoxémica manejados fuera de la uci, el 63% amci ® fue capaz de tolerar pp durante más de 3 horas. sin embargo, la oxigenación aumentó durante el pp solo un 25% y no se mantuvo en la mitad de los pacientes después del regreso a la posición supina. estos resultados son consistentes con los hallazgos de pequeños estudios previos de pp en pacientes no intubados (289) . un ensayo clínico controlado que evalúe el uso del pp en pacientes no intubados puede ser un mecanismo para seleccionar pacientes que bien puedan beneficiarse de esta estrategia terapéutica. dada la evidencia débil que soporta el uso del pp en pacientes no intubados en términos de la disminución de la necesidad de entubación o ingreso a cuidados intensivos y la duda razonable de aumentar desenlaces deletéreos en aquellos pacientes en los cuales se retarde el tiempo de intubación, no se emite recomendación, a favor o en contra, del empleo de esta estrategia de manera rutinaria. en situaciones en las cuales hay limitación de recursos y de disponibilidad de camas en cuidados intensivos el uso de la pp asociada a vni o cánula de alto flujo podría ser una estrategia útil para mejorar la oxigenación en pacientes infectados con covid-19 e hipoxemia. se recomienda considerar la elevación de biomarcadores como la troponina i o t y el nt-pro-bnp en el paciente con covid-19 como indicadores de injuria miocárdica aguda, sin embargo, no reemplazan la ecocardiografía en el enfoque del paciente con sospecha de disfunción miocárdica. fuerte a favor fundamento la injuria miocárdica aguda asociada a covid-19 se reporta con frecuencia teniendo en cuenta los cambios en biomarcadores como la troponina y cambios electrocardiográficos, pero su impacto en la función cardíaca se desconoce y mucho menos su correlación con los cambios ecocardiográficos. los pacientes con covid-19 pueden desarrollar una serie de complicaciones cardiacas desde injuria miocárdica, arritmias, infarto, hasta miocarditis fulminante con falla cardiaca aguda y shock cardiogénico (292) . la troponina i, se ha encontrado más elevada en pacientes con curso fatal por covid-19 (37) . los niveles de nt-pro-bnp han sido reportados con elevación severa en pacientes con miocarditis y disfunción sistólica, con una disminución progresiva en relación a la mejoría de los pacientes, pero no parece tener un correlación significativa con el cambio de la fracción de eyección (fevi) (293) . la evidencia clínica sugiere que la elevación de los biomarcadores es más relacionada al compromiso sistémico que el daño miocárdico directo, q. deng y colaboradores en un análisis retrospectivo de 112 pacientes, reportaron niveles iniciales de troponinas normales casi en la mayoría, en el 37,5% de los casos los niveles incrementaron significativamente, principalmente en los que fallecieron y solo 6 pacientes tenían fevi menor al 50% y ninguno inferior al 40%, lo cual no sugiere una asociación entre las dos amci ® pruebas (294) . en una publicación donde se compara el fenotipo de 18 pacientes con covid-19 con un histórico de 23 pacientes con sdra por influenza (295) , se encontró que los primeros tenían mayor elevación de troponinas 73% vs 53%, pero en los parámetros ecocardiográficos contrario a lo que se esperaría los índices de rendimiento ventricular fueron mayores para el grupo de covid-19: índice cardiaco 3.1 vs 2.5 l/m/m 2 ; fevi 52 vs 44%; tapse 25 vs 18mm, nuevamente aunque no fue uno de los objetivos del estudio, parece no encontrarse correlación entre los biomarcadores que sugieren injuria miocárdica y los parámetros ecocardiográficos, el cual constituye uno de los pilares de la exploración cardiaca. se recomienda considerar como marcadores iniciales de mal pronóstico en el paciente crítico con covid-19 con sospecha de disfunción miocárdica aguda la elevación persistente de troponina i, mioglobina o creatin kinasa; independiente de la fracción de eyección del ventrículo izquierdo evaluada mediante ecocardiografía. fundamento los pacientes con covid-19 admitidos a la unidad de cuidados intensivos presentan con frecuencia disfunción cardiaca primaria, que puede corresponder a cardiomiopatía por estrés o miocarditis viral, pero también pueden ser consecuencia del compromiso sistémico (294, 296) . aunque parece que en los fenotipos cardiovasculares estudiados, el compromiso hemodinámico severo de la función sistólica izquierda y derecha es menor (295) . en el estudio de deng y colaboradores con 112 pacientes con covid-19, la fiebre, la disnea, hipoxemia, la obesidad y niveles elevados de cpk, troponina y nt-pro-bnp se relacionaron significativamente con mayor severidad (294) . en el subgrupo de pacientes con miocarditis frente a controles, el perfil clínico se describe con mayor edad, niveles de temperatura más elevados (38.8 ± 0.8 vs 38.2 ± 1.0; p:0.03), mayor proporción de disnea (92,8 vs 51%), y de dolor torácico (92,8 vs 61,2%). en los 14 pacientes fallecidos el 100% tuvieron picos de elevación de troponina i y de nt-pro-bnp dentro la semana que precedió la muerte, el 78% presentaron alteraciones electrocardiográficas y solo el 28% presentaron fracción de eyección menor o igual al 45% (294) . shi y colaboradores, enrolaron 671 pacientes para describir el significado clínico del compromiso miocardio de pacientes con covid-19 en wuhan, 62 pacientes fallecieron, de los cuales el 75% presentaron injuria miocárdica aguda (297) . el área bajo la curva (auc) de la troponina i inicial para predecir muerte intrahospitalaria fue de 0,92 (ic 95%, de 0,87-0,96) con una sensibilidad y especificidad del 86%, el auc para mioglobina fue de 0.88 y para cpk-mb fue de 0,87(297). un punto de corte para el pico más alto de troponina i de 4.5, tuvo un hazard ratio para mortalidad de 1.25 (ic 95%, 1.07-1.46; p= 0.004). en un análisis multivariado la edad avanzada, la respuesta inflamatoria y las enfermedades cardiovasculares subyacentes se asociaron con mayor riesgo de lesión miocárdica en pacientes con covid-19. con la información disponible parece que los biomarcadores de lesión miocárdica aguda elevados amci ® al ingreso y de forma persistente pueden predecir el riesgo de mortalidad intrahospitalaria en los pacientes con sospecha o diagnóstico de covid-19 con afectación cardiovascular. se recomienda no realizar de forma rutinaria ecocardiografía en pacientes críticos con covid-19. se debe practicar ecocardiografía en pacientes con sospecha o diagnóstico de covid-19 si presenta alguna de las siguientes condiciones: 1. síntomas y signos de insuficiencia cardíaca aguda de novo. 2. shock o deterioro súbito hemodinámico refractario a líquidos y/o vasoactivos con sospecha de origen cardiogénico. 3. sospecha de infarto agudo de miocardio o embolismo pulmonar para determinar intervenciones terapéuticas con un beneficio clínico. 4. cambios en el electrocardiograma, arritmias ventriculares o paro cardiorrespiratorio no explicados por otra causa. para nuestro conocimiento, en el momento no existe estudios clínicos que evalúen los criterios para realización de ecocardiograma en el paciente con covid-19. las sociedades de ecocardiografía han recomendado realizar el ecocardiograma en el contexto clínico en el cual, la información obtenida proporcione un cambio en la conducta o se espere un beneficio clínico al realizar este procedimiento (298) (299) (300) (301) . igualmente, se recomienda realizar el examen a la cabecera del paciente y el escaneo debe ser dirigido a contestar preguntas específicas según el contexto clínico del paciente (298) (299) (300) (301) (302) . ward et al, en su publicación describe cómo el uso del ecocardiograma limitado (dirigido) en la university of chicago medicine (ucm), aumentó significativamente durante la pandemia (15% frente a 34%, p <0.001), posterior a la implementación de recomendaciones sobre el uso apropiado de la ecocardiografía en tiempos de pandemia (303) . los pacientes con infección por sars -cov-2 pueden presentarse con comorbilidades cardiovasculares que potencialmente estén descompensadas y/o compromiso cardiovascular por covid-19. en este último, podemos encontrar alguno de los siguientes fenotipos: falla cardiaca aguda en el marco de compromiso directo viral o secundario al estrés metabólico y liberación de citoquinas, síndrome coronario agudo, cor-pulmonar secundario a tep o por compromiso secundario al sdra (299, 300, 304, 305) . las manifestaciones cardiovascular puede sospecharse en el marco de choque que no esté explicado por causas extracardiacas evidentes que no responde a líquidos, dolor torácico con clínica de síndrome coronario agudo, cambios electrocardiográficos y elevación de biomarcadores de lesión miocárdica, signos de falla cardiaca descompensada, deterioro súbito de la oxigenación, arritmias o paro cardiorrespiratorio (301, 304, 305) . ante estas manifestaciones, el ecocardiograma podría ser útil para entender el origen de la descompensación aguda, al estar enfocado a amci ® responder preguntas acerca de la función ventricular global y segmentaria (en el abordaje de síndrome coronario agudo), compromiso del ventrículo derecho, alteraciones valvulares, derrame pericárdico, si existe una contribución cardiovascular al compromiso pulmonar, si en el marco del choque existe evidencia de componente cardiogénico y cómo podría guiarse/optimizarse el soporte hemodinámico de estos pacientes(300-304). se sugiere en pacientes críticamente enfermos con covid-19 que cursan con shock y sdom, ajustar la monitoria a las condiciones clínicas del paciente y recursos disponibles. se puede considerar el cap para el monitoreo del gasto cardiaco, la valoración de la perfusión y orientar los elementos hemodinámicos del tipo de shock, el cap de gasto cardiaco continuo puede disminuir la exposición del personal de salud frente al catéter de medición convencional. se sugiere la utilización de la tdtp dependiendo de la disponibilidad del recurso para orientar el diagnóstico diferencial del sdra versus edema pulmonar cardiogénico en los pacientes con covid-19. fundamento los pacientes con infección severa por sars-cov-2, cursan con alto riesgo de falla renal y cardiovascular, con necesidad de un manejo restrictivo de líquidos, lo que justifica la monitoria estricta en uci (306, 307) . el catéter venoso central es útil para la monitoria inicial de estos pacientes, sin embargo, su predicción a respuesta a volumen está limitada (306) (307) (308) . la monitoría no invasiva tiene limitaciones en casos severos de inestabilidad hemodinámica, ventilación espontánea y en presencia de peep alto, lo que limita su uso para el cálculo de gasto cardiaco y la predicción de respuesta a líquidos (308, 309) . la monitoria con cap puede ser considerada en pacientes con covid-19 que cursan con choque y doms, con el objetivo de realizar un diagnóstico definitivo de los componentes del choque, valorar la hipoperfusión, la función cardiaca y el estado de volemia (307, 308) . igualmente, los pacientes con sospecha tep o compromiso del ventrículo derecho pueden beneficiarse de esta monitoria(308). richard et al, en su estudio determinaron los desenlaces asociados al uso de cap vs cvc en pacientes con shock, sdra, o ambos, sin evidenciar diferencias en mortalidad (49.9% vs 51.3% p =.70) o estancia hospitalaria. el uso de cap no garantiza la mejoría de desenlaces en pacientes con covid-19, sin embargo, la presencia de una monitoria continua ayudaría a optimizar los recursos y disminuiría la interacción con el paciente, con menor exposición del equipo médico (310) . la monitoria por tdtp puede utilizarse en pacientes con covid-19 que cursan con choque, buscando optimizar el manejo hídrico, valorar el agua extravascular pulmonar (evlw) y el índice de permeabilidad vascular pulmonar (pvpi) con el fin de establecer el diagnóstico amci ® definitivo del edema pulmonar: sdra vs cardiogénico (311) (312) (313) . hu et al, en su estudio evaluaron los desenlaces del uso de evlw y la presión de cuña de la arteria pulmonar (pawp) como estrategias para el manejo de líquidos en pacientes sdra, no encontraron diferencias significativas en las tasas de supervivencia (p = 0,542). no obstante, en el grupo de evlw la duración de la ventilación mecánica y la estancia en la uci fueron significativamente menor (p <0,05), al igual que el balance hídrico (p <0.05), con mejoría significativa en los índices de oxigenación (p = 0.006)(314). no se puede emitir una recomendación a favor o en contra para la utilización de un protocolo de ultrasonido rutinario a la cabecera del paciente (pocus). sin embargo, se podría considerar el uso en pacientes seleccionados, con los adecuados epp y desinfección de los equipos; donde el pocus pueda tener ventajas sobre otras modalidades de monitoria o en pacientes con limitaciones para monitoria invasiva que requieren evaluación del estado hemodinámico o determinación de severidad del compromiso pulmonar. las recomendaciones sobre la utilidad de pocus en pacientes con covid-19 están enfocadas principalmente en la evaluación de la severidad/progresión de la lesión pulmonar, diagnóstico de manifestaciones cardiovasculares, monitoria hemodinámica y en la guía de fluidoterapia (302, (315) (316) (317) . en la valoración del compromiso pulmonar por covid-19, el pocus ofrece una ventaja sobre otras modalidades de monitoreo, debido a la capacidad de enmarcar el compromiso pulmonar en una línea de tiempo según sus hallazgos: desde la aparición de un patrón de "líneas b", consolidaciones subpleurales con evolución a consolidaciones multilobares, irregularidades en el artefacto de la línea pleural y finalmente aparición de patrón de "líneas a" una vez inicie la recuperación, con adecuada correlación tomográfica (318) (319) (320) (321) . en la diferenciación del origen del choque, el pocus ha demostrado superioridad versus el concepto clínico al evaluar: función ventricular (incluyendo ventrículo derecho), vena cava inferior, líquido libre abdominal, lesiones aórticas, compromiso pulmonar y búsqueda de trombosis venosa profunda identificando tep (322, 323) . en cuanto a la monitoria hemodinámica de pacientes con covid-19, adicional a la función y gasto cardíacos, se recomienda variables dinámicas de respuesta a líquidos y ultrasonido pulmonar en el diagnóstico de sobrecarga hídrica (205) . la variabilidad de gasto cardiaco calculado por pocus durante la elevación pasiva de miembros inferiores, identifica los respondedores a líquidos con sensibilidad del 88% y un lr (-): 0.13 [95%ci, 0.07-0.22]) (324) . la variabilidad de la vena cava inferior muestra limitaciones en pacientes con aumento de presiones de cavidades derechas y respiración espontánea (325) . en cuanto a otras modalidades de monitoría no invasiva, es importante conocer las limitaciones en el marco de compromiso hemodinámico severo, ventilación espontánea, alteraciones valvulares aórticas, entre otras (309) . marik (326) . el ultrasonido tiene limitaciones específicas como la necesidad de un operador experimentado y la adecuada calidad de las imágenes. adicionalmente, en los pacientes con covid-19, esta modalidad de monitoreo requiere una mayor interacción con el paciente, mayor uso de epp en comparación con otras modalidades el pac(307). se recomienda perseguir al inicio de la reanimación del paciente críticamente enfermo con covid-19, metas clínicas de fácil medición, como la presión arterial media (entre 60 y 65 mmhg) o el gasto urinario (mayor a 0,5 cc/k/h) y metas de perfusión como el lactato en sangre arterial (menor a 2 mmol), la saturación venosa central de oxígeno (entre 65 y 70%) y la diferencia veno arterial de co2 (menor a 6 mmhg). se han reportado casos de disfunción ventricular como causa de choque asociado a covid-19, sin embargo, no se ha descrito un manejo específico o cambios en las metas de reanimación para estos pacientes, las manifestaciones de hipoperfusión tisular son: alteración de la conciencia, oliguria, piel fría y moteada y pulso débil. a nivel de gases sanguíneos las metas de reanimación pueden ser globales como el lactato (en sangre arterial vn< 2 mmol) y la diferencia veno arterial de co2(pv-aco2 vn < 6 mmhg) o regionales como la saturación venosa central de oxígeno medida en la sangre venosa tomada de un catéter central (vn: 65-70%). se puede optimizar la perfusión, interviniendo los principales determinantes: fluidos para aumentar el volumen intravascular, inotrópicos para aumentar la fuerza de contractilidad, vasopresores para recuperar la presión de perfusión y transfusión de glóbulos rojos para aumentar la hemoglobina como transportador de oxígeno (44) , las recomendaciones dadas en el documento anterior siguen siendo válidas e incluyen entre otras que todo paciente con covid-19 en estado de shock debe ser ingresado de forma inmediata a la unidad de cuidados intensivos, garantizando el aislamiento indicado, procurando recuperar la presión arterial media a valores > 65 mmhg, para ello la utilización de un catéter venoso central en los pacientes que no responden al manejo inicial y el procedimiento debe ser realizado por el médico con mayor entrenamiento, idealmente guiado por ecografía si hay disponibilidad y las competencias, así mismo las estrategia de control estricto de fluidos para no generar efectos deletéreos relacionados a la sobrecarga de volumen, es lo más indicado. se recomienda en la reanimación inicial de pacientes en estado de shock con sospecha o amci ® diagnóstico de covid-19, guiar la fluidoterapia con el uso de índices clínicos como el tiempo de llenado capilar, temperatura de la piel y depuración de lactato; en fases avanzadas donde el monitoreo clínico es insuficiente utilizar medidas dinámicas como la variabilidad de presión de pulso (vpp), la variabilidad de volumen sistólico (vvs), la respuesta a la maniobra de elevación pasiva de piernas o la prueba de oclusión teleespiratoria de acuerdo a los recursos disponibles y la experiencia. fuerte a favor fundamento sobre los objetivos de intervención y el tipo de agente vasoactivo a utilizar en pacientes con covid-19 y shock no existe una evidencia directa y las recomendaciones se basarán en evidencia indirecta de pacientes críticos con diversos tipos de shock en especial el séptico y vasopléjico. la falla circulatoria aguda asociado a sdra en covid-19 se presenta con una frecuencia del 6-30% y en la admisión a urgencias la hipotensión y un lactato ≥2 es infrecuente(38, 327). la baja sensibilidad del qsofa y crb-65 para predecir la severidad del covid-19 y la necesidad de intervenciones de terapia intensiva refleja lo infrecuente del shock en esta condición. factores como la vasoplejia, fuga capilar asociada al estado hiperinflamatorio, altos requerimientos de peep y disfunción cardiaca pueden ser generadores o contribuyentes del shock y deben ser considerados en el abordaje diagnóstico, en su interpretación para lograr tomas de decisiones adecuadas. en pacientes con sdra, una reanimación óptima de líquidos debe tomar en cuenta aspectos como tiempo (oportunidad), tipo (cristaloides balanceados y/o no balanceados o coloides) y volumen (ni mucho, ni poco) con el objetivo de disminuir la mortalidad, el tiempo de vm y de cuidados intensivos, sin que ello afecte los índices de oxigenación, de perfusión tisular y la morbilidad asociada con su uso inadecuado. la administración agresiva de líquidos puede empeorar la oxigenación y la disfunción ventricular, lo que potencializa un mayor tiempo de ventilación mecánica e incluso la mortalidad. la evidencia ha demostrado que una estrategia conservadora de fluidos (balance -136+/amci ® en una revisión sistemática y un metaanálisis de 7 rct (n = 1.301) una terapia dirigida al aclaramiento temprano de lactato frente a una terapia guiada por la saturación venosa central de oxígeno (svo2), se asoció con una reducción significativa de la mortalidad (rr 0,68), menor estadía en la uci (dm 1,64 días), y menor duración de la ventilación mecánica (dm -10,22 horas). pero se debe resaltar que un nivel alto de lactato no siempre indica hipovolemia; también puede ser causada por uso de adrenalina, agonistas beta o por disfunción mitocondrial, insuficiencia hepática e isquemia mesentérica (331) . por otra parte, el llenado capilar (crt), una prueba técnicamente fácil y accesible, realizada cada 30 minutos se asoció con una reducción no significativa de la mortalidad (hr 0,75) en comparación con la medición de lactato sérico cada 2 horas. dado el potencial beneficio sobre mortalidad, duración de estancia en uci y la duración de la ventilación mecánica, así como su accesibilidad, sugerimos utilizar parámetros dinámicos de temperatura de la piel, tiempo de llenado capilar y / o medición de lactato sobre parámetros estáticos para evaluar la capacidad de respuesta a la fluidoterapia en pacientes con covid-19 y shock(332). se recomienda en pacientes adultos con covid-19 y estado de shock, escoger la norepinefrina como el vasopresor de primera línea y a la vasopresina el de segunda. si no se cuenta con norepinefrina el uso de vasopresina o epinefrina serían la primera elección; la dopamina no se recomienda por el mayor riesgo de arritmias. se recomienda iniciar dobutamina frente al aumento de la dosis de norepinefrina en pacientes en estado de shock con evidencia de disfunción cardíaca e hipoperfusión persistente a pesar de la reanimación inicial. fuerte a favor fundamento sobre los objetivos de intervención y el tipo de agente vasoactivo a utilizar en pacientes con covid-19 y shock no existe una evidencia directa y las recomendaciones solo pueden basarse en evidencia indirecta de pacientes críticos con sepsis y sdra. en pacientes en shock séptico los agentes vasoactivos para alcanzar una pam de 60-65 es un objetivo razonable. una presión media más alta puede incrementar 2.5 veces el riesgo de arritmias cardiacas y no está exento de riesgo de isquemia en las extremidades (333) . para aproximarnos a la escogencia de los vasoactivos en shock séptico, basados en su perfil de riesgo/beneficio, la guía scandinavian society of anaesthesiology and intensive care medicine (ssai ) task force for acute circulatory failure(334), la revisión sistemática de cochrane database 2 con 28 rct con un n:3497 (335) y el ensayo clínico controlado de honarmand k et al con un n:3,737 (336) amci ®  la noradrenalina es el agente vasoactivo más ampliamente estudiado con el menor riesgo a priori de efectos no deseados, razón por la cual se sugiere usar como el agente vasoactivo de primera línea en pacientes con covid-19 y shock.  si la noradrenalina no está disponible la vasopresina o epinefrina se muestran como la mejor alternativa. los factores que determinan la elección entre vasopresina y epinefrina pueden incluir disponibilidad y el perfil de seguridad de estos agentes. con la vasopresina, la isquemia digital puede ser una preocupación y con epinefrina, la taquicardia, la isquemia miocárdica y el exceso de producción de lactato.  el uso de dopamina se ha asociado un 2.5 veces mayor de riesgo de aparición de arritmias frente a la norepinefrina y un posible aumento del riesgo de mortalidad. por ello la dopamina no debe utilizarse en pacientes con covid-19 y shock donde haya disponible de norepinefrina o las alternativas señaladas  en shock distributivo la adición de vasopresina a las catecolaminas evidenció baja certeza de reducción de la mortalidad (rr 0,91; ic del 95%: 0,85 a 0,99), alta certeza de una reducción de la fibrilación auricular (rr 0,77; ic del 95%: 0,67 a 0,88) y certeza moderada de un mayor riesgo de isquemia digital (rr 2,56; ic del 95%: 1,24 a 5,25). en vista de estos hallazgos se plantea la vasopresina como un agente vasoactivo de segunda línea a ser utilizado si la pam objetivo no se ha alcanzado con norepinefrina en pacientes con covid-19 y shock. no existe evidencia directa en pacientes con covid-19 y shock, para establecer una recomendación sobre cuál es el agente inotrópico óptimo. en una guía de práctica clínica de 2018 que evalúa el agente inotrópico óptimo en pacientes con insuficiencia circulatoria aguda (shock), no se identificaron rct que comparen dobutamina versus placebo o ningún tratamiento. con base en una justificación fisiopatológica, sugerimos agregar dobutamina, más que no suministrar ningún tratamiento, en pacientes con covid-19 y shock con evidencia de disfunción cardíaca e hipoperfusión persistente a pesar de la reanimación con líquidos y altas dosis de norepinefrina. el uso de dobutamina en estado de shock, incluso en pacientes con covid-19 con shock, debe ser investigado. recomendación se recomienda no suspender la medicación estándar para falla cardiaca en pacientes con sospecha o diagnóstico de covid-19, especialmente los iecas, ara-ii, y b-bloqueadores, si la condición clínica permite continuar el uso de esta medicación, ya que no se ha podido confirmar una asociación nociva. amci ® previos alrededor de la relación independiente de la edad avanzada, enfermedad cardiovascular subyacente (enfermedad coronaria, insuficiencia cardíaca y arritmias), tabaquismo activo y epoc con muerte por covid-19 (337) (338) (339) ; esos mismos reportes sugieren que las mujeres son proporcionalmente más propensas a sobrevivir a la infección por covid-19 que los hombre; existen además consideraciones especiales desde el punto de vista cardiovascular, que se deben tener en cuenta al decidir cualquier terapia en paciente afectados por covid-19 y existe la hipótesis de un efecto nocivo de la terapia estándar para falla cardiaca en estos pacientes (338) . en un estudio observacional que incluye 8910 paciente con infección por covid-19, se evaluó la relación entre la enfermedad cardiovascular subyacente, y la asociación entre la terapia farmacológica cardiovascular y la mortalidad (337); respecto a los factores de riesgo cardiovascular, el 30.5% de los pacientes tenían hiperlipidemia, el 26.3% tenía hipertensión, el 14.3% tenía diabetes mellitus, y en relación a los medicamentos, los sobrevivientes usaron más comúnmente ieca y las estatinas que los no sobrevivientes, mientras que no se encontró asociación entre la supervivencia y el uso de ara ii; respecto a los otros medicamentos incluidos b-bloqueadores, antiplaquetarios e insulina no se encontraron diferencias significativas; sin embargo, y teniendo en cuenta el impacto sobre mortalidad del uso de betabloqueadores en la falla cardiaca, consideremos que la decisión de continuar su uso debe basarse en el análisis clínico de cada paciente y su estabilidad clínica. se recomienda establecer un protocolo de reanimación ajustado al contexto del paciente con covid-19 con una organización administrativa ajustada a la pandemia que incluya las siguientes estrategias:  desarrollar una estrategia de prevención del paro cardiorrespiratorio en el paciente con sospecha o diagnóstico de covid-19 basada en la detección oportuna.  formar un equipo multidisciplinar formado en rcp con líderes médicos, de en enfermería y en terapia respiratoria, los cuales deben educar a todo el equipo de trabajo en la identificación de signos de alerta temprana, cambios abruptos de variables clínicas, técnicas de monitoreo, interpretación de paraclínicos y de alarmas de monitoreo.  entrenamiento del personal sanitario a través del uso de la simulación clínica en manejo de crisis, epp, y procesos de atención fundamentales en la atención del paro cardiaco en el paciente con sospecha o diagnóstico de covid-19  promover la comunicación asertiva, planeación y retroalimentación de las intervenciones realizadas antes y después de un evento de paro cardiaco (briefing y debriefing), con el fin de establecer modificaciones que conllevarán a mejoras en la atención de futuros eventos. amci ® el pronóstico y sobrevida de un paciente con sospecha o diagnóstico de covid-19 que presenta paro cardiaco depende de la prevención a través del reconocimiento oportuno de las causas reversibles de éste, la no presencialidad y un ritmo de paro no desfibrilable lo hacen de mal pronóstico. la prevención va a depender del nivel de entrenamiento del equipo previamente, y en época de pico de pandemia cuando el talento humano especializado disminuya, se hace necesario que en los equipos de trabajo estén liderados por especialistas en la disciplina para que puedan guiar al equipo. los nuevos procesos de atención del paciente, la alta contagiosidad del virus, y el uso de nuevos medicamentos hacen que se requiera un entrenamiento del personal para estandarizar los procesos y disminuir el error médico. la crisis de covid-19 está ejerciendo una presión sin precedentes sobre las personas, los equipos y los sistemas organizacionales, conllevando a errores médicos que van desde la infección cruzada por el personal sanitario con la posibilidad de cometer errores en la atención. cada día trae nuevos desafíos: picos en volumen y gravedad, escasez de equipos y estrés en los médicos sobrecargados, que se manifiesta según la experiencia de wuhan en insomnio y depresión. se propone implementar una estrategia antes, durante y después del trabajo clínico, denominada circle up covid-19 desarrollada por center of medical simulation dirigida a convertir equipos de trabajo muchas veces insustituibles , en eficientes , seguros, fuertes y que se apoyan mutuamente incluyendo en mejora de la salud psicológica . impactando en el rendimiento del equipo , y promoviendo el bienestar y la resiliencia(340-342) se recomienda establecer un protocolo de reanimación ajustado al contexto clínico del paciente con covid-19 que incluya las siguientes modificaciones:  implementar criterios de selección e inicio de maniobras de rcp en la atención del paro cardíaco basados en la bioética y en el pronóstico de supervivencia a corto y largo plazo de los pacientes.  promover la prevención del paro cardiaco mediante la detección oportuna del riesgo y definir intubaciones programadas.  asegurar la correcta protección con los epp necesarios al abordar el paro cardiaco y la intubación que son procedimientos generadores de aerosoles.  priorizar el manejo de la vía aérea antes del inicio de las compresiones torácicas, haciendo énfasis en la reducción de la exposición de aerosoles (código azul protegido).  utilizar filtro de alta eficiencia contra virus para todas las estrategias de ventilación (bolsa mascarilla con cierre hermético y en el circuito del ventilador).  promover la realización de la intubación por el operador de mayor experticia con uso de videolaringoscopio si está disponible y considerar el acceso supraglótico solo si el intento de intubación es fallido. amci ®  en caso de parada cardiaca en ventilación mecánica iniciar el masaje cardiaco evitando las desconexiones del circuito del respirador.  en caso de paro en posición prono si el paciente se encuentra vigil retornar rápidamente a la posición supino y si está en ventilación mecánica es razonable realizar compresiones en la espalda. fuerte a favor fundamento se hace necesario el entrenamiento en el manejo de los procedimientos generadores de aerosoles y se sugiere que el que realiza la intubación orotraqueal debe ser el más experto. el riesgo de aerosolización es de 6.6 en el proceso de intubación orotraqueal, el de compresiones torácicas es de 4,5, ventilación mecánica no invasiva de 3,1, ventilación manual pre-intubación de 2,8, succión después de intubación 1,3. se ha descrito que si no se ha capacitado previamente en el retiro de los epp existe más riesgo de auto contaminación y aumenta ésta sin un líder supervisor al retirarlo. según revisión de cochrane sobre ropa y equipo de protección para los trabajadores sanitarios para evitar que se contagien con el coronavirus y otras enfermedades altamente infecciosas da a conocer que la capacitación presencial, la simulación por ordenador y la capacitación por vídeo dieron lugar a menos errores a la hora de quitarse el epp que la capacitación impartida solo como material escrito o una conferencia tradicional (343) (344) (345) (346) (347) (348) . se recomienda no considerar la existencia de manifestaciones neurológicas específicas o típicas atribuidas a la infección por sars-cov-2. se recomienda realizar la valoración neurológica integral del paciente con diagnóstico o sospecha de sars-cov-2 teniendo en cuenta manifestaciones frecuentes relacionadas a covid-19: disgeusia, anosmia, cefalea, vértigo, confusión, delirium, alteración de estado de consciencia, eventos cerebrovasculares, ataxia, polineuropatías inflamatorias y convulsiones. una revisión sistemática realizada por asadi-pooya et al. entre diciembre y marzo de 2020 mostró que el 25% de los pacientes con covid-19 presentaron sintomatología neurológica. analizaron cinco artículos (n=765) donde 4 eran retrospectivos, y 1 era prospectivo, encontrando cefalea entre el 6 y el 13%, vértigo entre el 9 y el 17%, confusión en el 9%, alteración del estado de consciencia en el 8%, eventos cerebrovasculares en un 3%, ataxia en un 0,5% y convulsiones en un 0,5% (349) . amci ® menor a 1000 participantes donde recolectarán información sobre el compromiso neurológico en pacientes con covid-19 con un seguimiento hasta febrero de 2021 (350) . la hiposmia y la disgeusia de aparición súbita son manifestaciones clínicas muy prevalentes en pacientes con covid-19 evidentes aun en ausencia de sintomatología respiratoria alta. lechien et al publicaron un estudio multicéntrico que incluyeron 12 hospitales europeos reclutando 412 pacientes infectados con covid-19 levemoderado donde 85,6% presentaron alteraciones relacionadas con el olfato y 88,5% presentaron alteraciones relacionadas con el gusto, donde la anosmia se presentaba antes que cualquier otro síntoma en el 11,8% de los casos y el 18,2% de los casos no presentaba rinorrea u obstrucción nasal, la recuperación del olfato fue presente en el 44% de los pacientes y las mujeres fue el grupo poblacional más afectado (p=0,001) (351) . otras manifestaciones clínicas son las alteraciones de la agudeza visual, y dolor tipo neuralgia (352) . respecto a las patologías psiquiátricas; la serie de mao comenta que el 7,5% de los pacientes tiene clínica de alteración del estado de consciencia, concepto que se aproxima a la defunción de delirium. severance et al. encontraron que 106 pacientes con sintomatología psicótica aguda presentaron niveles elevados de inmunoglobulina g para coronavirus del tipo hku1, nl63 y oc43 con diferencias estadísticamente significativas respecto a los individuos controles (n=106) (p<0,001). donde la respuesta inmune para nl63 fue asociado con el espectro-esquizofrenia (or: 3.10, ci 5 1.27-7.58, p= 0.013) pero no se correlaciona con desórdenes afectivos (353) . aún no se ha descrito una correlación directa de este trastorno psicótico con covid-19. los síntomas musculares se han observado en pacientes infectados por covid-19 incluyendo la miopatía del paciente en estado crítico (miopatía difusa no necrotizante con degeneración grasa de fibras musculares), la miopatía necrotizante (ligada a falla orgánica múltiple) y la miopatía de filamentos gruesos(354). se recomienda considerar como predictores clínicos neurológicos de alerta para sospechar covid-19: anosmia, disgeusia, delirium y alteraciones neuromusculares inespecíficas sin otra causa aparente de explicación. se recomienda no establecer de rutina predictores neurológicos específicos de mal pronóstico en el paciente críticamente enfermo con covid-19. se deben tener en cuenta los factores de riesgos generales de mal pronóstico para la población general como la edad avanzada, las comorbilidades cardiovasculares y el tabaquismo. page la proteína spike (s) del covid-19 es reconocida por la enzima convertidora de antígenos 2 (eca2) de la célula huésped cuyo papel es el punto de entrada molecular a tejidos pulmonares, gastrointestinales y neuronales (355) . la forma como el covid-19 ingresa al sistema nervioso central es desconocido, pero se especula que inicialmente invade terminales nerviosas periféricas y después llega al sistema nervioso central a través de una ruta guiada por sinapsis nerviosas con un patrón ascendente (ruta dada por el coronavirus hev67 y el oc-43) (352, 356) . en modelos de roedores el covid-19 ingresaría al cerebro a través del nervio olfatorio, atravesando la lámina cribiforme propagándose por el tálamo y el tallo cerebral; explicándose por la expresión de los receptores de la enzima convertidora de antígenos (eca2) en la superficie de las mucosas nasales, las neuronas y la glía (352, 357, 358) . una segunda forma de ingreso es a través de la vía hematológica mediante arterias cerebrales atravesando la barrera hemato-encefálica utilizando las células inflamatorias como un modelo similar al del caballo de troya (352, 359, 360) logrando una ubicación definitiva en células neuronales y endoteliales del lóbulo frontal como lo demostraron en estudios post-mortem descritos por paniz -mondolfi et al, lo que explicaría los cambios comportamentales de paciente (360) . la tercera forma de acceso al sistema nervioso central es mediante el drenaje del sistema linfático cerebral invadiendo ganglios linfáticos hiliares y mesentéricos con sintomatología gastrointestinal asociada (361) . una vez ha logrado ingresar tiene la capacidad de infectar macrófagos, microglía, y astroglía los cuales secretan factores proinflamatorios como interleuquina 12, interleuquina 15, y factor de necrosis tumoral alfa (362) . esta condición se exacerba con el desencadenamiento de la tormenta de citoquinas liderada por la interleuquina 6, interleuquina 2, interleuquina 7 e interferón gamma (355) . de esta forma los coronavirus siendo neurotrópicos ocasionan múltiples manifestaciones clínicas ya mencionadas, así como encefalitis, parálisis flácida, incluyendo la asociación con guillain-barré (357) . los síntomas que harían sospechar la presencia de neurocovid-19 son la náusea, el vómito y la anorexia, estos síntomas pueden ser el reflejo del compromiso del virus en el área postrema del piso del cuarto ventrículo que hace parte del complejo vagal dorsal de la médula oblonga. sin embargo, estos síntomas pueden enmascararse como una respuesta inespecífica relacionada con un compromiso gastrointestinal (363) . como se mencionó previamente la anosmia y la disgeusia son síntomas significativos para sospechar en covid-19 (358) ; esto es debido a una lesión directa sobre el nervio olfatorio (i par craneal), y la lesión de alguno de los tres nervios encargados de registrar el sentido del gusto como lo son el vii, ix y x pares craneales, así como el compromiso del núcleo solitario y del tálamo como zona de relevo; de hecho el núcleo del tracto solitario es muy cercano al centro respiratorio que podría ocasionar disnea de origen central (361) , otros núcleos como el núcleo dorsal motor del vago y el núcleo ambiguo están relacionados con funciones cardiovasculares a tener en cuenta (364) . respecto a los factores de riesgo destaca el tabaquismo el cual aumenta la posibilidad de neuroinfección debido a interacciones funcionales entre el receptor nicotínico de acetilcolina y el receptor eca2 el cual está sobreexpresado en pacientes fumadores (365) . amci ® en pacientes con infecciones severas vs infecciones no severas (45.5% vs 30.2%, p = 0.02), incluyendo eventos cerebrovasculares (5,7% vs 0,8% p=0,03), alteración del estado de consciencia (14.8% vs 2.4%; p<0.001) y lesiones musculoesqueléticas (19,3% vs 4,8% p< 0001) (366) . la encefalopatía que se manifiesta como una alteración aguda o subaguda del estado de consciencia presentándose en pacientes con comorbilidades, factores de riesgo cardiovasculares, edad avanzada y deterioro cognitivo previo (362, 366, 367) . así como aquellos individuos con hipoxemia la cual induce metabolitos anaerobios en el sistema nervioso central, edema celular, intersticial e isquemia (362) . los eventos cerebrovasculares pueden ser desencadenados por cuadros de hipoxia, inmovilización, un incremento de la respuesta proinflamatoria o por predisposición a la hipercoagulabilidad (359) . respecto a este último rubro tanto la edad (hazard ratio 1,05/por año 95% ic 1,004 -1,01) y la coagulopatía definida como como un tiempo de protrombina mayor a 3 segundos, o tiempo de tromboplastina mayor a 5 segundos (hr 4,1 95% ic 1,9 -9,1) fueron considerados predictores independientes de complicaciones trombóticas (352) ; otros trabajos reportan incremento del conteo plaquetario y niveles elevados de dímero d (352) . de hecho, un scoping review realizado por wilson y jack muestra que la presencia de eventos cerebro vasculares es un factor de riesgo de mal pronóstico para pacientes infectados por covid-19 (368) . mao et al. reportaron 14 eventos cerebro vasculares en 214 pacientes con covid-19, los factores de riesgo más relevantes fueron los clásicos factores de riesgo cardiovasculares (diabetes, hipertensión y edad avanzada), así como una presentación sistémica severa, teniendo como un denominador común el compromiso estructural de grandes vasos (366) . la presencia de convulsiones (clínicas o subclínicas) puede ser una manifestación de eventos cerebro vasculares, meningoencefalitis o hipoxia cerebral. siendo los factores de riesgo más importantes en su exacerbación las alteraciones electrolíticas como hipocalcemia, las reacciones adversas a medicamentos y la epilepsia como comorbilidad de base (359, 368) . otros tipos de coronavirus como lo son el 229e, 293, y oc43 se han aislado de líquido cefalorraquídeo (lcr) de pacientes con esclerosis múltiple sugiriendo posiblemente sean agentes etiológicos en la exacerbación de brotes de esta patología sin embargo aún no se ha documentado la asociación entre covid-19 y ésta condición (356) . otras patologías en las cuales se ha asociado la presencia de esta familia de microorganismos es la enfermedad de parkinson, la esclerosis lateral amiotrofia, la neuritis óptica y la encefalitis aguda diseminada (356, 362) . múltiples trabajos han documentado la asociación entre polineuropatía y coronavirus. la mayoría de ellos consideran que existe una estrecha relación entre una polineuropatía autoinmune exacerbada por la infección por coronavirus o bien un compromiso nervioso periférico inducido por bloqueo neuromuscular, alteraciones hidroelectrolíticas o disvitaminosis(356). amci ® se recomienda que todo paciente con acv isquémico se considere sospechoso de infección por covid-19 si presenta: sintomatología asociada sospechosa de infección por covid-19, contacto cercano con individuos con sintomatología infecciosa, allegados con viajes recientes, si la historia clínica es atípica, si la información suministrada no es clara, si presenta deterioro del estado de alerta inexplicable, y si al examen físico presenta hallazgos compatibles con una infección por covid-19. se recomienda que todo paciente con acv isquémico de quien no se pueda recibir información se considere sospechoso de covid-19 ya que el evento cerebro vascular es una complicación que se ha reportado en pacientes con infección por covid-19. hay una gran evidencia que correlaciona la presencia de infección por covid-19 con factores de riesgo cardiovasculares. esto se demostró en un metaanálisis que incluyó 7 estudios de china (n=1576) donde las comorbilidades más frecuentes fueron hipertensión (21,1%, 95% ic: 13 -27,2%), diabetes (9,7%, 95% ic 7,2 -12,2%), enfermedad cardiovascular (8.4%, 95% ic: 3.8-13.8) y patologías respiratorias (1.5%, 95% ic: 0.9-2.1%). al comparar severidad vs no severidad la presencia de hipertensión tuvo un or de 2.36 (95% ci: 1.46-3.83), y la enfermedad cardiovascular un or de 3.42 (95% ci: 1.88-6.22) respectivamente (369) . existieron pocos casos de hipercoagulabilidad en pacientes sin factores de riesgo cardiovasculares (356) . la cohorte de wuhan (n=138) publicada por wang et al. mostró otros factores de riesgo que podrían eventualmente estar asociados a estado de embolia y trombosis como shock en 8,7%, arritmias 16,7% y miocarditis en un 7,2%. situaciones que conllevarían a hipercoagulabilidad, lesión endotelial y eventualmente la aparición de acv. (174) . en este orden de ideas existe una estrecha correlación entre la presencia de factores de riesgo cardiovasculares que ocasionarían acv y que podrían eventualmente estar relacionados con la patogenia de covid-19. ante esta inquietud khosravani et al. publicaron en stroke un informe especial donde realizan ciertas recomendaciones para el abordaje de los pacientes con acv en el contexto de la pandemia por covid-19 de una forma rápida, eficaz y segura para los diferentes profesionales de la salud. surge así el código stroke protegido el cual consiste en:  usar elementos de protección personal y una mascarilla al paciente  ejecutar protocolo de aislamiento de contacto y gotas  ejecutar protocolo de aerosoles si el paciente está sometido a ventilación mecánica no invasiva, manejo de aspiración de secreciones o maniobras de reanimación cardiopulmonar básica y avanzada  si el paciente presenta deterioro del estado de alerta con necesidad de soporte ventilatorio alto con fracción inspirada de o2 mayor a 50% se recomienda intubar temprano y proceder con el transporte. se debe proceder con el código stroke protegido si el paciente presenta alguna de las siguientes condiciones:  si el paciente presenta sintomatología sospechosa de covid-19 (fiebre, tos, dolor torácico, disnea, cefalea, mialgias, emesis)  si existe algún contacto cercano con sintomatología infecciosa  si el paciente o alguno de sus allegados ha presentado viajes recientes amci ®  si el paciente es covid-19 positivo  si refiere al interrogatorio una historia clínica atípica o poco clara  si el paciente o alguno de sus acudientes es incapaz de suministrar información  si el paciente presenta deterioro del estado de alerta  si al examen físico se encuentran signos compatibles con patologías diferentes a covid19 por último, estas son las recomendaciones en el momento de realizar el traslado a saber:  no apresurarse dentro de la sala de reanimación o dentro de la unidad de cuidados intensivos y mantener la calma  designar un líder para el traslado del paciente y para supervisar el uso adecuado de los elementos de protección personal  limitar el número de personas encargadas del transporte  evitar la contaminación con otras áreas del hospital(370). se recomienda no realizar neuroimagen de rutina en pacientes críticos por covid-19 con cefalea y anosmia, dado que no existe una evidencia concluyente que demuestre una estrecha correlación entre estos síntomas y hallazgos imagenológicos. fuerte en contra fundamento en la mayoría de los casos la cefalea es un síntoma no específico que no es característico de irritación meníngea la ocurrencia de cefaleas aisladas en ausencia de otros síntomas sugiere un mecanismo benigno más que un compromiso de sistema nervioso central (356) . sin embargo, el covid-19 al tener una capacidad neuroinvasiva, se han reportado casos de encefalitis virales con o sin necrosis hemorrágicas de compromiso temporal mesial y talámico que ameritarían estudio de imagen diagnóstica (368) . un estudio retrospectivo publicado por kandenmirli et al. evaluó 749 pacientes en 8 hospitales infectados con covid-19 de los cuales 235 requirieron manejo en uci donde el 21% de ellos (n=50) presentaron sintomatología neurológica. la resonancia magnética cerebral fue realizada en 54% (n=27) de estos pacientes. el 44% tuvieron hallazgos agudos, el 37% tuvieron alteraciones corticales de la captación de señal en el modo flair, 3 pacientes tuvieron anormalidades en la señal flair en la sustancia blanca profunda y subcortical, 4 pacientes con lesiones en el lóbulo frontal, 3 en el lóbulo parietal, 4 en el lóbulo occipital, 1 en el lóbulo temporal, 3 en la corteza de la ínsula, y 3 en el giro cingular (371) . amci ® un paciente presentó trombosis de seno venoso y otro presentó un infarto en el tercio medio del territorio de la arteria cerebral media. en 56% de los pacientes no se encontraron hallazgos que sugieran compromiso intracraneal de covid-19. una correspondencia escrita por helms et al. reportaron 58 pacientes con sdra y covid-19 en dos unidades de cuidados intensivos en francia entre marzo y abril del 2020, el 84% presentaron signos neurológicos como delirium evaluados mediante cam-icu (65%), agitación (69%), signos del tracto cortico espinal (67%), síndrome disejecutivo (36%). de ellos se realiza resonancia magnética en 13 pacientes encontrando alteraciones en la perfusión en un 100%, un realce de leptomeninges en un 62%, y un acv isquémico en un 23%; dos pacientes asintomáticos presentaron áreas isquémicas con hiperintensidad focal (372) . ante estos hallazgos los principales diagnósticos diferenciales son las patologías autoinmunes, encefalitis, convulsiones e hipoglucemia. los pacientes con compromiso frontal bilateral poseen hipoxemia que ocasionan hipoperfusión fronto temporal. las microhemorragias corticales (y no) son consecuentes de la ruptura de la membrana hematoencefálica resultando en este patrón mencionado. el estado postictal muestra un compromiso simétrico de la sustancia blanca. de esta forma hay que considerar otras condiciones como las comorbilidades cardiovasculares, las reacciones adversas a los medicamentos, e hipoxia inducida por sdra que ocasionarían patrones imagenológicos de confusión, que ponen en duda la estrecha relación entre covid-19 y hallazgos de resonancia magnética (371) . en este orden de ideas necesitamos más datos para determinar cuáles son los hallazgos imagenológicos relacionados con neurotropismo y qué patrones pueden encontrarse directamente relacionados con la presencia de convulsiones, hipoxia o el desencadenamiento de una tormenta de citoquinas(362, 371, 372). se recomienda la valoración neurológica completa en los pacientes con sospecha o infección por covid-19. se recomienda la monitorización electroencefalográfica continua por al menos 24h o según la consideración del especialista en neurociencias en el paciente en estado crítico con sospecha o infección por covid-19 en quien se sospeche crisis epilépticas o estatus no convulsivo. las manifestaciones neurológicas en pacientes con infección por covid-19 pueden estar presentes en el 36% de los casos (366, 373, 374) . en el paciente en estado crítico con infección por covid-19 se han observado complicaciones vasculares que puede causar ataque cerebrovascular agudo isquémico o hemorrágico con tazas de entre el 5 al 6% por lo que el examen neurológico debe realizarse para documentar la presencia de déficit amci ® neurológico focal que haga sospechar esta patología (366, 375, 376) . es conocido que los pacientes en unidades de cuidado crítico tienen patologías que aumenta el riesgo de crisis o estado epiléptico, entre las cuales se encuentran (377) (378) (379) (380) :  pacientes sin patologías neurológicas hospitalizados en unidad de cuidado intensivo  hemorragia subaracnoidea  hemorragia intracraneal  trauma cráneo encefálico moderado a severo  infección del sistema nervioso central  tumor cerebral  encefalopatía hipóxico-isquémica algunas de estas patologías se presentan más frecuentemente en pacientes por covid-19 por lo que la monitorización electroencefalográfica continuar es requerida en este grupo de pacientes. el virus puede producir descompensación de paciente con epilepsia conocida, crisis por fiebre, crisis producidas por el estado crítico del paciente o las patologías subsecuentes que se han observado en esta infección (381) . el tiempo de monitorización requerido debe ser entre 12 a 24 horas para lograr una sensibilidad de 82 a 88%(380, 381). se recomienda realizar tomografía cerebral simple ante las manifestaciones neurológicas focales que nos hagan sospechar ataque cerebrovascular isquémico o hemorrágico. la resonancia cerebral puede ser necesaria como estudio complementario para determinar otros diagnósticos diferenciales en los pacientes con sospecha o infección por covid-19. las manifestaciones neurológicas en pacientes con infección por covid-19 pueden estar presentes en el 36% de los casos (366, 373, 374) . en el paciente en estado crítico con infección por covid-19 se han observado complicaciones vasculares que puede causar ataque cerebrovascular agudo isquémico o hemorrágico con tazas de entre el 5 al 6% por lo que el examen neurológico debe realizarse para documentar la presencia de déficit neurológico focal que haga sospechar esta patología (366, 375, 376) . la tomografía cerebral hace parte de la valoración inicial del ataque cerebrovascular isquémico y del estudio para determinar la presencia de otros diagnósticos diferenciales como ataque cerebro vascular hemorrágico en paciente con dicha patología puede ser necesario realizar angiotac con extensión a tórax en caso de sospecha de oclusión proximal o estudios endovasculares en pacientes que sea indicado (382) . la realización de resonancia cerebral usualmente documenta alteraciones en los pacientes con covid-19 en el 37 -62 % de los casos evaluados no relacionada con el acv. se recomienda la realización de punción lumbar en el paciente con sospecha o diagnóstico de covid-19 con base en los reportes de casos disponibles:  paciente con crisis epilépticas de novo.  paciente con alteración del estado de conciencia persistente a pesar de encontrarse metabólicamente compensado, descartado ataque cerebrovascular u otra causa de encefalopatía.  paciente con manifestaciones como mielitis, neuropatía craneal múltiple o sospecha de polineuropatía desmielinizante aguda. las capacidades neurotrópicas de los coronavirus en general han sido expuestas desde la infección por sarscov. en cuanto al sars-cov-2, asadi-pooya y colaboradores(383), han descrito, la posibilidad de ingreso al sistema nervioso central tras el ingreso por la mucosa nasal o por una gran viremia en el torrente sanguíneo. se han descrito procesos inflamatorios asociados (encefalitis) y en previamente con el sars y el mers hasta lesiones desmielinizantes (encefalomielitis aguda diseminada). estas primeras manifestaciones en 2002 con el sars fueron presencia de crisis epilépticas de novo, en quienes excluyendo otras causas tanto por neuroimagen además de pruebas microbiológicas en lcr, les fue descubierto el sars cov mediante pcr rt. en la presente pandemia, takeshi moriguchi y colaboradores (384) describieron el primer caso de encefalitis asociado a sars-cov-2, en un hombre joven en japón, que, tras 7 días de clínica respiratoria, desarrollo crisis epilépticas y alteración del estado de conciencia, sin antecedente conocido de epilepsia. se realizo imagen por resonancia cerebral, demostrando hiperintensidades a nivel temporal y lcr que mostró pleocitosis linfocitaria, se descartaron otros virus ( herpes, herpes zoster) y se le realizó pcr rt para sars-cov-2 siendo positiva. inclusive en este paciente los primeros hisopados faríngeos fueron negativos, pero los hallazgos en tomografía de tórax hicieron sospechar la infección por sars-cov-2. otro caso descrito de encefalitis hemorrágica aguda, fue también descrito en la revisión de ahmad y colaboradores (385) . donde una mujer joven presentó cuadro respiratorio de fiebre de 3 días de evolución y compromiso del estado de conciencia. en esta paciente se aisló el sars-cov-2 en hisopado faríngeo y ante el compromiso severo del estado de conciencia, se realizó resonancia que mostró compromiso hemorrágico bitalámico, en regiones temporales e ínsula, apoyando que se tratara de una diseminación tras neuronal probablemente con puerta de entrada mucosa olfatoria y siguiendo la diseminación por el los tractos del primer nervio hasta la corteza entorrinal, que es la vía propuesta de infección descrita inclusive por grupos como el de montalvan (356) y natoli (386) . amci ® precisamente, en la revisión sistemática de montalvan (356) se describen 1 caso de mielitis en contexto de paciente con infección por sars-cov-2, en quien se documentó la infección en lcr. se recomienda la medición de ácidos nucleicos por rt-pcr para sars-cov-2 en líquido cefalorraquídeo en los pacientes con sospecha o confirmación de infección por sars-cov-2 que realice crisis epilépticas de novo, en quien se descarte otras causas de estructuralidad (acv, tumores) o causas metabólicas (alteraciones hidroelectrolíticas, hipoglicemia, uremia etc.). se recomienda la medición de ácidos nucleicos por rt-pcr para sars-cov-2 en líquido cefalorraquídeo en pacientes con sospecha o confirmación de infección por sars-cov-2 con alteración franca del estado de conciencia, en quien se haya descartado como causante hipoxia, ataque cerebrovascular, alteración hidroelectrolítica o estatus no convulsivo mediante imágenes y electroencefalograma. se recomienda la medición de ácidos nucleicos por rt-pcr para sars-cov-2 en líquido cefalorraquídeo en pacientes con sospecha de encefalitis, mielitis o síndrome de guillain barré. en pacientes críticos, se ha recomendado búsqueda activa de compromiso del snc por sars-cov-2, sobre todo en pacientes con crisis epilépticas que no sean sintomáticas a trastornos metabólicos, además de hallazgos imagenológicos y curso clínico. las descripciones hechas por asadi y takeshi (383, 384) , muestran pacientes con cursos tórpidos, en los que el común denominador es una alteración del estado de conciencia persistente a pesar que otras variables (metabólicas, vasculares e infecciosas diferentes al sars-cov-2). de igual forma pacientes que realicen en contexto de la enfermedad, un cuadro de debilidad generalizada aguda, con arreflexia e incluso compromiso de nervios craneales como los descritos por zahra sedaghat(387). page amci ® se recomienda en los pacientes críticos con compromiso pulmonar por covid-19, un manejo orientado de fluidos frente a una estrategia liberal, ajustando el balance de fluidos de acuerdo con la evaluación clínica y/o a la capacidad de respuesta a volumen para garantizar la perfusión renal. se recomienda ajustar la intensidad de la monitoria en el paciente crítico con covid-19 al grado de severidad de la enfermedad para alcanzar tempranamente metas de reanimación que se reflejen en menor riesgo de lesión renal aguda. se recomienda evitar el uso de medicamentos nefrotóxicos teniendo en cuenta la farmacocinética y farmacodinamia individual, así como las interacciones farmacológicas en el paciente crítico con covid-19. el manejo de la volemia en los pacientes críticos ha cambiado considerablemente en las últimas décadas orientándose a un manejo titulado, evitando la administración empírica de altos volúmenes de líquidos durante la fase de reanimación de los pacientes siendo el flujo sanguíneo el determinante primordial del aporte tisular de oxígeno; los principales componentes de este deben optimizarse y balancearse para evitar la disoxia tisular. en estados de bajo flujo, los mecanismos compensadores neurohumorales producen una redistribución del flujo a lechos no esplácnicos y a nivel renal una redistribución corticomedular convirtiendo el tejido medular renal en una zona vulnerable a la lesión. de igual forma, el flujo sanguíneo renal se ve reducido de forma refleja en presencia de hipoxemia y/o hipercapnia. diversas fuentes de información nos han indicado cómo orientar adecuadamente el manejo del estado de perfusión tisular en los pacientes críticos con o sin una condición de shock, siendo la estimación aproximada del estado de volumen del paciente el pilar fundamental sobre el cual se basará toda la estrategia de restablecimiento o mantenimiento de la volemia del paciente con el fin de mantener la perfusión adecuada. aunque históricamente se prioriza la normalización del volumen en la reanimación de un paciente inestable, hemos comprendido la importancia que tiene el tiempo para lograr las metas en el pronóstico general del paciente y evidencias como el trabajo de ospina y cols. soportan el uso temprano de vasopresores para lograr de forma temprana metas de perfusión mientras buscamos la normovolemia. los pacientes con enfermedad pulmonar asociada a covid-19 deben mantenerse normovolémicos para preservar el flujo sanguíneo renal siendo la evaluación del estado de volumen un verdadero reto clínico. la fiebre, el aumento de pérdidas insensibles, la baja ingesta o las pérdidas por el tracto digestivo, pueden hacer que un paciente con covid-19 tenga hipovolemia, situación que puede desencadenar daño renal de no ser revertida apropiadamente y a tiempo. del otro lado del espectro, la administración liberal de líquidos además del potencial de empeorar la lesión pulmonar en presencia de una membrana alveolo capilar seguramente alterada, puede producir por sí misma un incremento en el riesgo de desarrollar lesión renal como lo demostró el estudio de grissom. desde el punto de vista de las metas amci ® hemodinámicas que se deben tener con un paciente con covid-19, se recomienda seguir los lineamientos de la campaña sobreviviendo a la sepsis, orientadas a mantener un óptimo estado de volumen, unas presiones de perfusión en un rango que permita la regulación de los flujos regionales en los distintos órganos y un gasto cardíaco dentro de unos rangos establecidos para una perfusión sistémica óptima. el examen clínico sigue teniendo vigencia absoluta para una adecuada aproximación al paciente, por ello debemos buscar los indicadores clínicos tradicionales de hidratación (piel, mucosas, enoftalmos, edema, etc.), el llenado capilar como lo describe hernández y cols en el estudio andrómeda-shock, el estado de alerta, las funciones cognitivas y la rata urinaria son entre otros unos marcadores aceptables para hacernos una idea del estado de adecuación de la perfusión periférica. la oliguria como marcador de perfusión renal está presente en 1/4 parte de los pacientes al ingreso a uci sin tener en sí sola una implicación pronóstica, sin embargo, la persistencia de esta en el tiempo es un indicador de alerta y obliga a una evaluación más detallada de las diversas variables que pudieran ocasionarla. debemos recordar que la administración de cargas de líquidos solamente está justificada cuando hay una respuesta cardiovascular a dicha administración, situación que se puede prever con una prueba de elevación pasiva de las piernas o con métodos más invasivos como la variabilidad de la onda de pulso, del volumen sistólico y/o del gasto cardíaco, entre otros. el esfuerzo respiratorio del paciente, los volúmenes utilizados en las estrategias de ventilación protectora y las arritmias frecuentemente presentes en los pacientes con compromiso pulmonar limitan el rendimiento diagnóstico de diversos dispositivos utilizados para la evaluación del estado de volumen y el gasto cardíaco, situación que debemos conocer y manejar(332, 388-394). se recomienda no utilizar de forma rutinaria la administración de tratamientos específicos antivirales para el paciente crítico con covid-19, con lesión renal aguda o crónica se recomienda no utilizar de rutina remdesivir en los pacientes con falla renal crónica y debe suspenderse en los pacientes que desarrollan lesión renal aguda con tfg < 30 ml/min. las intervenciones farmacológicas en los ensayos clínicos deben ajustarse a la farmacocinética y farmacodinamia específicas de cada molécula. la incidencia de falla renal reportada por criterios de kdigo, en los estudios chinos fue de 0.5% de los pacientes críticamente enfermos y de 4.7% en los pacientes con covid-19 y amci ® sdra. sin embargo, otros estudios han demostrado que hasta un 40%de pacientes con covid-19 que ingresan a la uci pueden presentar falla renal aguda. la falla renal en los pacientes con covid-19 es multifactorial como se ha descrito en preguntas anteriores por lo que se recomienda la toma diaria de creatinina sérica y el seguimiento continuo del gasto urinario y otros parámetros de la función renal como hematuria, proteinuria, tasa de filtrado glomerular, nitrógeno ureico en sangre, dímero d. los medicamentos que se emplean en el manejo de la infección covid-19 que actualmente incluyen oseltamivir, lopinavir/ritonavir, ribavirina, y la cloroquina o hidroxicloroquina son metabolizados principalmente en el hígado, aunque en la orina se encuentran metabolitos derivados de oseltamivir, ribavirina y de la hidroxicloroquina. por esto en ninguno de los estudios realizados en torno a la infección por sars-cov-2 se ha realizado ninguna recomendación en cuanto a la modificación de su dosis. la hidroxicloroquina por su parte se metaboliza a cloroquina, que a su vez se metaboliza a monodesetilcloroquina y a bisdesetilcloroquina. este medicamento no es dializable en las diálisis intermitentes y la única recomendación en los pacientes con falla renal, es hacer seguimiento electrocardiográfico estrecho para vigilar la prolongación del qtc. el favipiravir es un inhibidor de la polimerasa dependiente de rna que se encuentra en fase experimental para el tratamiento de la infección por sars-cov-2. la eliminación de este medicamento se realiza por vía renal y en los pacientes con falla renal en estadios leves a moderados se ha encontrado una concentración dos veces mayor en el riñón que sus niveles en sangre; sin embargo, esto no se ha asociado con ningún evento adverso por lo que la recomendación actual es no disminuir la dosis en pacientes con falla renal. el remdesivir se elimina por vía renal por lo cual no se recomienda administrar en pacientes con falla renal y los pacientes que desarrollan falla renal con el medicamento durante los estudios han sido retirados de los ensayos clínicos. no se cuenta con estudios que evalúen el remdesivir en una tfg <30 ml/min. en la tabla 15 se describen algunas intervenciones farmacológicas propuestas en medio de la pandemia para el manejo del covid-19 y su relación con la tasa de filtración según tfg. recientemente , izzedine et al publicaron una carta editorial en el kidney international may 21, 2020 donde alertan sobre el posible efecto nocivo de la hidroxicloroquina en la aparición de falla renal aguda al inhibir la autofagia celular que es un proceso importante en la remodelación de los túbulos renales, siendo estas células de alto recambio, pudiendo todo esto contribuir a la aparición de falla renal aguda(166, 327, 395-398) se recomienda aplicar las indicaciones tradicionales de terapia de soporte renal en pacientes críticamente enfermos con covid-19. se recomienda el inicio de terapia de soporte renal en pacientes críticos con covid-19 con hipercalemia severa o acidosis metabólica severa, refractarias a pesar del manejo médico óptimo o cuando el balance positivo de fluidos es deletéreo, con mayor requerimiento de oxígeno suplementario y que no responde a diuréticos. se recomienda el inicio temprano de terapia de soporte renal dentro de las primeras 24 horas de una indicación absoluta, asegurando previamente una adecuada reanimación de la perfusión tisular. en ausencia de trastornos hidro-electrolíticos y severa sobrecarga de volumen, el tiempo de inicio de diálisis es controversial. amci ® se recomienda en pacientes críticos con covid-19 que requieren soporte renal, las modalidades de terapia continua o extendida si cursa con inestabilidad cardiovascular, de acuerdo con la disponibilidad institucional. se debe considerar en pacientes críticos con covid-19, que requieren inicio de soporte renal preferir la vía femoral para inicio de la terapia para disminuir el riesgo de contaminación por proximidad, la siguiente vía se establecerá de acuerdo con la evolución y condiciones del paciente. en pacientes diagnosticados con covid-19 se puede presentar la insuficiencia renal aguda como parte de su enfermedad. en estudios observacionales de usa y china la ira se reportó entre un 3 y 37% de los pacientes. la enfermedad renal en pacientes con covid-19 se puede manifestar como ira, hematuria o proteinuria, y conllevan un mayor riesgo de mortalidad. la ira se asocia con cambios hemodinámicos y liberación de citocinas, pero no se descarta citotoxicidad directa por el virus. en un estudio realizado en nueva york con 5450 pacientes covid-19 positivos se diagnosticó lesión renal aguda en 37% de ellos, siendo leve con aumento de creatinina dos veces por encima del nivel basal en 47% de los pacientes, moderada en 22% de los pacientes, y severa con más del triple de la creatinina basal en 31%. hubo hematuria en el 46% de los pacientes y proteinuria en el 42%. se requirió terapia dialítica en el 15% de todos los pacientes con diagnóstico de ira, y el 97% de los pacientes que requirieron diálisis estaban en ventilación mecánica. la ira fue notada dentro de las primeras 24 horas de admisión a uci en el 33% de los pacientes y se relaciona con la severidad de la enfermedad. existen además predictores independientes: edad, raza negra, diabetes, hipertensión, enfermedad cardiovascular, ventilación mecánica, y uso de vasopresores. la terapia dialítica debe instaurarse precozmente una vez realizado el diagnóstico, idealmente dentro de las primeras 24 horas, después de asegurado que se ha completado el proceso de reanimación correspondiente. las indicaciones te trr en pacientes críticos con ira en covid-19 no difieren del paciente crítico general y se debe considerar ante: manifestaciones severas de uremia, sobrecarga de volumen, trastornos ácidos básico, refractarios, hipercalemia severa con manifestaciones cardiovasculares. pero no hay datos clínicos que respalden el inicio temprano vs tardío en esta población particular. pero un planteamiento válido es que la sobrecarga de volumen en pacientes que desarrollan sdra es perjudicial, dificultando el soporte ventilatorio óptimo, por lo cual se puede considerar un umbral más bajo para el inicio de trr con esta indicación específica: sdra + sobrecarga de volumen + infección covid-19 (399) . amci ® el paciente debe ser dializado en el cubículo de cuidado intensivo o en la habitación de aislamiento en los casos en que esté disponible y siempre evitar traslado a unidades con otros pacientes. la crrt es la modalidad preferida para este tipo de pacientes, pero debe quedar claro que esto depende de las facilidades de la institución que albergue al paciente y de la experticia de los profesionales. el acceso vascular en el paciente crítico general debe ser en su orden: vena yugular interna derecha, venas femorales comunes, vena yugular interna izquierda, y debe ser colocado por el médico encargado del paciente si está capacitado para ello, para evitar exposiciones innecesarias del personal de la salud. sin embargo, por precaución por el riesgo de contaminación, recomendaciones de expertos basadas en seguridad sugieren la utilización el catéter femoral. el tipo de catéter recomendado es un catéter doble lumen transitorio. sería ideal el monitoreo a través de cámaras del procedimiento para evitar el contacto prolongado del personal de enfermería durante el procedimiento de diálisis. en algunos casos específicos y de acuerdo con la disponibilidad, la diálisis peritoneal puede ser una alternativa. en los casos de crrt el líquido efluente no es contaminante para el personal de la salud. para terminar, es importante hacer énfasis en que en algunos hospitales ha habido escasez de insumos y esto puede llegar a convertirse en un serio problema. se recomienda para casos de fuerza mayor:  un litro de solución salina al 0.9% con cloruro de potasio a necesidad  un litro de dextrosa al 5% en agua con 150 meq de bicarbonato de sodio  un litro de solución salina al 0.9% con 1 gr de cloruro de magnesio  un litro de solución salina al 0.9% con 1 gr de cloruro de calcio esto nos da una solución de cuatro litros que contienen: 153 meq/l de sodio, 37.5 meq/l de bicarbonato, 2.6 mmol/l de magnesio y 2.25 mmol/l de calcio, más una cantidad variable de potasio. esta solución se puede usar como líquido dializante en pacientes en terapias de reemplazo renal continuo. especial cuidado se debe tener en el proceso de anticoagulación, pudiéndose usar heparina no fraccionada, hbpm, y citrato en los centros donde se tenga experiencia (139, 339, (400) (401) (402) (403) (404) (405) (406) (407) (408) (409) (410) (411) . se sugiere no utilizar de rutina la trrc más hemoperfusión en el paciente crítico con covid-19. débil en contra page amci ® se puede considerar en el paciente crítico con covid-19 con lesión renal aguda en quien se considere inicio de trrc, considerar la utilización de filtros de fibra hueca con propiedades adsortivas o asociado con cartuchos para hemoperfusión directa. el síndrome de liberación de citocinas (tormenta de citocinas) es un importante determinante en la transformación de infección por covid-19 de leve a moderado y progresión de la lesión de un órgano como el pulmón con neumonía y sdra a compromiso sistémico con inestabilidad hemodinámica, cid y fom. los pacientes afectados de tormenta de citocinas se encuentran con niveles altos de il-6 especialmente, además de il-10, tnf, que se relacionan con pobres pronósticos y mayor mortalidad. la asociación entre la lesión alveolar y renal (eje pulmón-riñón) es evidenciada en estudio del 2019 por panitchote y cols con 357 pacientes con sdra secundaria a neumonía y sin enfermedad renal preexistente que desarrollaron lesión renal aguda en el 68% con aki 3 en el 50% de ellos. recientemente en estudio en china zhou, con 191 pacientes afectados de covid-19 se encontraron como indicadores de mal pronóstico pacientes con altos niveles de dímero d, il-6, troponina i, dhl, ferritina y choque séptico. las terapias de depuración extracorpórea han sido utilizadas como tratamiento en pacientes con lesión severa por covid-19; dentro de estas se cuentan la crrt, hemoperfusión aislada, intercambio plasmático (tpe), plasmafiltración y adsorción (cpfa) y crrt + hemoperfusión. dentro de los beneficios de la crrt se cuentan la estabilidad hemodinámica, estabilidad del medio interno, depuración de toxinas pequeñas y medianas, incluidos mediadores inflamatorios, cuando se utiliza terapia convectiva, además de permitir soporte nutricional. la asociación de este procedimiento con membranas especiales (an69 + metilsulfonato y polietilamina oxiris) permiten hacer adsorción de citocinas (il-6) y endotoxinas, por periodos de 24h por 2 días consecutivos para manejo de tormenta de citocinas. la hemoperfusión aislada o asociada a crrt, también permite la remoción de il-6, utilizando cartuchos ha330, con procedimientos de 2 a 4 horas de duración por 3 días consecutivos (37, (412) (413) (414) (415) (416) (417) . no se puede emitir una recomendación a favor o en contra sobre el uso rutinario de la plasmaféresis como opción terapéutica en la fase de inflamación del paciente con covid-19. amci ® el coronavirus covid-19 puede inducir el síndrome respiratorio agudo severo (sars), que conduce a la disfunción inmune, la liberación excesiva de citoquinas inflamatorias, y a una serie de reacciones en cascada de activación de citoquinas, que resultan en lesiones alveolares difusas, formación de membrana hialina, exudación de fibrina y otras manifestaciones de lesión del pulmón. en casos severos, la tormenta de citoquinas sistémicas invade el sistema circulatorio, lo que lleva a una inestabilidad hemodinámica, shock y mods (418) . los niveles de il-6, il-10, tnf-a y otras citoquinas inflamatorias en pacientes con covid-19 grave son significativamente más altos, lo que puede estar relacionado con un mal pronóstico (419) . por lo tanto, la plasmaféresis se puede usar con seguridad y efectividad en pacientes con covid-19 grave, para eliminar mediadores inflamatorios de gran peso molecular. la seguridad depende como todas las terapias extracorpóreas de un personal de la uci entrenado, preparado y capacitado para aplicar las intervenciones en forma óptimas (420) . las terapias extracorpóreas de soporte de órganos pueden representar una parte importante de la respuesta y los médicos y otros profesionales de la salud deben estar familiarizados con estas terapias sofisticadas. se debe hacer un llamado a la acción, para crear conciencia sobre las diferentes técnicas extracorpóreas, cada una con criterios específicos y modalidades de prescripción, entrega y monitoreo(421, 422). se recomienda no utilizar de forma rutinaria el uso de un tratamiento específico dirigido a pacientes con infección por sars-cov-2/covid-19 comparado con el manejo estándar para mejorar desenlaces clínicos fuertes. actualmente no existe una terapia dirigida que se a efectiva para el manejo del virus; un número alto de estudios han surgido en los últimos dos meses, la mayoría sin el rigor metodológico suficiente para tomar decisiones adecuadas con respecto al manejo del amci ® paciente con infección por sars-cov-2. el conocimiento en la estructura del virus y el mejor entendimiento en la fisiopatología de la enfermedad genera un sinnúmero de potenciales fármacos que han sido ensayados para el manejo de la enfermedad. en tiempos de pandemia, con una patología catastrófica en términos de vidas humanas y costos hospitalarios; es importante encontrar soluciones a desenlaces importantes como mortalidad, días de estancia en uci y en el hospital, aumento en los días libres del ventilador, disminución de complicaciones mayores debido a la enfermedad entre otros. hasta el momento no se ha documentado ninguna terapia específica que pueda impactar sobre estos desenlaces; pero la calidad de los trabajos, tampoco dejan claro sin él no usar ningún tratamiento específico mejora los desenlaces al menos al disminuir el número de complicaciones. este nuevo beta-coronavirus es similar al coronavirus del síndrome respiratorio agudo severa (sars-cov) y del síndrome respiratorio del medio este (mers-cov); por lo tanto, varias moléculas que habían sido evaluadas en este tipo de enfermedad rápidamente se abrieron paso a ensayos clínicos en paciente con covid-19. estos ensayos principalmente observacionales, aleatorios pero abiertos con un número pequeño de pacientes no han permitido sacar adecuadas conclusiones y es frecuente como ver las diferentes guías de las principales sociedades del mundo cambiar de forma frecuente sus recomendaciones; no existes evidencia de estudios clínicos aleatorios y controlados que midan desenlaces fuertes, la premura de un tratamiento efectivo ha sacrificado el rigor metodológico que una investigación requiere. una estructura viral y replicación conocidas generan posibles dianas para que diferentes fármacos puedan ser investigados, antivirales tipo arbidol el cual inhibe la fusión de la membrana en la envoltura viral a algunos receptores; antimaláricos como la hidroxicloroquina y la cloroquina, las cuales inhiben la entrada viral y endocitosis por múltiples mecanismos, así como los efectos inmunomoduladores demostrados en el huésped; antivirales que impiden la replicación como el lopinavir o darunavir inhibiendo las proteasas o la ribavirina, el remdesivir o el favipiravir que actúan como análogos de nucleótidos o fármacos que actúan modulando la respuesta específica del huésped como el tocilizumab el cual se une al receptor de la il-6 inhibiendo el punto de acción de esta; los corticosteroides con múltiples efectos en la modulación del sistema inmunológico del paciente o los fármacos para evitar la respuesta secundaria a esta cascada inflamatoria como son los anticoagulantes. por último, se han buscado estrategias con el fin de mejorar la inmunización pasiva del huésped en el uso del plasma de pacientes convalecientes o el uso de inmunoglobulinas enriquecidas entre otros tratamientos propuestos para esta enfermedad. como vamos a ver más adelante, actualmente no existe un tratamiento específico con el nivel de evidencia suficiente para recomendar de manera generalizada; tampoco existe suficiente evidencia del manejo del soporte básico sin el uso de fármacos dirigidos, que demuestre que esta estrategia se deba implementar de manera sistemática en todos los pacientes; por lo tanto, a continuación trataremos de resolver las inquietudes con respecto a los diferentes medicamentos que han sido usados en la pandemia del sars-cov-2/covid-19. se recomienda no utilizar antimaláricos tipo hidroxicloroquina (hcq) o cloroquina (cq) para el manejo de pacientes con infección por sars-cov-2/covid-19. para la fecha no hay un adecuado sustento bibliográfico que soporte el uso de antimaláricos en la prevención o manejo de pacientes con infección por sars-cov-2 tanto leve, moderada como severa. los mayores estudios no muestran utilidad clínica y tendencia a mayores eventos cardiovasculares con el uso de antimaláricos en pacientes con infección por covid-19 comparado con no darlo. su utilidad se deriva principalmente de resultados en estudios preclínicos e in vitro; como los presentados por wang y cols donde evaluaron 7 medicamentos de manera in vitro contra el covid-19, siendo el remdesivir y la cq efectivos de manera in vitro contra el nuevo coronavirus(424); liu y cols, donde la hcq fue efectiva en inhibir la infección por sars-cov-2 in vitro que junto con su potencial antiinflamatorio tenía potencial para el uso clínico (425) y yao y cols, donde la hcq fue más potente que la cq para inhibir el sars-cov-2 in vitro y fue recomendado para el uso en humanos en dosis de 400 mg dos veces al día por el primer día, seguido de 200 mg dos veces al día por 4 días más mantendría la concentración efectiva del fármaco en el tejido pulmonar (426) . los pocos estudios clínicos, son de baja calidad y no han mostrado mejoría ni eficacia en el uso de antimaláricos para el manejo de paciente adultos con covid-19, algunos estudios iniciales con pocos pacientes con resultados favorables (427) e incluso con recomendaciones para uso en las primeras versiones de guías internacionales para la amci ® hcq y cq, encontrando superioridad en estudios observacionales, de pocos pacientes, sin comparadores para inhibir la exacerbación de la neumonía, hallazgos de las imágenes pulmonares, promover una conversión negativa al virus y acortar el curso de la enfermedad; la cq tuvo un efecto notable tanto en términos de resultado clínico como de eliminación viral (428) ; considerando la hcq y la cq como un tratamiento costo efectivo (429) . estudios posteriores con un mayor número de pacientes no han logrado reproducir los estudios preclínicos iniciales; mahévas y cols, evaluaron la efectividad de la hcq en 181 pacientes admitidos a cuatro hospitales en francia, con neumonía por covid-19 quienes requieren oxígeno, pero no se encontraban en uci, comparado con una población con manejo estándar; la hcq se usó a dosis de 600 mg día en las primeras 48 horas a la admisión, este estudio no soporte el uso de la hcq en pacientes admitidos al hospital con covid-19 que requieren oxígeno al no reducir de forma significativa la admisión a la uci, el sdra o muerte en el día 7 después del ingreso (430) ; por el contrario, se han reportado efectos secundarios frecuentes (prolongación del intervalo qt, hipoglucemia, cambios en el estado mental, alteraciones gastrointestinales y retinopatía); silvia borda y cols, evaluó la seguridad y eficacia de dos dosis de cq en pacientes con covid-19 severo en un estudio aleatorizado, doble ciego fase iib en 81 pacientes adultos hospitalizados con infección por sars-cov-2, los pacientes fueron expuestos a dosis altas de cq (600 mg dos veces al día por 10 días) o dosis bajas (450 mg dos veces al día en el día 1 y una vez al día por 4 días), los hallazgos preliminares de este estudio sugieren que la dosis más alta de cq no debe recomendarse para pacientes críticos con covid-19 debido a sus posibles riesgos de seguridad, especialmente cuando se toman simultáneamente con azitromicina y oseltamivir; estos hallazgos no pueden extrapolarse a pacientes con covid-19 no severo (431); tang y cols, evaluaron la eficacia y seguridad de la hcq con el manejo estándar en un estudio multicéntrico, abierto, aleatorio y controlado en china, 150 pacientes con covid-19 positivo se incluyeron en el análisis de intención a tratar (75 en el grupo de hcq y 75 en el grupo estándar), la hcq fue administrada a dosis de 1200 mg día por tres días y mantenimiento con dosis de 800 mg día (duración del tratamiento: dos a tres semanas en pacientes con enfermedad leve a moderada o enfermedad severa respectivamente); la administración de hcq no resultó en una significativa mayor probabilidad de conversión negativa comparado con el tratamiento estándar, los efectos adversos fueron mayores en el grupo de hcq (432) . con todo esto la hcq y la cq, si se usan deberá ser bajo estudios experimentales aprobados con una estricta monitorización y vigilancia clínica de la frecuencia cardíaca y el intervalo qt, los niveles de glucosa, la función hepática y renal, y el cribado clínico de trastornos mentales y visuales en pacientes que reciben estos fármacos. debe evitarse hcq/cq en pacientes con enfermedades cardiovasculares subyacentes. nuevas evidencias con un mayor número de pacientes podrían sacar la hcq y la cq inclusive de estudios clínicos; barbosa y cols, evaluaron en un estudio cuasialeatorio comparativo el uso fuera de registro de la hcq en pacientes positivos por el sars-cov-2, el pronóstico primario fue la necesidad de escalar el soporte ventilatorio, cambio en el conteo de linfocitos o cambio en el índice de neutrófilos/linfocitos, un total de 63 pacientes fueron incluidos, 32 en el brazo de hcq. la administración de hcq fue asociada con la necesidad de aumentar el nivel del soporte ventilatorio comparado con aquellos que no recibieron hcq al día 5 del estudio, no hubo beneficios en la mortalidad, reconstitución inmunológica y riesgo de intubación (433) . el estudio con un mayor número de pacientes proviene de la ciudad de new york; geleris y cols, examinaron la asociación entre el uso hcq y la intubación o muerte en un centro médico de ny, se analizaron 1. amci ® estaban más enfermos en términos de oxigenación, en este estudio observacional la administración de hcq no fue asociada con una disminución en el riesgo compuesto de intubación o muerte (434) . se recomienda no utilizar antimaláricos tipo hidroxicloroquina (hcq) o cloroquina (cq) en combinación con azitromicina (az) para el manejo de pacientes con infección por sars -cov-2/covid-19. fundamento para la fecha la evidencia no favorece el uso combinado de los antimaláricos en combinación con la azitromicina; por el contrario, la combinación de estos dos medicamentos puede ser deletérea, inclusive con un aumento reportado en la mortalidad y la aparición de arritmias ventriculares de novo; estudios iniciales fueron promisorios, gautret y cols, evaluaron inicialmente el efecto de la hcq en la carga viral respiratoria en conjunto con el uso de azitromicina, la presencia del virus al día 6 fue el pronóstico primario; 20 pacientes con tratamiento mostraron una significativa reducción en la carga viral al día 6 de la inclusión comparado con los controles; la azitromicina adicionada a la hcq fue significativamente más eficiente en la eliminación viral (435) ; nuevamente gautret y cols, realizaron un estudio observacional, no controlado, no comparativo de 80 pacientes tratados con la combinación de hcq más azitromicina, presentando una mejoría significativa en disminución de la carga nasofaríngea del virus y una menor tiempo de enfermedad (436) ; luego million y cols, evaluaron la combinación de hcq y az en un estudio retrospectivo de 1.061 pacientes con sars-cov-2 tratados con hcq (200 mg tres veces al día por 10 días) + az (500 mg en el día 1, seguido de 250 mg al día por los próximos 4 días), el pronóstico fue mortalidad, empeoramiento clínico (ingreso a uci) o persistencia viral; la administración de hcq+az en combinación antes de que aparecieran las complicaciones del covid-19 es segura y asociada a una baja mortalidad en los pacientes (437) ; soportado además por estudios in vitro que demuestran que la combinación de hcq y az tienen efectos sinérgicos para el sars-cov-2 a concentraciones compatibles con las que se obtienen en pulmones humanos (438) . otros estudios por el contrario no han encontrado resultados positivos, es así como, magagnoli y cols, en un análisis retrospectivo de pacientes confirmados con infección por sars-cov-2 en centros de veteranos de los eeuu, un total de 368 pacientes fueron evaluados (hcq, n=97; hcq+az, n=113; no hcq, n=158), en este estudio no hubo evidencia que el uso de la hcq tanto sola o en combinación con la az, redujo el riesgo de ventilación mecánica en pacientes hospitalizados con covid-19; una asociación con un aumento en la mortalidad fue identificada en pacientes tratados con hcq sola (439) . nuevamente los estudios con un mayor número de pacientes se encuentran en la ciudad de new york; rosenberg y col, describieron la asociación entre hcq, con o sin az en el pronóstico de pacientes hospitalizados con covid-19; un estudio de cohorte multicéntrico retrospectivo en pacientes hospitalizados con covid-19 en 25 hospitales de ny, los pacientes recibieron ; en pacientes hospitalizados en el área metropolitana de ny con covid-19, el tratamiento con hcq, az o ambos, comparado con ningún tratamiento, fue no significativamente asociado con diferencias en la mortalidad hospitalaria (440) . recomendación se recomienda no utilizar de forma rutinaria el uso rutinario del lopinavir/ritonavir para el manejo de pacientes con infección por sars-cov-2/covid-19. en la actualidad no existe evidencia a favor o en contra en el uso del tratamiento con antirretrovirales con lopinavir/ritonavir en el manejo de pacientes adultos hospitalizados con covid-19; no se observó ningún beneficio con lopinavir/ritonavir más allá de la atención estándar. se está en espera de cierre de diferentes ensayos futuros que confirme o excluyan el uso de lopinavir/ritonavir en el paciente covid-19. en diciembre de 2019, un nuevo coronavirus, designado sars-cov-2, ha causado una pandemia (115, 142, 174, 441) ; cuando hablamos de enfermedad producida por covid-19 hablamos de enfermedades que van desde las enfermedades leves autolimitantes del tracto respiratorio hasta neumonía rápidamente progresiva, neumonía grave, falla multiorgánica y muerte. hasta este momento no existen agentes terapéuticos específicos para las infecciones por coronavirus. después de la aparición del síndrome respiratorio agudo grave (sars) en 2003, entre los fármacos aprobados se identificó lopinavir, un inhibidor del aspartato proteasa tipo 1 del virus de inmunodeficiencia humana (vih), que tiene actividad inhibitoria in vitro contra el sras-cov, el virus que causa el sars en los seres humanos y el ritonavir combinado con lopinavir para aumentar su vida media plasmática a través de la inhibición del citocromo p450 (442) . se comenzaron estudios evaluando la respuesta antiviral in vitro de la combinación de lopinavir/ritonavir y ribavirina en 41 pacientes con sars; comparados con 111 pacientes tratados con ribavirina sola, que sirvieron como controles históricos; el pronóstico adverso (sdra o muerte) fue significativamente más bajo en el grupo de tratamiento comparado con los controles históricos (2.4% vs 28.8%, p = 0.001) al día 21 del inicio de los síntomas; una reducción adicional en el uso de esteroides y de infecciones nosocomiales fue vista en el grupo de tratamiento con una disminución en la carga viral y aumento en el conteo de linfocitos (443) ; del mismo modo, el lopinavir tiene actividad, tanto in vitro como en modelo animal, contra el coronavirus del síndrome respiratorio de oriente medio (mers-cov) (444) . estos estudios previos son el soporte inicial para el uso del lopinavir/ritonavir en la epidemia del covid-19; cao y cols, en mayo de 2020 publicaron en china, un estudio controlado, aleatorizado en pacientes hospitalizados con prueba ; los efectos adversos gastrointestinales fueron más comunes con el lopinavir-ritonavir, pero los eventos adversos serios fueron más común con el grupo control; el tratamiento con lopinavir-ritonavir fue suspendido en 13 pacientes (13.8%) secundario a los eventos adversos (445) . otro estudio hung y cols, en hong kong, evaluaron en un trabajo multicéntrico, prospectivo, aleatorizado, fase 2 la eficacia y seguridad de la terapia combinada por 14 días de lopinavir 400 mg y ritonavir 100 mg cada 12 h, ribavirina 400 mg cada 12 h y tres dosis de 8 millones de ui de interferón beta-1b en días alternos en pacientes con covid-19 comparado con lopinavir/ritonavir cada 12 h (grupo control); el resultado primario fue tiempo en la negativización de la pcr viral en el hisopado nasofaríngeo en paciente con covid-19; 127 pacientes fueron ingresados, 86 en el grupo de combinación y 41 en el grupo control; en el grupo de intervención de forma significativa se negativizo la prueba de pcr de forma más rápida (7 días [iqr 5-11]) que el grupo control (12 días [8] [9] [10] [11] [12] [13] [14] [15] ; hr 4.37 [ic 95% 1.86-10.24], p = 0.0010); los eventos adversos fueron similares entre los grupos; ningún paciente murió durante el estudio (446) . por último, un pequeño estudio de zhu y cols en china, con 50 pacientes con sars-cov-2; evaluaron de forma retrospectiva los efectos antivirales y seguridad del lopinavir/ritonavir y el arbidol (antiviral aprobado en china y rusia para el sasr y la influenza), 34 pacientes en el grupo de lopinavir/ritonavir y 16 en el grupo de arbidol; los pacientes lopinavir/ritonavir presentaron un mayor tiempo para la negativización de la prueba de pcr viral (p < 0.01)(447). se recomienda no utilizar de forma rutinaria remdesivir como antiviral para el manejo de pacientes con infección por sars-cov-2/covid-19. se debe considerar su uso en escenarios de estudios de investigación clínica aprobados. actualmente no hay disponibilidad del medicamento en el país (colombia) por lo cual no se incluye en los protocolos de manejo de paciente con covid-19. en estados unidos el primer paciente con covid-19 mostró una mejoría significativa de sus síntomas con 24 horas de tratamiento con remdesivir (448) , lo que abrió la puerta a un nuevo tratamiento para el sars-cov-2; el remdesivir (gs-5734) es un análogo de los nucleótidos que inhibe la rna polimerasa; con un amplio espectro antiviral, puede inhibir la replicación de múltiples coronavirus en las células epiteliales del sistema respiratorio (449) ; estudiado (451) . por último, un estudio publicado por antinori y cols, en milán, italia; de manera prospectiva (compasional) incluyó pacientes con neumonía por sars-cov-2 mayores a 18 años bajo ventilación mecánica o con una saturación de oxígeno ≤ 94% al aire ambiente o un puntaje del national early warning score 2 ≥ 4; el pronóstico primario en cambio en el estado clínico en una escala ordinal de 7 categorías (1 = no hospitalizado de regreso a sus actividades diarias normales; 7 = muerte); de los 35 paciente ingresados, 18 se encontraban en uci y 17 en un piso de hospitalización de enfermedades infecciosas; un curso de 10 días de remdesivir fue completado por 22 pacientes (63%) y suspendido en 13, de os cuales 8 (22.8%) se descontinuo por eventos adversos; a los 28 días, 14 (82.3%) pacientes de piso fueron egresados, 2 permanecían hospitalizados y uno murió (5.9%), en la icu 6 (33.3%) fueron egresados, 8 (44.4%) pacientes murieron, 3 (16.7%) aún se encontraban en ventilación mecánica y 1 (5.6%) estaba con mejoría pero aún hospitalizado; la hipertransaminasemia y la injuria renal aguda fueron los eventos adversos más frecuentes reportados (42.8% y 22.8%, respectivamente); los datos sugieren que el remdesivir puede beneficiar a pacientes con neumonía por sars-cov-2 hospitalizados por fuera de la unidad de cuidado intensivo (452). page se recomienda no utilizar de rutina la ivermectina para el manejo de pacientes con infección por sars-cov-2/covid-19. para la fecha no se cuenta con la suficiente evidencia para emitir una recomendación para el uso de la ivermectina en pacientes con covid-19, en estudios iniciales in vitro, caly y cols, demostró como la ivermectina, una droga autorizada por la fda como antiparasitario tiene un efecto antiviral de amplio espectro de manera in vitro, con una reducción significativa de la replicación viral en modelos experimentales (453) , un estudio aún sin publicar, observacional multicéntrico de casos y controles (n: 704 casos y n: 704 controles), realizado entre el 1 de enero y 31 de marzo de 2020, incluyó pacientes diagnosticados con covid-19 confirmados por laboratorio, la dosis fue de 150 mcg/kg de ivermectina más la terapia médica de soporte en comparación con terapia médica sin ivermectina, el resultado principal fue la medición de supervivencia; en pacientes que requirieron ventilación mecánica, la mortalidad fue menor en el grupo de ivermectina (7,3% y 21,3% respectivamente) y las tasas de mortalidad global fueron más bajas con ivermectina ( no se puede emitir una recomendación a favor o en contra sobre el uso compasivo o rutinario de tocilizumab en pacientes con infección por sars-cov-2/covid-19. en pacientes individualizados se ha reportado desenlaces clínicos favorables. se puede considerar su uso en pacientes que cumplan con todos los siguientes criterios: ver tabla 16. el tocilizumab (tcz) un anticuerpo monoclonal humanizado igg1k, el cual se puede unir de manera específica a los receptores solubles de membrana para la il-6 (sil-6r and mil-6r) y ha sido ampliamente usado en el tratamiento de enfermedades autoinmunes, tales como la artritis reumatoide, la enfermedad de still del adulto o vasculitis de grandes vasos (459) . un primer estudio de xiaoling xu y cols, describió en china, 21 pacientes tratados con tocilizumab, se documentó una mejoría en los síntomas, en los requerimientos de oxígeno y en los hallazgos imagenológicos de la tomografía de tórax; los niveles promedio de il-6 antes de la terapia fueron de 132.38 pg./ml; todos los pacientes recibieron lopinavir y metilprednisolona antes de la terapia. se trata de una serie con una muestra pequeña de pacientes en donde solo 4 (19%) pacientes estaban en condición crítica (148) . posteriormente luo y cols, en china, reportan el uso de tocilizumab en 15 pacientes, con mejoría en el aumento de la pcr en todos los pacientes, excepto uno, y una disminución de la il6. el nivel sérico de il-6 tendió a aumentar inicialmente y luego disminuyó en 10 pacientes. los niveles medios de il-6 antes de la terapia fueron de 111.05 pg./ml; 53% de los pacientes recibieron metilprednisolona; el 20 % fallecieron. es otra serie pequeña, con 7 pacientes (46,6%) en condición crítica (147) . roumier y cols, en francia, estudiaron 30 pacientes que recibieron tcz, observando que se redujo la necesidad de ventilación mecánica en comparación con los controles ( amci ® 0.001); en este estudio, no hubo diferencias en la reducción de la mortalidad y 7 pacientes (23%) se encontraban en uci (460) . klopfenstein y cols, también en francia, en un estudio retrospectivo de casos y controles, encontraron que pacientes que recibieron tcz (n=20), a pesar de tener más requerimiento de oxígeno, con resultados biológicos más pobres (mayor linfopenia y un nivel de pcr superior) al inicio del estudio que los pacientes sin tcz (n = 25), presentaron el objetivo combinado (ingreso a uci y mortalidad) menor que los pacientes sin la terapia (25% vs 72%, p = 0.002); es otra serie, que disminuye la necesidad de ventilación mecánica (0% vs 32%, p = 0.006) de manera significativa (461) . luego rimland ca y cols informan los primeros datos de 11 pacientes con covid-19 tratados con tcz en los estados unidos, 9 de ellos en ventilación mecánica; la pcr y el fibrinógeno mejoraron rápidamente, pero no hubo mejoría en otros marcadores o resultados clínicos. sólo a seis pacientes les tomaron niveles previos de il 6 y de ellos dos tenían niveles bajos (462) . en otro estudio mikulska y cols, próximo a salir en jama, en pacientes con sdra moderado a severo, hay mayor disminución de la mortalidad con el tratamiento combinado de tocilizumab y esteroides, en relación con cada una de estas terapias. por último, no todos los estudios han mostrado resultados positivos; kimmig y cols, de chicago (eeuu), en 28 de los 60 pacientes críticos con covid-19, que recibieron tcz, se asoció con una mayor incidencia de infecciones bacterianas secundarias, incluida la neumonía asociada al ventilador (64.3% vs. 31.3% p = 0.010) (463) . posterior a la recomendación hay nueva evidencia publicada y estudios aún sin publicar que puede soportar el uso de los inhibidores de la il-6 en pacientes con sars-cov-2/covid-19; morena y col, en un estudio de tocilizumab como uso "off-label" en el tratamiento de neumonía por sars-cov-2 en milán, italia, este estudio abierto, prospectivo, describe las características clínicas y el pronóstico de 51 pacientes con covid-19 confirmado y severo tratados con tcz iv, todos los pacientes, presentan niveles plasmáticos elevados de il-6 (> 40 pg/ml) y saturación de oxígeno < 93% al aire ambiente, 45 pacientes (88%) se encontraban con sistema de alto flujo de oxígeno y 6 en ventilación invasiva, a los 7 días luego del tratamiento se observa una caída dramática en la temperatura corporal y la pcr, con un incremento significativo en el conteo de linfocitos (p < 0.001); a los 34 días del tratamiento, 34 pacientes (67%) mostraron una mejoría en la severidad del cuadro; 31 fueron dados de alta; 17 (33%) mostraron empeoramiento de su cuadro clínico y de estos, 14 murieron (27%). la mortalidad fue significativamente asociada con el uso de ventilación mecánica al inicio (83.3% vs 20% de los pacientes en soporte de oxígeno no invasivo, p = 0.0001), el efecto adverso más frecuente reportado fue la elevación de las enzimas hepáticas (29%), trombocitopenia (14%) e infecciones bacterianas serias e infecciones fúngicas en un (27%); los autores concluyen que el tcz ejerce un rápido beneficio sobre los marcadores inflamatorios y la fiebre, aunque no se consiguió un impacto clínico sobre el pronóstico, el riesgo aumentado de infecciones severas no es despreciable (464) . capra y col, describieron 85 pacientes en un hospital de italia con neumonía por covid-19 y falla respiratoria sin soporte ventilatorio y al menos uno de los siguientes: frecuencia respiratoria ≥ 30 respiraciones/min, saturación ≤ 93% o pao2/fio2 <= 300 mmhg, los pacientes recibieron la terapia estándar para el momento (hidroxicloroquina, lopinavir y ritonavir) y fueron considerados el control; 62 pacientes recibieron tzc con 4 días de la admisión más el manejo estándar, los pacientes en el grupo de tratamiento mostraron de manera significativa una mayor sobrevida comparado con los pacientes control (hr para muerte, 0.035; 95% ic], 0.004 a 0.347; p = 0.004), ajustado para las características clínicas de base; 2 de 62 pacientes en el grupo de tcz y 11 de 23 en el grupo control murieron; 92% y 42.1% de los pacientes que se dieron de alta en el grupo de tcz y en el control se recuperaron; la función respiratoria mejoró en el 64.8% de los amci ® pacientes con tcz que aún se mantenía hospitalizados, donde el 100% de los controles empeoro y requirieron ventilación mecánica, dando al tcz un espectro positivo en términos de curso clínico y sobrevida en pacientes con covid (465). guaraldi y col; evaluaron el papel del tcz en reducir el riesgo de ventilación mecánica invasiva en pacientes con neumonía severa por covid-19 quienes recibían tratamiento estándar para el momento (hidroxicloroquina, azitromicina, antirretrovirales y heparinas de bajo peso molecular) en un estudio retrospectivo, observacional en bologna, reggio emilia y módena, italia; el tcz fue dado a dosis de 8 mg/kg de peso corporal de forma iv (con un máximo de 800 mg) en dos infusiones separadas 12 h o 162 mg sc administradas en dos dosis simultáneas, una en cada muslo (324 mg en total), cuando la formulación iv no se encontraba disponible; el pronóstico primario fue la combinación de ventilación mecánica invasiva o muerte; de 1351 pacientes ingresados, 544 (40%) tenían neumonía severa por covid-19 y fueron incluidos, 57 (16%) de 365 pacientes en el grupo estándar requirieron ventilación mecánica, comparados con 33 (18%) de 179 pacientes tratados con tcz (p = 0·41; 16 [18%] de 88 pacientes tratados iv y 17 [19%] de 91 pacientes tratados sc); 73 (20%) pacientes en el grupo estándar murieron, comparado con 13 (7%; p < 0.0001) pacientes con tcz (6 [7%] del grupo iv y 7 [8%] sc); luego de ajustar para sexo, edad, centro de reclutamiento, duración de los síntomas y puntaje de sofa, el tratamiento con tcz fue asociado con una reducción en el riesgo de ventilación mecánica invasiva o muerte (hr 0.61, 95% ic 0.40-0.92; p = 0.020); 24 (13%) de 179 pacientes tratados con tcz fueron diagnosticados con nuevas infecciones en comparación con 14 (4%) de 365 pacientes en el grupo estándar (p < 0.0001) (466) . campochiaro y col, en un solo centro evaluó la eficacia y seguridad del tcz en pacientes con covid-19 severo, se diseñó un estudio retrospectivo en pacientes con características de hiper-inflamación (definida como una elevación tanto en la pcr, ≥ 100 mg/l, normal <6 mg/l o ferritina ≥ 900 ng/ml, normal <400 ng/ml en presencia de un incremento en la dhl > 220 u/l), acompañado de un compromiso respiratorio severo, definido como hallazgos típicos en la radiografía y/o tomografía, la presencia de una saturación de oxígeno ≤ 92% al aire ambiente o una pao2:fio2 ≤ 300 mmhg ingresados a la uci, comparando pacientes con tcz iv al manejo estándar, 65 pacientes fueron incluidos de los cuales 32 fueron tratados con tcz; los pacientes se encontraban con alto flujo o ventilación mecánica no invasiva, a 28 días de seguimiento, 69% de los pacientes con tcz experimentaron mejoría clínica comparado con un 61%del tratamiento estándar (p = 0.61); la mortalidad fue 15% en el grupo de tcz y 33% en el grupo estándar (p = 0.15); la incidencia de infección y trombosis pulmonar fue similar en ambos grupos (467); somers y col, evaluaron un estudio observacional en pacientes con neumonía por covid-19 severo que se encontraban en ventilación mecánica, evaluando como pronóstico la probabilidad de sobrevida posterior a la extubación; 154 pacientes fueron incluidos, 78 recibieron tcz y 76 no; en los modelos ajustados, el tcz, fue asociado con una reducción del 45% en el riesgo de muerte [hr 0.55 95% ic 0.33 a 0.90]; aunque el tcz, fue asociado con un incremento en la proporción de pacientes con superinfecciones (54% vs. 26%; p < 0.001), no hubo diferencias en la mortalidad a 28 días entre los pacientes tratados con tcz con o sin superinfecciones [22% vs. 15%; p=0.42] (468). price y col, también publicaron un estudio observacional de pacientes hospitalizados con covid-19, los pacientes recibieron tcz si cumplían criterios del síndrome de liberación de citoquinas, se evaluaron 239 pacientes; de los cuales 153 (64%) recibieron tcz, estos pacientes que recibieron ventilación mecánica la sobrevida fue del 75% (95% ic, 64-89), luego del tcz pocos eventos adversos fueron reportados y tanto la oxigenación como los biomarcadores de inflamación mejoraron (469) y por último, en un estudio preliminar con datos aún sin publicar perrone y col, evaluaron la eficacia del tcz en pacientes con neumonía por covid-19, en un estudio amci ® multicéntrico fase 2 en italia; se utilizó tcz, a dosis de 8 mg/kg iv, una o dos administraciones con 12 horas de diferencia; 301 y 920 casos fueron disponibles para un análisis de intención a tratar, 67 pacientes murieron; las tasas de letalidad fueron de 18.4% (97.5% ic, 13.6-24.0, p = 0.52) y 22.4% (97.5% ic, 17.2-28.3, p < 0.001) a 14 y 30 días; el tcz redujo la tasa de letalidad a 30 días pero no a 14 días comparado con las esperadas sin presentar una toxicidad significativa; la eficacia fue más evidente en los paciente que no requerían ventilación mecánica (469). recomendación se recomienda no utilizar de rutina bloqueadores de interleuquina-1 (anakinra) en pacientes con infección por sars-cov-2/covid-19. aunque su ventaja está en el perfil de seguridad, su vida media corta (3 horas) y porque las infecciones oportunistas son raras ,no hay suficiente evidencia para emitir una recomendación sobre el uso de este medicamento; cavalli y cols, de milán, italia, realizaron un estudio de cohorte retrospectivo en pacientes con sdra moderado a severo con hiperinflamación (pcr ≥ 10 mg/dl, ferritina ≥ 900 ng/ml o ambos), manejados con ventilación mecánica no invasiva fuera de la uci y que recibieron tratamiento con hidroxicloroquina y lopinavir, los pacientes que recibieron anakinra, 5 mg/kg dos veces al día intravenosa (n= 29, dosis alta) o 100 mg dos veces al día subcutánea (n= 7 pacientes, dosis baja) fueron comparados con una cohorte retrospectiva que no recibió anakinra (tratamiento estándar); la duración del tratamiento se prolongó hasta el beneficio clínico sostenido (reducción del 75% en la pcr, y una pafi > 200, durante al menos 2 días consecutivos) o hasta la muerte, bacteriemia, o efectos secundarios (alt > 3 veces valores de referencia); el tratamiento con anakinra a bajas dosis se interrumpió después de 7 días debido a la escasez de efectos sobre la pcr y el estado clínico. a los 21 días, el tratamiento con dosis altas de anakinra se asoció con una reducción en la pcr y mejoría en la función respiratoria en 21 de 29 pacientes (72%); en el grupo estándar, ocho de 16 pacientes (50%) mostraron mejoría respiratoria a los 21 días. en 21 días de seguimiento, la sobrevida fue del 90% en el grupo de dosis altas de anakinra y del 56% en el grupo estándar (p = 0.009). se trata del primer estudio que demuestra seguridad y mejoría en los pacientes covid-19, pero en el contexto fuera de la uci (470) . huet y cols, de parís, francia, realizaron el estudio llamado ana-covid-19 en el que compararon 52 pacientes tratados con anakinra subcutánea 100 mg dos veces al día durante 72 h, luego 100 mg diarios durante 7 días, con 44 pacientes históricos; su criterio de inclusión fue tener una saturación de oxígeno del 93% o menos con un soporte de mínimo de 6 l / min de oxígeno. la admisión a la uci por ventilación mecánica invasiva o muerte se produjo en 13 (25%) pacientes en el grupo de anakinra y 32 (73%) pacientes en el grupo histórico (hr 0. amci ® pacientes en el grupo histórico tuvieron un aumento en las aminotransferasas hepáticas (471). recomendación se sugiere que la terapia con interferón sólo sea considerada en pacientes con formas graves de infección por covid-19 en el marco de un estudio clínico. estudios preliminares muestran que el virus del covid-19 induce una expresión muy débil de interferones en las células infectadas, lo que obstaculiza la respuesta inmune innata temprana a la infección y sugiere que el uso de interferón (ifn) exógeno para estimular la inmunidad antiviral (473) . zhou q y col, en china, en un estudio observacional de 70 pacientes con covid-19 con gravedad mixta proporcionó evidencia de muy baja calidad que la adición de interferón-α a la terapia con umifenovir no afecta el tiempo de eliminación viral o la duración en la estancia hospitalaria cuando se comparó con el umifenovir solo (474) . hung if y cols, de hong kong, realizaron un ensayo multicéntrico, en adultos con covid-19, en los que 86 pacientes recibieron una combinación de lopinavir/ritonavir y tres dosis de 8 millones de unidades internacionales (0·25 mg) de interferón beta-1b en días alternos (grupo de combinación) y 41 pacientes recibieron lopinavir/ritonavir (grupo control); la terapia de combinación fue segura y superior al control, para aliviar los síntomas y acortar la duración de la eliminación del virus y la estancia hospitalaria; se trata de un estudio fase 2, en pacientes con covid-19 leve a moderado (ningún paciente con ventilación en el grupo de combinación), en el que el ifn se administró en los primeros 7 días de inicio de los síntomas y con el uso de un análogo de nucleósido oral (ribavirina), que no está en nuestras guías (446) . se necesitan estudios de ifn solo o combinado en pacientes críticos con covid-19. los efectos adversos de los ifn tipo i pueden limitar su uso para una intervención generalizada, como se propone en el brazo ifn-β con lopinavir/ritonavir del ensayo solidaridad de la oms. la administración por inhalación de vapor que se realiza actualmente en china ofrece la ventaja de acceso rápido al tracto respiratorio; sin embargo, la farmacodinamia y la farmacocinética de este modo de administración nunca se han evaluado. se sugiere no utilizar de rutina corticoides en el tratamiento de pacientes con sospecha o diagnóstico de covid-19. no se puede considerar su uso profiláctico ni en pacientes con enfermedad leve sin requerimiento de oxígeno. débil en contra page en diciembre de 2019, una serie de casos de neumonía de causa desconocida surgió en wuhan, hubei, china, con presentaciones clínicas muy parecidas a una neumonía viral; los análisis de secuenciación profunda de muestras del tracto respiratorio inferior indicaron un nuevo coronavirus, que se denominó novel coronavirus 2019 (covid-19-2019) (115) . en la actualidad, en ausencia de terapia preventiva para sars-cov-2, la piedra angular de atención para pacientes con covid-19 sigue siendo el manejo de apoyo, que va desde el tratamiento ambulatorio sintomático hasta el tratamiento intensivo completo con medidas de soporte en cuidados intensivos (475) . dentro del manejo farmacológico se ha planteado la opción del uso de corticoides, la justificación estaría basada en la disminución de la respuesta inflamatoria del huésped a nivel pulmonar; es decir, un efecto inmunomodulador, ya que esta infección puede conducir a un síndrome de distrés respiratorio agudo (sdra); sin embargo, el beneficio puede verse superado por los efectos adversos, incluido el retraso en el aclaramiento viral y mayor riesgo de infección secundaria. a pesar de que la evidencia directa de corticoides en covid-19 es limitada, revisiones de los resultados en otras neumonías virales nos podrían orientar en principio en esta actual situación (476) . teniendo en cuenta lo anterior; stockman y cols, en el 2.006, realizaron una revisión sistemática sobre ensayos en pacientes con sars; quince ensayos examinan el uso de corticoides con diez o más pacientes en tratamiento; 13 ensayos también recibían ribavirina; trece de estos estudios no fueron concluyentes; dos estudios describen un daño potencial con el uso de esteroides; en la literatura china estos autores encontraron catorce estudios con uso de esteroides en sars; doce fueron suspendidos por posible daño, la mayoría de estos ensayos se realizaron con muestras pequeñas de pacientes y de manera retrospectiva (477) . arabi y cols, en noviembre 21 de 2.017, realizaron un estudio multicéntrico de cohorte retrospectivo en 14 hospitales de atención terciaria de arabia saudita, donde se incluyeron 309 pacientes; el uso de corticoides en pacientes con mers no se asoció con un cambio significativo a los 90 días en la mortalidad y se documentó un retraso en la eliminación del arn de mers-cov (478) . en cuanto hace referencia a la situación actual de pandemia por sars-cov-2 y compromiso pulmonar; wu y cols, en marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con covid-19 en china; para aquellos pacientes que desarrollaron sdra, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; hr, 0.38 [ic 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). zha y cols, en marzo de 2.020, describen el uso de corticosteroides en el tratamiento de pacientes con covid-19; no hallaron asociación entre la terapia con esteroides y el pronóstico de los pacientes sin sdra, siendo un estudio con una serie muy pequeña de pacientes (479) . yang y cols, en marzo de 2.020, en una revisión sistemática y meta-análisis que incluyó 5.270 pacientes de 15 estudios, describen como el tratamiento con corticoides estuvo asociado con una mayor mortalidad (rr = 2.11, ic 95% = 1.13-3.94, p = 0,019), mayor estancia (wmd = 6.31, ic 95% 5.26-7.37, p = <0,001) y una mayor tasa de infección bacteriana (rr = 2.08, ic 95% 1.54-2.81, p = <0.001); con algunas limitaciones en este metaanálisis, la mayoría de los estudios incluidos son estudios de cohorte retrospectivos, controles históricos, con un bajo nivel de evidencia y una falta de ensayos controlados aleatorizados con buen diseño, sin un estándar uniforme para el tiempo y la dosis de los corticoides utilizado en los estudios; los efectos de los corticosteroides pueden ser influenciado también por otras opciones terapéuticas, como los medicamentos antivirales (480) . por último, li y cols, en mayo de 2.020, en otra revisión sistemática y metaanálisis, con respecto al uso de corticosteroides en sujetos con amci ® infecciones por sars-cov-2, sars cov y mers-cov, se determinó que hubo retraso en la eliminación del virus sin mejoría en la supervivencia, reducción en la duración de la hospitalización o tasa de admisión en la uci y/o uso de ventilación mecánica; presentándose varios efectos adversos. debido a la preponderancia de los estudios observacionales en el conjunto de datos y los sesgos de selección y publicación, se concluye especialmente con respecto al sars-cov-2, que se necesita mayor investigación con ensayos clínicos aleatorizados. internamente en este meta-análisis sugiere precaución al usar esteroides en pacientes con covid-19 (481). horby y col en una rama del ensayo de evaluación aleatorizada de la terapia covid-19 (recovery), estudio aleatorizado, controlado, abierto que compara una gama de posibles tratamientos con la atención habitual en pacientes hospitalizados con covid-19, compararon el uso de la dexametasona a dosis de 6 mg día (oral o intravenosa) una vez al día por 10 días o el alta según lo que ocurriera primero contra el manejo habitual; en 2104 pacientes aleatorizados que recibieron dexametasona se compararon con 4321 pacientes en manejo estándar; 454 (21.6%) pacientes en el grupo de dexametasona y 1065 (24.6%) pacientes en el grupo control murieron a los 28 días, con un riesgo relativo ajustado para la edad (rr 0.83; 95% ic 0.74 a 0.92; p < 0.001). la mortalidad relativa y absoluta variaron significativamente en relación al soporte ventilatorio al momento de la aleatorización; la dexametasona redujo las muertes en una tercera parte de los pacientes que recibieron ventilación mecánica invasiva (29.0% vs. 40.7%, rr 0.65, 95% ic 0.51 a 0.82; p < 0.001), y una quinta parte en los pacientes que reciben oxígeno sin ventilación mecánica invasiva (21.5% vs. 25.0%, rr 0.80, 95% ic 0.70 a 0.92; p = 0.002), pero sin reducir la mortalidad en paciente que no recibieron soporte respiratorio al momento de la aleatorización (17.0% vs. 13.2%, rr 1.22, 95% ic 0.93 a 1.61]; p = 0.14) (482). se recomienda no utilizar plasma convaleciente como tratamiento de rutina en paciente con sars-cov2 -covid-19. se debe considerar su uso en el marco de un ensayo clínico y con alguno de los dos escenarios siguientes: escenario a (enfermedad severa), definida como uno o más de los siguientes: disnea, frecuencia respiratoria > 30/min, spo2 < 93%, pao2/fio2 < 300 o empeoramiento radiológico con aumento > 50% de los infiltrados pulmonares en 24 -48 horas. escenario b (enfermedad que amenaza la vida), definida como uno o más de los siguientes: falla respiratoria, choque séptico, o disfunción multiorgánica. se recomienda no utilizar plasma convaleciente para profilaxis clínica de rutina contra la infección por sars-cov-2, solo se debe considerar en el marco de un ensayo clínico. (485) . una revisión sistemática y meta-análisis exploratorio realizado en 2014 identificó 32 estudios de infección por coronavirus sars e influenza severa, el estudio reveló una reducción de la mortalidad, especialmente si el plasma convaleciente se emplea en la fase temprana de la enfermedad cuando se comparó con placebo o no tratamiento (or 0.25; ic del 95% 0.14 -0.45); sin embargo, hay que tener presente que los estudios son de baja calidad, carecen de grupos control y puede tener riesgo moderado a alto de sesgo (486) . se ha sugerido que el plasma convaleciente de pacientes que se han recuperado de covid-19 puede ser una terapia potencial, proporcionando inmunidad pasiva de los anticuerpos específicos contra sars-cov-2 y podría servir para prevenir y tratar la enfermedad (487) . las personas que se han recuperado de la infección por sars-cov-2 pueden generar anticuerpos neutralizantes (488, 489) que podrían tener aplicación en la prevención de infección en ciertos escenarios, como las personas con comorbilidades subyacentes que predisponen a enfermedad grave y aquellas con exposición de alto riesgo como los trabajadores de la salud y los expuestos a casos confirmados de covid-19. existen algunos riesgos asociados con el uso de plasma convaleciente, unos conocidos y otros teóricos; los riesgos conocidos son aquellos asociados con la transfusión de hemocomponentes, incluida la transmisión de virus (ej. vih, vhb, vhc, entre otros) (490); riesgo muy bajo, con los estándares de calidad actuales de los bancos de sangre; también se pueden presentar complicaciones no infecciosas, como las reacciones alérgicas, anafilaxia, reacción febril a la transfusión, lesión pulmonar aguda relacionada con la transfusión (trali), sobrecarga cardiaca asociada a transfusión (taco) y hemólisis si se administra plasma abo incompatible (491) . los riesgos teóricos incluyen el empeoramiento de la infección dependiente de anticuerpos (antibody-dependent enhancement of infection -ade); el ade puede ocurrir en varias enfermedades virales e implica una respuesta inflamatoria exagerada ante la presencia de ciertos anticuerpos (492) . otro riesgo teórico es que la administración de anticuerpos a las personas expuestas al sars-cov-2 puede evitar la enfermedad, pero modifica la respuesta inmune de tal manera que esos individuos monten respuestas inmunes atenuadas, lo que los haría vulnerables a la reinfección posterior, si se comprueba que este riesgo es real estos individuos podrían ser vacunados contra covid-19 cuando exista una vacuna disponible (487) . durante el brote actual en china, se utilizó plasma convaleciente en algunos pacientes con covid-19 (493), desde esta publicación se identificaron 9 publicaciones relacionadas con el tema, entre todos los estudios fueron tratados con plasma convaleciente un total de 5063 pacientes(494-502) (tabla 17). shen y cols en marzo 2020 describieron en china el primer reporte en el cual el plasma convaleciente puede ser una opción de tratamiento en pacientes con covid-19; reportaron una serie de casos de 5 pacientes críticamente enfermos con covid-19 y síndrome de dificultad respiratoria aguda (sdra), todos en ventilación mecánica, a quienes se les administró plasma convaleciente con anticuerpos neutralizantes [10 a 22 días después del inicio de la enfermedad (ddie)], todos ellos posteriormente mostraron mejoría clínica, la carga viral de los pacientes disminuyó y fueron negativas en los 12 días posteriores a la intervención (494) . de forma similar, duan y cols en mazo 2020 en china reportaron mejoría clínica en una serie prospectiva de 10 casos de paciente severamente enfermos con covid-19, que recibieron plasma convaleciente con un tiempo medio de 16.5 ddie (11 a 20 días) después del inicio de los síntomas, e hicieron amci ® una comparación con un grupo control histórico comparables en edad, género y severidad de la enfermedad (495) . zhang y cols en mazo 2020, en china reportaron una serie de 4 casos de pacientes con covid-19 críticamente enfermos, 3 en falla respiratoria con ventilación mecánica y dos de ellos con ecmo (membrana de oxigenación extracorpórea), a quienes se les dio tratamiento con plasma convaleciente en un tiempo medio 15.5 ddie, posteriormente todos tuvieron mejoría clínica (496) . posteriormente ahn y cols en abril 2020 en corea, describieron una serie de dos casos de paciente con covid-19 severamente enfermos, en falla respiratoria y con ventilación mecánica, quienes además de recibir hidroxicloroquina, lopinavir/ritonavir y metilprednisolona, fueron tratados con plasma convaleciente entre 6 -10 ddie, ambos pacientes se recuperaron y fueron liberados de la ventilación mecánica, uno fue dado de alta al momento del reporte (497) . ye y cols en abril 2020 en china, describieron una serie de 6 pacientes con covid-19 con anormalidades imagenológicas y deterioro clínico a pesar del tratamiento estándar y con pcr para sars -cov-2 persistentemente positiva, aunque no estuvieron en falla respiratoria o con ventilación mecánica, de hecho, una de las pacientes era portadora asintomática; todos recibieron plasma convaleciente entre 32 a 49 ddie, en todos los pacientes, excepto 1, hubo resolución de los cambios de vidrio esmerilado y consolidación, todos mejoraron y fueron dados de alta (498) . zeng y cols en abril 2020 en china, reportaron una serie de 6 casos con covid-19 en falla respiratoria y se compararon con 21 controles que no recibieron plasma convaleciente por limitación en la disponibilidad y compatibilidad abo; a este grupo de paciente, se les administró plasma convaleciente en promedio 21.5 ddie, en todos los casos se negativizó la pcr para sars-cov-2 a los 3 días después del tratamiento; sin embargo, contrario a los reportes de los 5 estudios previos, en este grupo se murieron 5 pacientes (83% vs 93%, p = 0.184), pero tuvieron mayor porcentaje de aclaramiento del virus (pcr sars-cov-2 negativa 100% vs 21.4%, p = 0.005) antes de la muerte e incluso el tiempo de sobrevida fue mayor en el grupo de tratamiento (p = 0.029) (499) . salazar y cols en mayo 2020, en houston, texas, reportaron una serie de 25 pacientes con covid-19 severa o amenazante para la vida, el desenlace primario fue seguridad y el secundario fue el estado clínico de los pacientes al día 14 luego de la transfusión; al día 7 posttransfusión, 9 pacientes (36%) mejoraron con relación a su estado clínico basal, 13 (52%) no tuvieron cambios y 3 pacientes tuvieron deterioro clínico. siete de los nueve pacientes que mejoraron (28%) habían sido dados de alta; para el día 14 post-transfusión, 19 (76%) de los pacientes presentaron mejoría y 4 pacientes más, habían sido dados de alta; tres pacientes permanecían sin cambios, 3 pacientes se deterioraron y uno murió por una condición no relacionada con el plasma; el promedio de estancia hospitalaria fue de 14.3 días y la estancia hospitalaria luego de la transfusión fue en promedio 11 días; hubo una disminución de los valores promedio de pcr desde 14.66 mg/dl el día 0, a 2,9 mg/dl y 0.45 mg/dl los días 7 y 14 respectivamente; al momento de la publicación del artículo, solo permanecían intubados 2 pacientes; todos los pacientes que requirieron ecmo ya se habían liberado y 20 (80%) fueron dados de alta (500) . también en texas, estados unidos, ramachandruni y col en mayo 2020, reportaron una serie de 5 casos con covid-19 severa, falla respiratoria y en ventilación mecánica o pao2/fio2 < 100, todos con comorbilidades; a los cuales les administraron metilprednisolona y posteriormente plasma convaleciente; compararon los valores basales de pao2/fio2 y posterior a la intervención; encontrando, mejoría de la pao2/fio2 en 48% luego del tratamiento con esteroides y en 26% luego de la administración de plasma convaleciente (501) . finalmente, en respuesta al brote de covid-19 en los eeuu y las tasas de mortalidad reportadas, la fda en colaboración con la mayo clinic y la comunidad nacional de bancos de sangre desarrollaron un programa nacional de acceso ampliado para recolectar y distribuir plasma convaleciente donado por amci ® individuos que se han recuperado de covid-19; entre abril 3 y mayo 11, 2020; fueron incluidos 14.288 pacientes con covid-19 severa o potencialmente mortal o con riesgo alto de progresión a covid-19 severa o potencialmente mortal en el programa nacional de acceso ampliado; en ese tiempo, un total de 8.932 pacientes inscritos recibieron transfusión de plasma convaleciente covid-19. en una publicación reciente, joyner y cols en mayo 2020, en estados unidos, hicieron un análisis de seguridad después de la transfusión de plasma convaleciente covid-19 humano con compatibilidad abo en 5.000 adultos hospitalizados con covid-19 grave o potencialmente mortal, 66% de los cuales se encontraban en uci; la incidencia de eventos adversos serios (eas) durante las 4 horas siguientes a la transfusión de plasma convaleciente fue < 1%, incluyendo mortalidad (0.3%); de los 36 eas reportados, hubo 25 incidentes reportados como eas relacionados, incluyendo 4 muertes, 7 eventos de taco, 11 trali y 3 reacciones alérgicas graves asociadas a la transfusión; sin embargo, solo 2 (de 36) eas fueron considerados definitivamente relacionados con la transfusión de plasma convaleciente por el médico tratante; en este grupo de pacientes, la tasa de mortalidad a los siete días luego de la administración del plasma convaleciente, fue del 14,9% (502) . a pesar que la tasa general de letalidad para la covid-19 parece ser aproximadamente 6.4% (503), la tasa de mortalidad reportada parece no ser excesiva si la comparamos con los informes de wuhan que sugieren tasas de letalidad del 14% para los pacientes hospitalizados (504) y 57% entre los pacientes en unidad de cuidados intensivos (139) . los nueve estudios mostraron mejoría en muchos aspectos, incluyendo el aclaramiento del virus, la disminución del suplemento de oxígeno y la ventilación mecánica, la normalización de los valores de laboratorio, y la recuperación en los hallazgos pulmonares radiológicos. todos los estudios, reportaron que no se presentaron eventos de seguridad o reacciones adversas serias relacionadas con la administración de plasma convaleciente en pacientes con covid-19, excepto en 2 casos relacionados, según criterio de los médicos tratantes, en el estudio publicado por joyner y cols (502) . esta serie de estudios son alentadores; sin embargo, la mayoría de los reportes de casos tienen limitaciones significativas: carecen de los ajustes para factores de confusión críticos, incluidos los co-tratamientos, las características basales, la gravedad de la enfermedad y el momento de administración del plasma y deben ser seguidas de investigaciones adicionales. para establecer mejor el papel del plasma convaleciente es necesario realizar estudios dirigidos a los siguientes escenarios: 1. el uso como profilaxis post-exposición 2. evaluar si el plasma convaleciente es útil en paciente con enfermedad leve 3. el efecto del plasma convaleciente en pacientes con enfermedad moderada 4. el tratamiento de rescate con plasma convaleciente en pacientes que requieren ventilación mecánica debido a covid-19 5. finalmente, trabajos que evalúen la seguridad y farmacocinética del plasma convaleciente en los pacientes pediátricos con alto riesgo. actualmente están en curso varios estudios para evaluar el tratamiento de pacientes infectados con sars-cov-2 con plasma convaleciente. una búsqueda realizada el 23 de mayo de 2020 en clinicaltrials.gov con los términos "plasma convaleciente y covid-19" mostró 82 ensayos en curso sobre el uso de plasma convaleciente en pacientes con amci ® covid-19, que nos ayudarán a resolver las inquietudes relacionadas con esta intervención (505) . page se recomienda no utilizar de rutina las las inmunoglobulinas hiperinmunes en pacientes con infección por sars-cov-2/covid-19. la inmunoglobulina hiperinmune (h-igiv) se deriva de individuos con altos títulos de anticuerpos contra patógenos específicos y se ha utilizado con éxito en el tratamiento de infecciones, como el citomegalovirus y la gripe h1n1 (506) . se propone que la inmunoglobulina hiperinmune combinada con medicamentos antivirales puede ser efectiva en el tratamiento de pacientes con covid-19, estos anticuerpos (ac) recogidos de los pacientes recuperados serán específicos contra covid-19 al aumentar la respuesta inmune en pacientes recién infectados (507) . existe evidencia más sólida para el uso de h-igiv en el tratamiento de enfermedades virales. cheng y cols en enero de 2005, realizaron una revisión retrospectiva en hong kong, que reveló que el plasma convaleciente de los sobrevivientes de sars-cov administrados a pacientes con sars-cov que tenían enfermedad progresiva resultó en tasas de alta significativamente más altas en el día 22 y tasas de mortalidad más bajas, en comparación con los controles históricos (485) . hung y cols en febrero de 2011, realizaron un estudio de cohorte prospectivo sobre la efectividad del plasma convaleciente de los sobrevivientes de h1n1 con un título de ≥ 1:160 ofrecido a pacientes de la uci con infección grave por h1n1; los pacientes que rechazaron las infusiones de plasma convalecientes fueron controles; veinte de los 93 pacientes recibieron sueros convalecientes, el tratamiento con plasma convaleciente condujo a una reducción significativa de la carga viral respiratoria, los niveles séricos de citocinas (il-6, il-10, tnfα) y la mortalidad (484) . posteriormente hung y cols en agosto de 2013, publicaron un estudio multicéntrico prospectivo, doble ciego, aleatorizado y controlado en el que compararon la efectividad de la inmunoglobulina hiperinmune (h-igiv) del plasma convaleciente de los sobrevivientes de h1n1 versus la inmunoglobulina iv (igiv) normal, en pacientes con h1n1 en uci con soporte respiratorio y recibiendo oseltamivir; este estudio mostró, una reducción de la carga viral y una mayor supervivencia en el grupo que recibió h-igiv dentro de los 5 días posteriores al inicio de los síntomas, demostrando la superioridad de la inmunoglobulina hiperinmune sobre la igiv en el tratamiento de la infección grave por h1n1(508). el uso de inmunoglobulina hiperinmune ha demostrado una clara efectividad en el tratamiento de la gripe y el sars-cov; sin embargo, el plasma se debe recolectar y procesar de pacientes convalecientes y verificar que tenga títulos adecuados. según la experiencia con el sars-cov, lo ideal es recolectar plasma de pacientes con un curso de enfermedad más leve (506) . poco se sabe sobre la seguridad de la inmunoglobulina hiperinmune cuando se usa para el tratamiento de infecciones por coronavirus, los riesgos incluyen la exacerbación de la infección dependiente de anticuerpos (antibody-dependent enhancement of infection -ade)(509); el ade puede ocurrir en varias enfermedades virales, e implica una respuesta inflamatoria exagerada ante la presencia de ciertos anticuerpos; sin embargo, los estudios en sars y mers no proveen información suficiente para extrapolarse a la infección por sars-cov-2. no se encontraron estudios con inmunoglobulina hiperinmune en el tratamiento de pacientes con covid-19. no se puede emitir una recomendación a favor o en contra para el uso de la inmunoglobulina intravenosa como tratamiento adyuvante en pacientes con covid-19 severo. se debe considerar la inmunoglobulina intravenosa como tratamiento adyuvante en pacientes con covid-19 severo, en el contexto de estudios clínicos en los siguientes escenarios. escenario a (enfermedad severa), definida como uno o más de los siguientes: disnea, frecuencia respiratoria > 30/min, spo2 < 93%, pao2/fio2 < 300 o empeoramiento radiológico con aumento > 50% de los infiltrados pulmonares en 24 -48 horas. escenario b (enfermedad que amenaza la vida), definida como uno o más de los siguientes: falla respiratoria, choque séptico, o disfunción multiorgánica. en las enfermedades virales, los anticuerpos ejercen su efecto por neutralización viral (bloqueo de la entrada de células virales y, por lo tanto, replicación), activación del complemento, opsonización y mediación de citotoxicidad celular dependiente de anticuerpos. la neutralización viral es específica de antígeno; otras actividades antivirales son antígeno-inespecíficas y se realizan en parte a través de interacciones fc: fc receptor. en la infección por sars-cov-2, el principal antígeno objetivo asociado con la neutralización es la proteína spike, que es responsable de la unión del sars-cov-2 a las células epiteliales, incluidos los neumocitos; los anticuerpos en las inmunoterapias pasivas covid-19 son de naturaleza policlonal, con múltiples epítopos contra los paratopes de sars-cov-2, incluido el dominio de unión al receptor en la proteína spike (509) . la inmunoglobulina intravenosa (igiv) es un producto derivado del plasma de miles de donantes utilizados para el tratamiento de inmunodeficiencias primarias y secundarias, afecciones autoinmunes/inflamatorias, trastornos neuroinmunológicos y secuelas relacionadas con infecciones; la igiv proporciona protección inmune pasiva contra una amplia gama de patógenos; actualmente, la experiencia con el uso de igiv en el tratamiento de la infección por sars-cov-2 es muy limitada; sin embargo, la justificación del uso de ivig en la infección por sars-cov-2 es la modulación de la inflamación (506) . la igiv se ha usado en el tratamiento de otros coronavirus, incluido el sars cov. stockam y cols, en septiembre de 2006, en respuesta a una petición de "the world health organization -who", realizaron una revisión sistemática de los efectos del tratamiento en los pacientes con síndrome respiratorio agudo, incluida la igiv o el plasma convaleciente; se evaluaron cinco estudios sobre el uso de igiv o plasma convaleciente administrado además de corticosteroides y ribavirina, se consideró que estos estudios no fueron concluyentes ya que los efectos de la igiv o el plasma convaleciente no podían distinguirse de otros factores que incluían comorbilidades, estadio de la enfermedad o el efecto de otros tratamientos (477) . wnag y cols, en mayo 2004, hicieron un estudio prospectivo, en un solo centro, de infección por sars en taiwán, se administró igiv si el paciente tenía leucopenia amci ® o trombocitopenia, o si había progresión rápida de la enfermedad en la radiografía; un total de 40 pacientes recibieron igiv, de los cuales 22 tenían citopenias graves, uno de ellos tenía evidencia de síndrome hemofagocítico y 18 paciente tuvieron progresión radiológica de la enfermedad; el estudio sugiere que la igiv condujo a una mejora significativa en el recuento de leucocitos y plaquetas, pero reconoce que no había un grupo de control para evaluar objetivamente las respuestas (510) . lew y cols, en julio 2003, reportaron un estudio retrospectivo de un solo centro en singapur, se encontró que los pacientes adultos con sars tratados con un régimen de pulso de metilprednisolona (400 mg) e igiv (0.4 mg/kg) diariamente durante tres días consecutivos tuvieron una hazard ratio ajustada de 0.41 para mortalidad en comparación con el grupo no tratado, con una tendencia hacia una recuperación más temprana; sin embargo, este hallazgo no fue estadísticamente significativo (ic del 95%: 0.14 a 1.23; p = 0.11); además, este resultado tuvo como factor de confusión el uso concurrente de esteroides (511) . aunque algunas de las preparaciones de igiv comercializadas actualmente (gamunex-c y flebogamma) contienen anticuerpos que reaccionan de forma cruzada contra el sars-cov-2 y otros antígenos de virus, in vitro(512), hasta la fecha, ningún ensayo clínico de alta calidad ha demostrado eficacia y seguridad convincentes de igiv en epidemias de coronavirus. a pesar de que los datos para el uso de igiv en la infección por sars y mers son débiles, la dosis alta de ivig puede ser útil en la infección grave por sars-cov-2 a través de la modulación inmune, saturando fcγr y reduciendo ade (506) . en general, la inmunoglobulina intravenosa es bien tolerada y el perfil de seguridad es bien conocido. las reacciones adversas comunes son leves y autolimitadas, pero se sabe que en pacientes de alto riesgo se producen efectos adversos graves, como trombosis, disfunción renal y muerte. en cuanto la evidencia (tabla 18); xie y cols en abril, en wuhan, china, realizaron un estudio retrospectivo, revisando 58 casos de covid-19 severa (disnea, fr > 30/min, spo2 < 93% en reposo, pao2/fio2 < 300, progresión imagenológica > 50% en 24 -48 horas) o críticamente enfermos (falla respiratoria con ventilación mecánica, choque, disfunción orgánica múltiple) en el cual evaluaron la mortalidad a 28 días como desenlace primario y como desenlace secundario evaluaron la mortalidad a 14 días, días de estancia hospitalaria, de uci y la necesidad de ventilación mecánica; reportaron que el tratamiento con igiv dentro de las 48 horas posteriores al ingreso no sólo redujo el uso de la ventilación mecánica comparado con el tratamiento luego de 48 horas del ingreso (6.67% vs 32.14%, p = 0.016), sino que también redujo la duración de la estancia en el hospital (11.50 ± 1.030 vs 16.96 ± 1.620 días, p = 0.0055) y la uci (9.533 ± 1.089 vs 13.50 ± 1.632 días, p = 0.0453); mejorando en última instancia la mortalidad a los 28 días (p = 0.0215); concluyen, que el estudio demostró que el tratamiento con igiv en pacientes con covid-19 con neumonía grave puede mejorar los indicadores en poco tiempo y mejorar la eficiencia del tratamiento de los pacientes con alta efectividad (513) . el tratamiento con dosis altas de igiv (25 g/día durante 5 días) al inicio del distrés respiratorio, sumado al tratamiento de soporte y en un caso combinados con antivirales (lopinavir/ritonavir) y metilprednisolona en covid-19 grave publicado por cao y cols en marzo, en wuhan, china (514), demostró la elevación de los recuentos de linfocitos, disminución de los marcadores inflamatorios, recuperación de la oxigenación, resolución parcial/completa de las alteraciones radiológicas pulmonares y las pruebas de hisopos nasales y orofaríngeos negativos dentro de unos pocos días después del inicio tratamiento (< 6 días). lanza y cols en mayo 2020, reportaron en nápoles, italia, el caso de una mujer de 42 años que tenía covid-19 severa y que venía con deterioro clínico a la cual se le venía dando tratamiento con hidroxicloroquina más azitromicina, no se le administraron amci ® esteroides por el riesgo de disminuir la depuración de la viremia, a quién se le administró igiv el día 16 después de iniciados los síntomas con mejoría clínica rápida, normalización de los gases arteriales y disminución marcada de los infiltrados pulmonares al día 5 y 8 respectivamente; como evento adverso, reportaron hipotensión durante el inicio de la infusión que se mejoró al disminuir la velocidad de infusión. la paciente finalmente se recuperó, negativizó rt-pcr sars-cov-2 y fue dada de alta (515) . se recomienda la tromboprofilaxis farmacológica en todos los pacientes confirmados o sospechosos de covid-19 severo, a menos que está contraindicada, en cuyo caso es razonable la implementación de profilaxis no farmacológica. en términos generales se reconoce que los pacientes hospitalizados con enfermedad médica aguda, incluidas infecciones como la neumonía, tienen un mayor riesgo de eventos tromboembólicos (516) . tang y cols, en china describieron múltiples trastornos de la coagulación en pacientes con covid-19, aquellos pacientes que no sobrevivieron tenían significativamente mayores niveles de dímero-d y productos de degradación de la fibrina y con tiempos de coagulación convencionales más alargados al ingreso (p < 0.05); 71.4% de los no sobrevivientes y 0.6% de los sobrevivientes cumplían criterios para coagulación intravascular diseminada(517); este mismo grupo realizó un estudio con 449 pacientes con covid-19 severo, pacientes con coagulopatía asociada a covid-19 (cac), definida por un sic score ≥4 la utilización de tromboprofilaxis redujo de manera significativa la mortalidad a 28 días (40.0% vs 64.2%, p = 0.029) así como también en aquellos con un se recomienda no utilizar de rutina antiagregación en pacientes con covid-19 severo con el fin de prevenir desenlaces neurológicos adversos. no se encuentran estudios en la literatura para el uso de antiagregantes para el manejo específico del covid-19; el manejo de los eventos cardiovasculares en pacientes covid-19 no difiere de la población general sin la enfermedad. no se establecen diferencias en los estudios descritos, ni en las publicaciones hasta la fecha de la revisión (518) . no se puede emitir una recomendación a favor o en contra sobre el uso de la anticoagulación terapéutica de rutina con heparinas de bajo peso molecular o heparina no fraccionada en pacientes con bajo riesgo de sangrado y con un curso clínico grave o crítico, que además tengan elevación del dímero d mayor a 1 mcg/ml (1000 ng/ml) y/o fibrinógeno mayor a 900 mg/dl. diferentes publicaciones describen como una estrategia de tratamiento basada en profilaxis con heparina de bajo peso molecular (hbpm) para tratar la coagulopatía grave por covid-19 podría no ser suficiente. especialmente porque estos pacientes tienen dentro de su coagulopatía, una predisposición mayor a la presencia de trombosis que al sangrado. además, los bajos niveles de antitrombina que se han descrito en estos pacientes, los hace más resistentes a la heparina, lo que sugiere que las dosis profilácticas ya sea de heparina no fraccionada o hbpm pueden ser inadecuadas(519-521). 135 asociación colombiana de medicina crítica y cuidados intensivos. amci ® no se puede emitir una recomendación a favor o en contra sobre la anticoagulación terapéutica de rutina con heparinas de bajo peso molecular en pacientes con covid-19 en estado crítico, que presenten elevación del dímero d mayor a 1 mcg/ml (1000 ng/ml). tang y cols, en china con un estudio retrospectivo donde se incluyeron 449 pacientes con covid-19 severo, se evaluó la presencia de trombosis como desenlace asociado. este estudio describe como niveles de dímero d por encima de 1500 ng/ml estaban asociados a una mayor probabilidad de muerte y en estos pacientes el tratamiento anticoagulante reduce de manera significativa la mortalidad (0.44, ic 95% 0.22-0.86) (156, 521) . no se puede emitir una recomendación a favor o en contra para la medición rutinaria de niveles de anti xa en pacientes con covid-19 en los que se decide hacer anticoagulación terapéutica con hbpm. se puede considerar la medición de niveles anti xa si se cuenta con la disponibilidad del recurso. harr y cols, en un estudio en donde se incluyeron pacientes con hiperfibrinogenemia relacionada a trauma, se evidenció como los niveles de fibrinógeno se correlacionaron significativamente con la consistencia del coágulo y adicionalmente como se genera una relación inversa entre los niveles de fibrinógeno y la actividad de las hbpm, lo que sugeriría una potencial resistencia a la heparina. basados en que los pacientes covid-19 presentan niveles de fibrinógeno en muchas ocasiones con niveles > 700 mg/dl e incluso >900 mg/dl lo que hace razonable considerar que aquellos pacientes covid-19 que requieren dosis terapéuticas de hbpm y es posible evaluar los niveles de anti xa, hacer ajustes y monitoreo del nivel de anticoagulación sería una opción razonable (522) . se recomienda el uso de hbpm o hnf para la anticoagulación terapéutica en pacientes con una indicación específica con diagnóstico de covid-19. amci ® como previamente se describió, una revisión sistemática comparó las dosis fijas de hbpm subcutánea con dosis ajustadas de hnf intravenosa o subcutánea en personas con clínica sugestiva de tep, esta revisión demostró que la incidencia de tep recurrente fue menor con hbpm que en los participantes con hnf (or 0.71, ic 95% 0.56 a 0,90), también se asoció con una reducción en el tamaño del trombo (or 0.71, ic 95% 0.61 a 0.82), evidencia de baja calidad. sin embargo, no hubo diferencias en la mortalidad general entre los participantes tratados con hbpm y los tratados con ufh (or 0.84, ic 95% 0.70 a 1.01). por otra parte, los protocolos de manejo en escenarios de coagulación intravascular diseminada (cid), proponen el uso de hnf por encima de la hbpm en pacientes en los que se indica la anticoagulación. más aún, la presencia de falla renal aguda es común en los pacientes con covid-19, por lo que la opción de tratamiento con hnf tiene también escenarios en donde podrían ser de elección (519, 523) . capítulo 8. procedimientos y covid-19 recomendación se recomienda realizar la preoxigenación en pacientes con sospecha o diagnóstico de covid-19, cuando estén disponibles, en áreas de presión negativa con mínimo 12 recambios de aire por hora o en instalaciones con ventilación natural o que tengan un recambio de aire de mínimo 160 l/seg si están disponibles. se recomienda como complemento opcional durante la preoxigenación en el paciente crítico con diagnóstico o sospecha de covid-19 la caja de acrílico para protección durante la intubación, la caja no protege contra la generación de aerosoles fuera de esta y requiere para su uso, entrenamiento previo. si es difícil su uso retírela inmediatamente. se recomienda utilizar en la mascarilla quirúrgica sobre la mascarilla de oxigenación en el paciente crítico con sospecha o diagnóstico de covid-19. se recomienda utilizar filtros hpfa entre la máscara y el dispositivo disponible para la preoxigenación en el paciente crítico con sospecha o diagnóstico de covid-19. se recomienda en el paciente con sospecha o diagnóstico de covid-19 preoxigenación por 3 a 5 min, si el paciente luego de 3 minutos no tiene incremento en la mejoría inicie la administración de medicamentos. se recomienda en caso de compromiso hemodinámico considerar ventilación a dos manos con cierre hermético de la máscara sobre la cara del paciente con frecuencias altas (>25 por minuto y baja presión). amci ® fundamento el manejo de la vía aérea es un procedimiento considerado generador de aerosoles, la enfermedad covid-19 tiene una alta tasa de transmisión y el personal de salud requiere el uso estricto del epp (524, 525) , revise el enunciado para epp recomendado en esta guía. la posibilidad de permanencia del virus en algunos ambientes puede durar hasta 4 horas, por esto una estrategia para proteger al equipo de salud y otros pacientes podrías ser estar en áreas con presión negativa, lo cual no es fácil de encontrar en nuestro contexto o que tenga un adecuado recambio de aire(526). como medidas complementarias se pueden utilizar opciones como las cajas acrílicas para intubación, esta disminuye el riesgo de contaminación por gotas, pero no elimina los aerosoles, es necesario previo entrenamiento. en caso de que la caja sea una limitante retírela inmediatamente (527) . los pacientes covid-19 , clásicamente se presentan con tos, esto es un factor de riesgo para quienes manipulan la vía aérea, la utilización de mascarilla por parte del paciente debajo del dispositivo bolsa mascarilla , la cual también deberá tener un filtro de alta eficiencia para disminuir el número de partículas que pueden estar en el ambiente durante la preoxigenación y posible ventilación, ésta última la cual será evitada al máximo (524, 526, 528) . la preoxigenación es una técnica que pretende barrer el nitrógeno y aumentar la disponibilidad de oxígeno para que cuando el paciente presente apnea por los medicamentos para la intubación o por su condición clínica, se disponga de un tiempo mayor sin desaturación crítica y riesgo de colapso cardio-respiratorio. considere que los pacientes con formas moderadas y severas de covid-19, pueden tener más comprometida esta reserva respiratoria y puede no ser efectiva la preoxigenación y cuando inicia la apnea, la desaturación será más precoz. si después de 3 minutos de preoxigenación no hay mejoría de la saturación arterial, considere fallida esta maniobra y considere mayor riesgo de hipoxemia severa con probabilidad de bradicardia extrema y paro cardiorrespiratorio. en caso de requerir ventilación por disminución rápida de la saturación de oxígeno arterial y considere necesario ventilación manual bolsa mascarilla a dos manos no debe ser vigorosa y debe utilizar filtros hpfa, estos reducirán los aerosoles en el ambiente(526, 529). se recomienda la utilización de cajas de acrílico para intubación del paciente con sospecha o diagnóstico de covid-19 como complemento durante la intubación para disminuir el riesgo de contaminación por gotas, sin embargo, no protege 100 % la generación de aerosoles y si ésta hace más difícil la intubación retírela inmediatamente. amci ® se recomienda minimizar los intentos de intubación orotraqueal en el paciente con sospecha o diagnóstico de covid-19, el primer intento debe procurar ser realizado por el más experimentado en el manejo de la vía aérea. se recomienda la intubación con videolaringoscopio en pacientes con covid-19 teniendo en cuenta disponibilidad y entrenamiento); esta alternativa puede ofrecer ventajas frente a la laringoscopia tradicional. se recomienda administrar medicamentos para asegurar la vía aérea en secuencia de inducción rápida, para obtener en el menor tiempo posible condiciones para la intubación (45 a 60 s). se recomienda en caso de intubación fallida por personal experto, considerar dispositivos supraglóticos como las máscaras laríngeas como medida de rescate con el riesgo de generación de aerosoles. se recomienda contar con disponibilidad de vasopresor y atropina en el sitio donde se realizará la intubación. en caso de contar con lidocaína se recomienda utilizar a dosis de 1 mg/kg sin epinefrina. administrada 3 minutos antes de la intubación. como se describió en el aparte de preoxigenación, se deben garantizar todas las medidas basadas en bioseguridad y protección adecuada para el personal de la salud, ubicación en áreas que cuenten con presión negativa o salas con un óptimo recambio de aire pueden ayudar a disminuir el riesgo de contagio. las medidas complementarias como la caja de taiwán o caja de intubación puede complementar de forma opcional estas medidas durante el proceso de aseguramiento definitivo de la vía aérea pero no garantiza 100 % la eliminación de aerosoles, pudiendo ser un obstáculo para quien realiza la intubación, de ser así, se deberá retirar inmediatamente, por eso sólo es un complemento al epp, que es la verdadera protección en estos escenarios (se debe incluir máscaras n95 o ffp2 fpp3) (524, 527) . el paciente críticamente enfermo puede tener comprometida de forma significativa su reserva respiratoria y hemodinámica por su cuadro clínico y puede empeorar por los medicamentos utilizados durante la intubación orotraqueal. las complicaciones en el manejo de la vía aérea se presentan cuando se realiza más de un intento dentro de los cuales están el traumatismo, desaturación e hipoxemia (530) . es por esto por lo que se debe procurar que el primer intento sea realizado por el más experimentado en el manejo de la vía aérea e idealmente se logre la intubación en el primer intento con la menor hipoxemia secundaria (166, 526, (531) (532) (533) . basado en el planteamiento anterior y considerando la ventaja de intubar pacientes críticamente enfermos en el primer intento dadas sus condiciones clínicas, la revisión de amci ® demandas asociadas a manejo de vía aérea en los estados unidos sigue siendo preocupante al considerar posibles causas la falta de entrenamiento y falta de aplicación de las guías y recomendaciones de manejo así como en la utilización de equipos adecuados para pacientes específicos (534) ; se ha planteado especialmente en los pacientes covid-19 los cuales tienen un importante compromiso pulmonar y alto riesgo de desaturación, la posibilidad de encontrar una vía aérea difícil no predicha y dificultades en su manejo(526, 533). es por esto que se requiere del mejor dispositivo para manejo de vía aérea invasiva disponible, siempre y cuando se cuente con el adecuado entrenamiento previo en su uso, la ventaja de los videolaringoscopio se debe a la superioridad al compararla con la laringoscopia convencional, siendo en algunos grupos la primera opción para intubaciones electivas (535, 536) . como se ha mencionado, el riesgo de una rápida desaturación en pacientes con enfermedad pulmonar, así como en pacientes con covid-19, se debe utilizar la inducción de secuencia rápida la cual se utiliza para pacientes con estómago lleno en los cuales se quiere lograr condiciones de inconciencia y de intubación óptimas en el menor tiempo posible para disminuir el riesgo de broncoaspiración. en estos casos de falla respiratoria con tan mala reserva se quiere aprovechar la ventaja que ofrece esa técnica para tener en poco tiempo al paciente intubado con menor riesgo de desaturación. es así como los medicamentos en una inducción de secuencia rápida incluyen el opioide, hipnótico y relajante, estos dos últimos administrados simultáneamente y lavados con un bolo de 20 cc. la opción del opioide en nuestro contexto suele ser fentanilo a dosis de 2 a 5 mcg / kg iv, dando 2 a 3 minutos de latencia para su efecto, luego el hipnótico que puede ser propofol entre 1 y 1,5 mg / kg si la estabilidad hemodinámica lo permite o considera usar vasopresor simultáneo. en caso de preferir evitar la hipotensión la ketamina a dosis de 1 a 1, 5 mg / kg es una opción más estable hemodinámicamente. con relación al relajante neuromuscular la succinilcolina es la clásicamente utilizada dosis de 1 a 1,5 mg/kg pero debido a sus efectos secundarios como hiperpotasemia, fasciculaciones, mialgias y un importante riesgo de hipertermia maligna algunos grupos no lo consideran, el rocuronio a dosis de 1,2 mg/kg ha demostrado lograr tiempos y condiciones de intubación similar a la succinilcolina sin los efectos secundarios de esta (533, 535) algunos grupos han considerado no utilizarlos si la condición clínica del paciente es crítica pues éste período de latencia puede ser acompañado de una hipoxemia severa y paro cardíaco, por lo tanto sólo usan hipnótico y relajante neuromuscular. ante una vía aérea difícil no predicha en la cual no se logre la intubación, considere los dispositivos supraglóticos como las máscaras laríngeas los cuales son más fáciles de insertar en comparación con la técnica de intubación orotraqueal, y deben estar dentro del planeamiento y organización de elementos para manejo de la vía aérea invasiva. al lograr ventilar con este dispositivo se logrará una recuperación del paciente, pero se pueden generar aerosoles pues este mecanismo de cierre puede permitir escape de aire y macropartículas durante el ciclo respiratorio ya sea manual o mecánico (535, 536) . el cuadro clínico de pacientes críticos y particularmente covid-19, puede asociarse a inestabilidad hemodinámica y requerimiento de soporte vasopresor. la adición de medicamentos como los opioides o hipnóticos pueden asociarse a hipotensión la cual puede no responder a volumen, es necesario evitar episodios de hipotensión en especial en pacientes ancianos, con enfermedades cardiovasculares de base las cuales pueden tolerar menos estos cuadros de hipotensión, así como también pueden favorecer amci ® desbalance en la relación ventilación/perfusión a nivel pulmonar empeorando los cuadros de hipoxemia. la hipoxemia puede acompañarse de bradicardia y si no se corrige la ventilación o la bradicardia es muy probable que el paciente presente paro cardiorrespiratorio, por lo cual se recomienda utilizar una dosis de atropina para corregir la bradicardia, no mejorará la oxigenación, pero tendrá un tiempo adicional para recuperar la oxigenación y ventilación del paciente. en estos casos debe tener disponibles vasopresores y atropina desde el planeamiento de los medicamentos necesarios para el manejo de la vía aérea (166) . se recomienda la intubación orotraqueal oportuna y no retrasar el inicio de la ventilación mecánica invasiva en los pacientes con sdra severo por covid-19 debido a mayor riesgo de desenlaces adversos. fundamento definir el momento de la intubación en esta población es un reto. la mayoría de los autores recomiendan el inicio "temprano" de la ventilación mecánica, sin embargo, la definición de cuando es temprano no es clara. este punto es motivo de análisis dado que a la luz de la evidencia actual la utilización de métodos no invasivos como la ventilación no invasiva y la cánula de alto flujo, para manejo inicial de pacientes con algún grado de hipoxemia es controvertido entre otras por el riesgo que supone al personal sanitario al ser un procedimiento generador de aerosoles. en el 2015 un estudio mostró que la intubación retrasada después de la falla al utilizar cánula de alto flujo o la ventilación no invasiva para pacientes con insuficiencia respiratoria moderada y grave se asoció con una mayor mortalidad. publicaciones recientes muestran que solo la quinta parte de los pacientes que murieron por covid-19 recibieron ventilación mecánica invasiva y soporte respiratorio más agresivo antes de la muerte, lo que indica que en muchos pacientes se habría retrasado la intubación. de los pacientes fallecidos solo el 27% recibieron tratamiento de oxígeno nasal o con mascarilla facial antes de su muerte. esta baja proporción puede tener varias explicaciones. primero, algunos pacientes con hipoxemia severa no tenían otros síntomas, como dificultad para respirar o disnea, es decir, desarrollaron una especie de hipoxemia silenciosa. en segundo lugar, la falta de suficientes ventiladores mecánicos invasivos es una razón importante que evitaría que los pacientes reciban intubación. tercero, el manejo de estos pacientes por un equipo de médicos no intensivistas; por lo tanto, pueden no estar seguros del momento en que un paciente requiere intubación. la serie de casos de la epidemia de covid-19 en wuhan mostró que la intubación tardía era común en la etapa inicial de la epidemia, mostrando que una de esas posibles razones del retraso incluía falta de ventiladores mecánicos invasivos y falta de capacitación clínica específica para el soporte respiratorio. recomendación se recomienda tomar la decisión de intubación orotraqueal en el paciente crítico con sospecha o diagnóstico de covid-19 utilizando una combinación de variables clínicas, gasométricas y hemodinámicas. tabla la intubación orotraqueal (iot) efectiva y segura, programada debe prevenir el colapso respiratorio y hemodinámico. siempre es necesario asegurar la escena del procedimiento de intubación con las consideraciones técnicas y de protección personal adecuadas. conocer los pasos para la realización del procedimiento de intubación orotraqueal (iot) contextualizados al paciente covid-19, reduce los riesgos innecesarios. la iot es un procedimiento generador de aerosoles por lo tanto lo ideal es realizarlo en una habitación con presión negativa, sin embargo, la baja disponibilidad en el país obliga a utilizar otras alternativas de seguridad. una habitación de presión negativa es un cuarto que tiene una presión más baja que las áreas adyacentes, lo que mantiene el flujo de aire fuera de la habitación y hacía habitaciones o áreas contiguas. las puertas de la sala deben mantenerse cerradas, excepto al entrar o salir de la sala, y la entrada y la salida deben minimizarse. la intubación en el paciente crítico con covid-19 es de los procedimientos que mayor riesgo de aerosolización tiene, por lo tanto, se debe adoptar una posición de intervención oportuna, pero también segura, para evitar desenlaces desfavorables en el paciente y disminuir el riesgo de contaminación en el personal de salud, se recomienda individualizar cada caso mediante la combinación y análisis de los criterios clínicos, gasométricos y hemodinámicos de cada paciente. (533, (537) (538) (539) se recomienda no realizar de rutina broncoscopia en los pacientes con sospecha o diagnóstico de covid-19, debido al riesgo de generación de aerosoles. se puede considerar en atelectasias masivas con compromiso significativo de la oxigenación adicional a la lesión pulmonar per sé y la hemorragia alveolar para control local directo. en general la realización de broncoscopia en pacientes con sospecha o confirmación de covid-19 debe ser evitada y realizarse sólo con indicación de emergencia como cuerpo extraño en la vía aérea, hemoptisis masiva, obstrucción grave de la vía aérea central o atelectasia lobar o pulmonar completa(540). esto debido a la alta carga viral en la mucosa nasal y faríngea de los pacientes con infección por sars-cov-2 (102) y la alta producción de aerosoles infecciosos que se generan durante este procedimiento. en caso de ser necesaria su realización, deberá ser llevada a cabo por el operador con mayor experiencia amci ® minimizando el tiempo de exploración y el personal expuesto en la sala. es mandatorio utilizar epp completo que incluya respirador fpp2 o fpp3, bajo protocolo supervisado de donning y doffing (541) . son de elección los broncoscopios desechables de un solo uso, pero de no ser posible se prefiere el uso de un broncoscopio flexible por encima de uno rígido por la más fácil manipulación de este. idealmente el procedimiento se llevará a cabo en el mismo cubículo del paciente que deberá contar con presión negativa y recambio de aire de 12 a 15 veces por hora. recomendación se recomienda no realizar de rutina la broncoscopia para la recolección de muestras para el diagnóstico de covid-19 en el paciente críticamente enfermo. la broncoscopia es una prueba de segunda elección para la toma de muestras respiratorias en los pacientes con sospecha o confirmación de covid-19 (542) . la toma de muestras del tracto respiratorio superior por hisopado nasofaríngeo u orofaríngeo es el método primario y de elección para determinar la infección por sars-cov-2. solo si resultaran dos pruebas negativas y persistiera una alta sospecha diagnóstica estaría indicado tomar muestras del tracto respiratorio inferior por broncoscopia, ya sea aspirado endotraqueal (bas) o lavado bronco alveolar (bal) (543), prefiriendo la realización de minibal para la recolección de muestras (540). las muestras deberán ser recogidas en un recipiente estéril, e introducidas en una bolsa con autocierre. deben manejarse con cuidado extremo evitando manipulaciones innecesarias y bajo protocolos de protección para el personal que las maneja, y trasladarse al laboratorio para su análisis. pueden almacenarse a 2-8ºc las primeras 72 h de su recolección; si se demorara más el análisis, precisa almacenarse a temperatura de -70ºc (124) . en una serie china la sensibilidad del bal fue de 93% frente a 72% en muestra de esputo (no recomendada) y 63% en hisopado nasofaríngeo (128) por lo que el especialista que realiza el procedimiento deberá sopesar el riesgo de este procedimiento en cada caso, valorando que se beneficiarán aquellos pacientes que tengan una indicación adicional para su realización. se recomienda la realización de la traqueostomía cuando está indicada, en los pacientes covid-19 sospechosos y confirmados con pronóstico razonable de vida, después del 5 o 7 día de ventilación , previa valoración y consenso por el equipo quirúrgico y de cuidado intensivo, asegurando que las condiciones clínicas, ventilatorias y hemodinámicas se encuentran controlada. en el contexto de pacientes hospitalizados en cuidado intensivo, la traqueostomía se realiza para facilitar el destete de la ventilación mecánica, mejorar la limpieza de la vía aérea y el manejo de las secreciones, aumentar la comodidad de los pacientes y la movilización y disminuir la probabilidad de complicaciones como la estenosis traqueal; sin embargo no hay una clara disminución en la mortalidad (544) (545) (546) . la infección actual por sars-cov2, tiene diferentes estadios de gravedad, uno de ellos es el compromiso pulmonar el cual se caracteriza por un síndrome de dificultad respiratorio agudo (sdra). de acuerdo con el comportamiento de la covid-19, entre un 10% a un 15% de los pacientes requieren ventilación mecánica (115, 121) , este grupo de pacientes con manifestación grave del compromiso pulmonar requiere estrategias de protección pulmonar en la ventilación mecánica, sedación profunda y posiblemente parálisis muscular y puede tener una mortalidad entre el 30% y el 50% (48, 547) . una de las principales características en éste grupo de pacientes es la mortalidad temprana, definida ésta como aquella que se produce en menos de 14 días; de acuerdo a la experiencia en wuhan, china; leung (548), reporta que la mortalidad se presenta en los primeros cinco días luego de la admisión hospitalaria y de acuerdo a lo referido por graselli et al (287) , en la región de lombardía, italia, la mediana de mortalidad se presenta al día siete después del ingreso. con estas consideraciones, al principio de la pandemia y en las aproximaciones iniciales no se recomendaba realizar la traqueostomía en los primeros 14 días posteriores a la intubación orotraqueal. sin embargo, con el conocimiento de la fisiopatología y las experiencias en otras series, como medida para facilitar la liberación de la ventilación mecánica, se ha podido realizar el procedimiento después de la primera semana de inicio de la ventilación. de acuerdo con el curso natural de la enfermedad, el paciente en promedio se intuba al día 10 a 12 de iniciado los síntomas, una semana posterior a la intubación para la traqueostomía, estaríamos alrededor del día 21 de la enfermedad, donde los pacientes ya tendrán una disminución de la carga viral. esto sin embargo no evita la utilización de los epp necesarios. esta medida en específico fue discutida y consensuada entre la sociedad de medicina critica amci y la asociación colombiana de cirugía. no existe evidencia que permita evaluar el riesgo real de infección del personal asistencial de los pacientes con sospecha o diagnóstico de covid-19 en la realización de traqueostomías. se debe considerar en la traqueostomía y la realización de ésta como un procedimiento generador de aerosoles (organización mundial de la salud). se recomienda que los epp requeridos para la realización del procedimiento, deben incluir máscaras ffp3 o n95, protección ocular, vestido antifluido idealmente desechable y amci ® guantes; este nivel de protección representa el mayor nivel de seguridad para realizar el procedimiento en el paciente con sospecha o diagnóstico de covid-19. no existe actualmente artículos que permitan evaluar cual es el riesgo real de infección del personal asistencial en la realización de traqueostomías en pacientes con covid-19; quizás el ejemplo más cercano, es una serie de casos, reportada durante la epidemia del síndrome respiratorio agudo grave en el 2004 (549), en el cual se realizaron 23 traqueostomías sin ninguna infección del personal, en este reporte se aseguró un adecuado uso del equipo de protección personal (epp), el cual incluía las medidas de barrera, máscaras ffp3 y cuando existía la disponibilidad, respiradores con suministro de aire purificado. la traqueostomía y la realización de ésta es considerada por la organización mundial de la salud (oms) un procedimiento generador de aerosoles, bajo esta perspectiva, el epp requerido para la realización del procedimiento, debe incluir máscaras ffp3 o n95, protección ocular, vestido antifluido idealmente desechable y guantes; este nivel de protección representa el mayor nivel de seguridad para realizar el procedimiento mencionado. es obligatorio, que todo el personal reciba el entrenamiento para la postura, el uso y el retiro de los epp, si estos pasos no se realizan de la forma adecuada, representan una fuente de contaminación(550). se recomiendan no esperar la negativización de la pcr para sars-cov2 para realizar la traqueostomía en el paciente con diagnóstico de covid-19. fuerte en contra fundamento los estudios de zou et al y lescure et al (102, 551) , muestran que la carga viral de los hisopados nasales y faríngeos es elevada en la primera fase de la enfermedad, con una disminución entre el día nueve al quince, pero esta puede permanecer detectable hasta por tres semanas (37) . existen recomendaciones acerca de la necesidad de realizar la traqueostomía una vez la pcr para sars-cov2 sea negativa (552, 553) ;aunque este esquema suena lógico, es importante tener presentes las siguientes consideraciones. la sensibilidad de una sola muestra para ruta-pcr puede ser sólo del 70%(554) y es posible que sea necesario realizar una segunda prueba para minimizar el riesgo para quien realiza el procedimiento, aunque esta aproximación no siempre puede ser viable desde el punto de vista clínico, epidemiológico y administrativo. amci ® recomendamos que la mejor estrategia es diferir la realización de la traqueostomía hasta 5 7 días luego de la intubación cuando esta indicada, con el conocimiento acerca de la evolución natural de la enfermedad, en ese momento en la mayoría de los pacientes, lo más probable es que la condición ya se encuentre en la tercera semana desde el inicio de los síntomas, en cuyo caso lo más probable es que ya exista una disminución de la carga viral; este hecho no evita que se deba utilizar de la forma correcta los epp. recomendación se recomienda escoger la técnica teniendo en cuenta la experticia que tenga en el grupo tratante y la anatomía del paciente para la decisión de la técnica. se recomienda la guía ecográfica para disminuir la probabilidad de complicaciones del procedimiento si la anatomía es desfavorable para la realización de traqueostomía percutánea. se recomienda la traqueostomía quirúrgica en pacientes de riesgo elevado de complicaciones donde se requiere un control más rápido y seguro de la vía aérea. se recomienda no utilizar de forma rutinaria la utilización de broncoscopia para la realización de traqueostomía por vía percutánea. no hay evidencia directa hasta la fecha de publicación del consenso si existe superioridad entre las dos técnicas en el paciente con sospecha o diagnóstico covid-19. en pacientes críticos no existen diferencia en los desenlaces cuando se evalúa el rendimiento de la técnica percutánea y la técnica quirúrgica, la elección de uno u otro método está dado por la anatomía del paciente, el entrenamiento de los profesionales y la disponibilidad de los diferentes insumos y técnicas. tampoco se ha logrado hasta la fecha evaluar durante la pandemia de covid-19 si existe una diferencia entre las dos técnicas y por lo tanto no es posible acercarse a una recomendación basada en la literatura. sin embargo, es importante que para la decisión de la técnica a utilizar se considere la anatomía del paciente y los siguientes aspectos:  no se recomienda la utilización de broncoscopia para la realización de traqueostomía por vía percutánea, ésta aumenta la generación de aerosoles y el número de personas expuestas a estos (555, 556) . amci ®  si la anatomía es desfavorable para la realización de traqueostomía percutánea, la guía ecográfica puede disminuir la probabilidad de complicaciones del procedimiento (557) .  la traqueostomía quirúrgica es una alternativa para la realización del procedimiento en las unidades de cuidado intensivo en momentos de sobrecarga laboral y adicionalmente puede tener un mejor y más rápido control de la vía aérea, especialmente en pacientes con riesgo elevado de complicaciones (549) . recomendación se recomienda el uso de la terapia ecmo en sdra severo refractario por covid-19 (pao2/fio2 < 150, posición prona, requerimiento de relajantes neuromusculares en algunos casos vasodilatadores pulmonares y maniobras de reclutamientos) sin respuesta clínica manifestado por:  pao2/fio2 < 60 mmhg por mas de 6 horas  pao2/fio2 < 50 mmhg por mas de 3 horas  ph < 7.20 + paco2 > 80 mmhg por mas de 6 horas además del criterio anterior, se recomienda tener en cuenta la edad, las comorbilidades y la expectativa de sobrevida del paciente con buena calidad de vida y en circunstancias donde no exista limitación de recursos. no hay estudios clínicos aleatorizados sobre el uso del ecmo en pacientes con covid-19 (166, 558) . existe el estudio eolia (216) , el cual fue detenido durante su realización, y de acuerdo a un análisis bayesiano posterior puede interpretarse como una disminución de la mortalidad en los pacientes en ecmo con sdra severo (211, 216, (559) (560) (561) (562) . de igual manera debe considerarse la racionalización de los recursos y el estado de prevalencia de la pandemia en un lugar determinado. el inicio de la terapia puede evaluarse en función de la cantidad de pacientes en falla respiratoria y la disponibilidad de personal y otros recursos; si el hospital debe comprometer todos los recursos en proveer medidas básicas de cuidado intensivo no debe utilizar el ecmo (563, 564) . los pacientes jóvenes sin comorbilidades son considerados de alta prioridad al igual que los trabajadores de la salud (565, 566) . amci ® se recomienda no desarrollar nuevos centros de ecmo en época de pandemia, sobre todo en situaciones con limitación de recursos. fuerte en contra fundamento actualmente se recomienda el uso del ecmo con las mismas indicaciones para sdra basado en la capacidad de las instituciones de salud para iniciar éste tipo de terapias (567) . en épocas de crisis la capacidad de los hospitales está saturada y obliga a la reubicación y optimización de los recursos (568, 569) . los centros que ofrecen la terapia en ecmo deben ser centros con resultados favorables y tiempos de soporte de pacientes relativamente cortos (570) . cuando estamos en tiempos de capacidad hospitalaria convencional y existe disponibilidad de camas de cuidado intensivo se pueden ofrecer los servicios de ecmo vv, va, e-cpr inclusive a pacientes no covid-19, cuando estamos en contingencia y capacidad nivel 1 se debe hacer un triage respecto a pacientes jóvenes y ofrecer ecmo vv, va, escoger muy bien los casos para pacientes no covid-19 y no ofrecer e-cpr, cuando estamos en contingencia y capacidad nivel 2 es porque ya se están usando sitios de expansión y están casi saturados se restringe el ecmo a todas las indicaciones y se prioriza a pacientes con indicaciones no covid-19 con mayor riesgo de sobrevida, el ecmo vv queda para pacientes jóvenes, con disfunción de 1 órgano y covid-19 positivo, no se ofrecerá ecmo va o e-cpr y cuando estamos en capacidad de crisis es porque la capacidad total hospitalaria está sobresaturada y no es posible realizar ecmo tanto en pacientes covid-19 como en los no covid-19 (564, 571) . se recomienda practicar e implementar medidas de capacitación y vigilancia continua para mejorar la higiene de manos, evaluando la adherencia a protocolos establecidos en los trabajadores de la salud mediante listas de chequeo y supervisión para evitar infecciones cruzadas en el entorno del paciente con sospecha o diagnóstico de covid-19. se recomienda establecer protocolos específicos para reducir el riesgo de infecciones que se deriven de la interacción y el cuidado del paciente crítico con sospecha o diagnóstico de covid-19. amci ® se recomienda implementar prácticas de cuidado para la prevención de contagio de covid-19. se debe utilizar el equipo de protección personal (epp) para la prevención de enfermedades de componente infeccioso asociado a exposición con fluidos corporales derivados del paciente crítico con sospecha o diagnóstico de covid-19. las infecciones relacionadas con la atención sanitaria (iras) son definidas por la organización mundial de la salud como aquellas "infecciones que se presentan en un paciente durante el proceso de atención en un hospital u otro centro sanitario que no estaban presentes o no se estaban incubando en el momento del ingreso; se incluyen las infecciones contraídas en el hospital pero que se manifiestan tras el alta hospitalaria y también las infecciones profesionales entre el personal del centro sanitario". las iras representan una importante carga de enfermedad que se asocia a un impacto negativo en la economía del paciente y del sistema sanitario. la organización mundial de la salud plantea la higiene de manos como la principal medida necesaria para reducir y prevenir las iras; por esta razón establece directrices sobre la higiene de manos en la atención sanitaria y basada en esta propone la estrategia multimodal para la mejora de higiene de manos. las estrategias mencionadas anteriormente han demostrado el incremento en el cumplimiento de higiene de manos y disminución en las infecciones relacionadas con la atención en salud. la estrategia multimodal se articula a través de cinco componentes: cambio del sistema, formación, evaluación/ retroalimentación, recordatorios en el lugar de trabajo clima institucional. a través de estos componentes, se garantiza que el centro sanitario cuenta con la infraestructura necesaria para practicar adecuadamente el lavado de manos incluyendo dentro de este el acceso a un suministro seguro continuo de agua, jabón, preparado alcohólico y toallas; a su vez se proporciona educación, evaluación y retroalimentación con regularidad a todos los profesionales sanitarios (572 se recomienda realizar un plan de cuidados organizado y específico en paciente crítico con sospecha o diagnóstico de covid-19, ofreciendo el uso óptimo de recursos e intervenciones. se recomienda evitar el uso de excesivo de papelería relacionada con los registros usados para gestión de insumos y atención de los pacientes. se recomienda realizar intervenciones educativas enfocadas a mejorar la adherencia y adecuado uso de los epp. se debe procurar el cuidado de los elementos de protección personal bajo un protocolo que conserve las condiciones de integridad de estos. la actual reserva de elementos de protección personal (epp) es insuficiente debido al aumento de la demanda global, por el incremento de casos de covid-19 y por la información errónea que ha conllevado a compras de pánico y almacenamiento. por esta razón la organización mundial de la salud a través de su guía: uso racional del equipo de protección personal para la enfermedad por covid-19 ha implementado las siguientes estrategias para optimizar la disponibilidad de (epp): usar los (epp) adecuadamente, minimizar la necesidad de (epp) y coordinar el suministro adecuado de (epp). (574) la duración máxima del uso continuo de la n95 es de 8 a 12 horas, siguiendo las recomendaciones del manual de medidas básicas para control de infecciones en ips de minsalud. pero en lo cotidiano, ningún trabajador tolera 8 a 12 horas continuas con un respirador. por esto, su uso continuo en el sitio de trabajo dependerá de la necesidad de pausar para comer, para ir al baño, etc. en este caso, se guardará en una bolsa de papel para su nueva colocación, si tiene menos de 12 horas, se desechará si está visiblemente contaminada o se torna húmeda. el reusó de la n95 dependerá de la casa del fabricante, de si contiene o no celulosa en su estructura del respirador. por ejemplo, la recomendación del consenso colombiano acin sobre la desinfección para los respiradores sin celulosa es con peróxido de hidrógeno vaporizado al 58% por 28 minutos. los respiradores n95 de uso industrial tienen mayor contenido de celulosa que los de uso médico por lo tanto para procesos de esterilización, solo los n95 de uso médico podrán ser esterilizados mediante de peróxido de hidrógeno vaporizado (sterrad®)(84-88). amci ® se recomienda elaborar el protocolo de pronación del paciente críticamente enfermo por covid-19, garantizando el entrenamiento al personal de salud, organizando el recurso humano, dispositivos de apoyo y tiempo establecido para cambios de posición para prevenir las lesiones por presión en el paciente. fuerte a favor fundamento la estrategia de pronación es una alternativa eficiente en el manejo del síndrome de dificultad respiratoria en pacientes críticos y es fundamental la gestión del profesional de enfermería en la prevención de complicaciones y eventos adversos, lo cual aportará significativamente a la calidad del cuidado ofrecido favoreciendo las mejoras en la oxigenación. es importante optimizar los cuidados de enfermería en torno de los cuidados de piel en los pacientes en ventilación mecánica en decúbito prono, los estudios han demostrado como principal complicación las lesiones de presión con una incidencia hasta de 25.7%, siendo las más frecuentes las grado 1 y 2(573). una lesión se puede producir si se supera una presión en el tejido capilar arterial de 32 mmhg denominándose interfaz de presión. basándose en lo anteriormente mencionado, el cambio de posición es un componente integral de la prevención y el tratamiento de las upp, con una justificación sólida y de amplia recomendación en la práctica de enfermería (575) . el uso de superficies especiales para el manejo de la presión (semp) a partir del estudio de defloor (576), se determinó un antes y un después en el uso de las semp en conjunción de los cambios posturales. este realizo un importante aporte para reducir la incidencia de lesiones por presión comparado con los colchones de estándar. se recomienda promover actividades para controlar el nivel de estrés en el personal durante las jornadas de trabajo: identificar y reconocer los propios límites, buscar o proponer ayuda psicológica profesional cuando sea requerido, promover estilos de vida saludables, y organizar los turnos de trabajo asegurando periodos de descanso. se recomienda compartir las emociones con pares y superiores, analizar objetivamente las situaciones adversas, manejar fuentes de información objetivas y científicas, realizar pausas activas durante el turno y brindar espacios grupales para expresar emociones, miedos e incentivar al equipo de trabajo reconociendo su labor. amci ® se recomienda utilizar recursos de salud mental ocupacional, apoyo por enfermedad y licencia familiar, además de garantizar una adecuada dotación de personal. los estilos de superación personal y el crecimiento psicológico desempeñan un papel importante en el mantenimiento de la salud mental de las enfermeras. es razonable suponer que los niveles de ansiedad y estrés entre los profesionales de la salud son proporcionalmente más altos que los de la población general debido al contacto directo con pacientes infectados. esto puede explicar por qué las enfermeras de primera línea son excepcionalmente vulnerables a la fatiga y al agotamiento (wang, okoli, et al.2020) , agotamiento mental, falta de moral del personal, control / autonomía de decisión, menor calidad de vida y baja satisfacción laboral (cheung y yip, 2015). (577) . una investigación reciente realizada en china continental menciona el impacto negativo de la pandemia de covid-19 en los trabajadores de atención médica de primera línea, incluidos los mayores niveles de ansiedad (shanafelt, ripp y trockel, 2020 ), depresión (xiang et al. 2020 ), estrés postraumático síntomas, soledad e impotencia (xiang et al.2020) (577, 578) . los aspectos traumáticos y estresantes de la participación en una pandemia también ponen en riesgo el daño psicológico a los médicos (579) . la experiencia psicológica de las enfermeras que atienden a pacientes con covid-19 se puede resumir en 4 temas: primero, las emociones negativas presentes en la etapa inicial consisten en fatiga, incomodidad e impotencia que fue causado por el trabajo de alta intensidad, el miedo y la ansiedad, y la preocupación por los pacientes y sus familiares. segundo, los estilos de auto afrontamiento incluyeron ajustes psicológicos y de vida, actos altruistas, apoyo de equipo y coordinación racional. tercero, encontramos crecimiento bajo presión, que incluía un mayor afecto y agradecimiento, desarrollo de posición de responsabilidad profesional y autorreflexión. finalmente, encontraron que las emociones positivas ocurrieron simultáneamente con emociones negativas(580). se recomienda ofrecer mecanismos de apoyo para amortiguar el estrés relacionado con la pandemia por covid-19. esto incluye intervenciones para pacientes y familias ofreciendo recursos de salud mental y educación al egreso, previo a este reforzar visitas virtuales. se recomienda anticipar las necesidades de salud mental de los pacientes, el personal y las familias para ofrecer una respuesta integral de salud pública. se debe incluir atención psicológica en la hospitalización para pacientes, familiares y personal afectado por covid-19. se recomienda proporcionar atención de salud mental en las comunidades, mientras que se requiere distanciamiento social y los recursos del sistema de salud son limitados. amci ® se recomienda mantener una estrategia de comunicación asertiva con la familia, teniendo en cuenta la formación del personal sobre las estrategias para comunicar malas noticias. ser solidarios con el duelo de las familias y acompañar el proceso de afrontamiento aún en la distancia, identificando factores de riesgo para patología mental o duelo complicado, utilizando los recursos institucionales de salud mental para mejorar las intervenciones. la pandemia tiene el potencial de crear una crisis secundaria de angustia psicológica y desbordamiento del sistema de salud mental. los miembros de la familia pueden experimentar angustia, miedo o ansiedad por la hospitalización de un ser querido, particularmente cuando las medidas de control de infecciones restringen las visitas. la telesalud (incluida la cobertura de seguro para la telesalud), el suministro extendido de medicamentos, el aumento de la capacitación en salud mental del proveedor, el apoyo virtual de pares y los grupos virtuales de apoyo al uso de sustancias pueden ayudar a garantizar que se satisfagan las necesidades de salud mental de la comunidad (581). el sistema de salud y los líderes de enfermería deben asegurarse de que su personal de enfermería clínica esté protegido y respaldado para que puedan proporcionar esta dimensión crucial de la atención de covid-19. se recomienda crear grupos centralizados y definidos para atención de pacientes con sospecha o diagnóstico de covid-19 que se encarguen de elaboración, socialización e implementación de protocolos. estos deben incluir los aspectos de infraestructura, áreas delimitadas, utilización de epp, listas de chequeo, observadores, insumos y recursos que permitan atención integral. se recomienda organizar el plan de atención del paciente con sospecha o diagnóstico de covid-19 de enfermería con la asignación de actividades, número de personas según escalas que midan escalas de carga laboral para definir el número adecuado de los miembros del equipo de trabajo, tiempo de atención, gestión de recursos, gestión de riesgo y un líder por turno que garantice el cumplimiento fuerte a favor fundamento la implementación de estrategias de gestión en contingencias genera un trabajo organizado, enfocado en la prevención y tratamiento centralizado, elaboración y socialización de protocolos claros, áreas específicas, delimitadas y asignadas, con un uso racional del recurso humano que se despliega en fases, desde el inicio de la emergencia considerado como detección temprana hasta la atención directa de pacientes con sospecha amci ® o confirmación de sars-cov-2. dentro de las fases tempranas, se busca la gestión de los recursos necesarios para la atención de estos pacientes, con una asignación de zonas o servicios y unas condiciones particulares, tratamientos específicos y actividades de atención especiales para las cuales se discriminan medicamentos, dispositivos e insumos necesarios para el cuidado de enfermería. los grupos de atención deben contar con capacitación, gestión y supervisión, apoyo logístico, apoyo psicológico y retroalimentación (573, 580) . el plan de atención de enfermería debe tener presente la minimización de exposición, la prevención de infecciones en el personal y cuidados especiales derivados de la condición clínica de los pacientes con esta infección, altamente contagiosa y con síntomas o necesidades que rompe el modo operacional convencional y que requiere implementación basada en la práctica clínica. por lo tanto, el plan debe ser centralizado oportuno, ordenado, seguro y eficiente e incluye: relación enfermería/paciente de acuerdo a criticidad, capacitaciones y entrenamiento al personal de enfermería de línea de frente en el área crítica de aislamiento mediante videos, infografías y procesos prácticos (el contenido de capacitación incluye el uso de elementos de protección personal, higiene de manos, desinfección de áreas, manejo de residuos y esterilización de dispositivos de atención al paciente y manejo de exposición ocupacional), asignación de actividades clínicas (atención directa) y administrativas (supervisión, observador, líderes, gestión de recurso humano y medicamentos), soporte y contratación de personal adicional ante la contingencia con preparación académica o inducción, asignación de turnos razonables con períodos de descanso (alimentación, eliminación), coordinación con otros departamentos y optimización de flujos de trabajo, estrategias de control de infecciones y trabajo en equipo (577, 579) . se recomienda que las muestras clínicas tomadas para el diagnóstico de covid-19 deben conservarse a temperatura entre -2 a 8°c, y luego de las 48 horas deben permanecer congeladas a una temperatura de -70°c. se recomienda que se realice el envío al laboratorio de salud pública de referencia dentro de las 48 horas posteriores a la toma de la muestra del paciente. se recomienda que el transporte de las muestras debe realizarse con geles o pilas congeladas. se recomienda considerar que las muestras del tracto respiratorio bajo presentan la mejor certeza diagnóstica en pacientes con neumonía para adultos intubados y ventilados mecánicamente con sospecha de covid-19. se recomienda contar con elementos de protección personal de acuerdo con las precauciones establecidas para el paciente con sospecha o diagnóstico por covid-19 para evitar la transmisión a profesionales de la salud. se debe evitar perder el circuito cerrado en los pacientes ventilados mecánicamente y valorar el riesgo de las acciones en pacientes con peep alta. se recomienda realizar la toma de muestra post mortem no invasiva por hisopado nasofaríngeo dentro de las primeras seis (6) horas posteriores al fallecimiento, para que esta sea útil para su análisis. las muestras clínicas tomadas para el diagnóstico de coronavirus deben conservarse a temperatura entre -2 a 8°c, y luego de las 48 horas deben permanecer congeladas a una temperatura de -70°c. sin embargo, la muestra puede conservarse en un tiempo máximo de refrigeración por 72 horas. no obstante, se sugiere que se realice el envío al laboratorio de salud pública de referencia dentro de las 48 horas posteriores a la toma. si no se conserva la cadena de frío adecuada, la muestra puede ser inviable. el transporte de las muestras debe realizarse con geles o pilas congeladas (128, 582, 583) .se debe tener en cuenta que no conservar la cadena de frío durante el transporte de la muestra, degradan la partícula viral, obteniéndose falsos negativos (583) . las muestras del tracto respiratorio bajo presentan la mejor certeza diagnóstica en pacientes con neumonía. para adultos intubados y ventilados mecánicamente con sospecha de covid-19 en comparación al tracto respiratorio superior (nasofaríngeo u orofaríngeo). en el caso de aspirado traqueal, es importante considerar que para la obtención de las muestras para el diagnóstico de covid-19 se deben contar con elementos de protección personal de acuerdo a las precauciones estándar para evitar la transmisión a profesionales de la salud, circuito cerrado y valorar su realización en aquellos pacientes con peep alta (128) . la toma de muestra post mortem no invasiva por hisopado nasofaríngeo se debe hacer antes de seis (6) horas post mortem, para que esta sea útil para su análisis(166, 582-585). se recomienda en los pacientes con diagnóstico covid-19, monitorizar continuamente la oxigenación mediante saturación arterial de oxígeno con pulso oxímetro y la aparición temprana de signos clínicos de dificultad respiratoria durante la monitorización (aleteo nasal, cianosis, tirajes intercostales). se recomienda no suministrar de forma rutinaria suministrar oxígeno si la saturación de oxígeno (spo2) está por encima de 94%, y no se evidencian signos clínicos de dificultad respiratoria durante la monitorización continua del patrón respiratorio. se recomienda como parámetro importante para evaluar la oxigenación y guiar el suministro de oxígeno mediante los diferentes dispositivos la transferencia de oxígeno, medida por la pao2/ fio2 o sao2/fio2. se propone iniciar la oxigenoterapia por cánulas de bajo flujo y ajustar el flujo (máximo 5 l) hasta alcanzar la spo2 objetivo ≥ 94%; si el paciente se encuentra en estado crítico iniciar con mascarilla con bolsa de reserva (a 10-15 l / min). una vez que el paciente esté estable, el objetivo de oxigenación es mantener niveles de spo2 entre 88 y 92% en pacientes no embarazadas y entre 92-95% en pacientes embarazadas. se recomienda no utilizar de forma rutinaria el uso de dispositivos que generan aerosoles durante la administración de oxígeno (dispositivos venturi o nebulizador de alto flujo o jet) en pacientes con sospecha o diagnóstico covid-19. en las diferentes guías publicadas para manejo de pacientes positivos para covid-19 las metas de oxigenación durante la terapia de oxígeno en adultos recomiendan iniciar la oxigenoterapia a 5 l / min y ajustar el flujo hasta alcanzar la spo2 objetivo ≥ 94% durante la reanimación; o use mascarilla con bolsa de reserva (a 10-15 l / min) si el paciente está en estado crítico. una vez que el paciente esté estable, el objetivo de oxigenación es > 90% de spo2 en pacientes, no embarazadas y ≥ 92-95% en pacientes embarazadas(165). los dispositivos para la oxigenoterapia se pueden dividir en dos grupos, dependiendo de si cubren la totalidad o una parte de los requerimientos respiratorios del paciente. unos son de bajo flujo o para esfuerzos mínimos del paciente, estos dispositivos completan su ventilación con aire ambiente y los sistemas de alto flujo cubren la totalidad de los requerimientos inspiratorios del paciente. escalones terapéuticos: oxigenoterapia convencional a diferentes concentraciones de bajo flujo (son las cánulas nasales, las mascarillas simples y las mascarillas con reservorio), es el primer escalón terapéutico ante cualquier paciente que presente una situación de hipoxemia (spo2) < 90% respirando aire ambiente. el objetivo debe ser ajustar la fio2 (hasta 0.4) para mantener un nivel de oxigenación adecuado, considerado este como una spo2 > 91%. la administración de oxígeno se considera un procedimiento generador de aerosoles de riesgo bajo y por lo tanto es adecuado para pacientes covid-19 positivos(586). b. en adultos con signos de emergencia (respiración obstruida o ausente, dificultad respiratoria severa, cianosis central, shock, coma y / o convulsiones) deben recibir vía aérea amci ® de emergencia manejo y oxigenoterapia durante la reanimación para apuntar a spo2 ≥ 94%. una vez el paciente está estable, objetivo> 90% de spo2 en adultos no embarazadas y ≥ 92-95% en mujeres embarazadas. c. para el manejo del paciente con covid-19 la máscara de no re inhalación se considera como la opción de preferencia para escalar el paciente antes de la intubación y considerar la transferencia a uci; esto se debe a que puede proporcionar altas fracciones inspiradas de oxígeno (587) . d. los dispositivos que generan aerosoles durante la administración de oxígeno (dispositivos venturi o nebulizador de alto flujo o jet), no están indicados para manejo de covid-19 (588). se recomienda aplicar las estrategias de retiro de la ventilación mecánica habituales para pacientes adultos críticos en general, hasta el momento no se ha construido una evidencia contundente para el destete en covid-19. se recomienda en el paciente críticamente enfermo por covid-19 un descenso de la presión de soporte (psv) según tolerancia clínica, de esta forma el paciente podrá ser sometido a la realización de prueba de respiración espontánea con una presión de soporte de entre 5-8 cm h2o. se recomienda que el destete automatizado puede ser considerado como una herramienta útil según disponibilidad de equipos para realizarlo. se recomienda no utilizar las maniobras que incrementan la aerosolización como la prueba de respiración espontánea en pieza en t o el cuff-leak test en el momento de realizar la medición de los predictores de éxito en el destete. fuerte en contra fundamento la realización de las pruebas de respiración espontánea sigue siendo un factor predictor importante en el éxito en el retiro del soporte ventilatorio mecánico y la indicación de tiempo de duración sigue siendo de 30 a 120 minutos debido a que las intubaciones realizadas en el mismo periodo de tiempo no han tenido diferencias significativas en el éxito del destete (589, 590) . en los pacientes que han sido ventilados por más de 24 horas y que el motivo por el cual fueron llevados a ventilación mecánica ya ha sido superado se debe establecer un protocolo de destete que debe incluir una prueba diaria de respiración espontánea y la minimización o retiro de la sedación (si no existe alguna contraindicación)(165, 591). la movilización temprana como factor coadyuvante en el éxito de la liberación mecánica ya se ha documentado en otros escenarios similares, razón por la cual la implementación amci ® temprana de este tipo de estrategias será un punto de vital importancia para recuperar la funcionalidad de los pacientes con covid-19 (121) . se recomienda que la extubación de los pacientes críticamente enfermos por covid-19 se debe realizar con los elementos de protección personal requeridos para el riesgo de aerosoles. se recomienda no estimular la tos y el esputo inducido en los pacientes con sospecha o diagnóstico de covid-19 posterior a la extubación inmediata. se recomienda no utilizar de forma rutinaria la vmni en la falla respiratoria post extubación en pacientes críticos que no tengan una enfermedad concomitante que sea respondedora a la vmni como el epoc o edema pulmonar de origen cardiogénico en pacientes con sospecha o diagnóstico de covid-19. fuerte en contra se recomienda mantener un umbral bajo para decidir intubación en caso de sospecha de fallo en la extubación en el paciente con sospecha o diagnóstico de covid-19. la estricta monitoria y manejo del paciente posterior a la extubación surgen como un reto insoslayable para el personal de cuidado intensivo, enfocando todos sus esfuerzos en evitar la re-intubación, lo que se traducirá en un descenso significativo de la morbilidad y la mortalidad que supone una re-intubación (592), la cual se puede definir como el no requerimiento de re intubación en las primeras 72 horas post extubación (593, 594) . en los últimos años la cánula nasal de alto flujo (caf) se ha convertido en una herramienta útil en el soporte de oxigenoterapia en los pacientes extubados que presenten riesgo de reintubación (595, 596), y a la vez no presenten hipercapnia (597) . la utilización de ventilación mecánica no invasiva de manera profiláctica en la falla respiratoria post extubación no ha demostrado tener éxito evitando la re-intubación en las primeras 48 horas (598, 599) excepto en las situaciones donde el paciente presente una enfermedad pulmonar o alteración cardiaca concomitante que sea respondedora a el manejo con vmni como lo son la enfermedad pulmonar obstructiva crónica (epoc) y el edema pulmonar de origen cardiogénico (267, 600) . los pacientes extubados en los que se halla documentado epoc, se sugiere posterior a la extubación la implementación de una estrategia de niv de manera protocolaria (600, 601), con una intensidad de 1 hora cada 3 horas durante un período mínimo de 48 horas (602). se recomienda utilizar en los pacientes con extubación reciente que no expresen predictores de riesgo de fracaso, sistemas de oxigenoterapia convencionales de bajo flujo que generen menos riesgo de aerosolización, fuerte a favor se podría considerar cánulas de alto flujo de oxígeno y/o la ventilación mecánica no invasiva (con una máscara facial adecuadamente ajustada y ramas inspiratorias y espiratorias separadas) como terapia de puente después de la extubación, pero se deben brindar las condiciones estructurales necesarias (habitaciones de presión negativa o habitaciones aisladas de puertas cerradas) y con epp estrictos para el personal sanitario. fuerte a favor fundamento las pautas de anzics establecen que la caf y/o la ventilación no invasiva (con una máscara facial bien ajustada y ramas inspiratorias y espiratorias separadas) pueden considerarse como terapia de puente después de la extubación, pero deben proporcionarse epp estricto en el aire. la terapia cpap o bipap (con alta presión espiratoria final) podría ser útil para prevenir la eliminación del reclutamiento en estos pacientes. en el momento de la extubación, los pacientes a menudo han estado enfermos durante más de una semana. es probable que su carga viral disminuya en ese punto, por lo que el riesgo de transmisión del virus puede ser menor (en comparación con la intubación inicial) (603) . de no contar con predictores de que nos indiquen que podría fracasar la extubación se deben utilizar entonces sistemas de oxigenoterapia convencionales de bajo flujo que generen menos riesgo de aerosolización(604). se recomienda limpiar y desinfectar con frecuencia el área de retiro de epp, incluso después de que se haya completado cada procedimiento de eliminación. se debe limpiar esta zona, pasando de las áreas más limpias a las más sucias, antes de ingresar a la habitación del paciente y realizar el manejo y disposición final de residuos. se recomienda realizar la limpieza de superficies con un desinfectante adecuado o con una solución de hipoclorito sódico que contenga 5000 ppm de cloro activo (por ejemplo, un producto con hipoclorito en una concentración de 40-50 gr/litro, se hará una dilución 1:10 en el momento de su utilización). amci ® se recomienda que los recipientes que contengan los residuos deberán quedar en el lugar designado a tal efecto, que permanecerá cerrado hasta que, según el procedimiento de gestión de residuos de la institución sean retirados. los circuitos, filtros, succión cerrada y tot deben ser dispuestos en bolsas de color rojo las cuales deben ser de polietileno de alta densidad de 1.6 milésimas de pulgada y deben contar con un rótulo donde se indiquen: el nombre del generador, las palabras residuos biológicos (covid19 2019) . una vez dispuesto, apretar y asegurar con nudo la bolsa de residuos y remover la bolsa de residuos del recipiente de residuos. posteriormente, desinfectar el exterior de la bolsa con solución desinfectante. luego colocar la bolsa de residuos en otra bolsa adicional de residuos y apretar y asegurar con nudo la bolsa de residuo. finalmente desinfectar la exterior bolsa de residuos con solución desinfectante. una vez terminada la disposición de los residuos de extubación, desinfectar los guantes con que manipuló los residuos con solución desinfectante y ubicar la bolsa de residuos dentro del vehículo de recolección interna de residuos. finalmente desinfectar el exterior de la bolsa de residuos con solución desinfectante. una vez terminada la disposición de los residuos de extubación, desinfectar los guantes con que manipuló los residuos con solución desinfectante y ubicar la bolsa dentro del vehículo de recolección interna. acogerse a la ruta sanitaria que asegure el menor riesgo de contaminación en el traslado interno de los residuos en la habitación del paciente (zona limpia) y zona sucia, se debe garantizar la ubicación de recipiente plástico de color rojo, liviano, resistente a los golpes, en material rígido impermeable, de fácil limpieza, y resistentes a la corrosión. los recipientes deberán ser lavados y desinfectados de acuerdo con los procedimientos establecidos por el prestador de servicios de salud(605-608). se recomienda utilizar un ajuste de peep del paciente crítico por covid-19, basado adicional a la tabla de peep, en las condiciones clínicas del paciente, en los índices de oxigenación, en la mecánica respiratoria del paciente y en los métodos de monitoreo disponibles. se recomienda titular la peep más alta que mantenga o mejore la relación safi y permita una presión plateau ≤ 30 cmh2o. se recomienda utilizar otras estrategias de titulación de peep probadas y con las cuales el equipo de trabajo esté familiarizado, dependiendo de la disponibilidad del recurso: ensayo peep decremental precedido por una maniobra de reclutamiento; titulación mediante la amci ® estimación de la presión transpulmonar con catéter esofágico o tomografía de impedancia eléctrica. fuerte a favor fundamento la titulación de la peep debe hacerse en función de la distensibilidad, oxigenación, espacio muerto y estado hemodinámico. puede titularse la peep mediante la estimación de la presión transpulmonar con catéter esofágico o tomografía de impedancia eléctrica. podría también titularse a partir de la fórmula (dp=plateau-peep) teniendo en cuenta que sea lógico el acoplamiento matemático fisiológico (lo que resultaría en una peep de 15 cmh2o si la presión plateau es de 30 cmh2o). la titulación de la peep requiere consideración de los beneficios (reducción de atelectrauma y mejora del reclutamiento alveolar) frente a los riesgos (sobre distensión inspiratoria final que conduce a lesión pulmonar y mayor resistencia vascular pulmonar)(165, 609, 610). se recomienda aplicar los protocolos de rehabilitación física como estrategia beneficiosa en el tratamiento respiratorio y físico de pacientes críticamente enfermos por covid-19. se recomienda realizar la movilización precoz del paciente críticamente enfermo por covid-19 durante el curso de la enfermedad siempre que sea posible hacerlo de forma segura, asegurando la protección personal del personal sanitario. derivado del tratamiento médico intensivo para algunos pacientes con covid-19, incluida la ventilación pulmonar protectora prolongada, la sedación y el uso de agentes bloqueantes neuromusculares, los pacientes con covid-19 que ingresan en la uci pueden presentar un elevado riesgo de desarrollar debilidad adquirida en la uci empeorando su morbilidad y mortalidad. por lo tanto, es esencial la rehabilitación temprana después de la fase aguda del síndrome de distrés respiratorio agudo (sdra) para limitar la gravedad de la debilidad adquirida en uci y promover la recuperación funcional. según la guía de la oms y la ops, enfatizan extremar el uso de los elementos de protección personal (epp) durante las intervenciones de rehabilitación física. la rehabilitación física proporciona intervenciones a través de movilizaciones, ejercicio terapéutico y programas individualizados a las personas que superan la enfermedad crítica asociada con covid-19 durante la ventilación mecánica y luego de esta, con el fin de permitir un retorno al hogar con funcionalidad. la prescripción de la movilización y ejercicio terapéutico debe de ser considera cuidadosamente en función del estado del paciente teniendo en cuenta, la estabilidad hemodinámica y clínica de la función respiratoria. cuando las movilizaciones, ejercicio terapéutico o programas de rehabilitación están indicados, debe realizarse una correcta planeación teniendo en cuenta amci ® la identificación/uso del personal mínimo necesario para realizar la actividad de manera segura. y el aseguramiento de todo el material que requerido esté a la mano y funcione correctamente y esté perfectamente limpio y desinfectado. si el material/equipo tiene que ser compartido con otros pacientes, límpielo y desinféctelo después de cada uso, entre paciente y paciente. se requiere personal entrenado específicamente para la limpieza y desinfección de los equipos, en una habitación aislada. y siempre que sea posible, evitar el traslado del material entre las áreas infectadas y no infectadas del hospital, manteniendo el equipamiento en las zonas aisladas (611) (612) (613) (614) (615) . ( basados en un estudio preliminar aún sin publicar, se podría sugerir el uso de dexametasona a dosis de 6 mg (oral o venosos) por 10 días o hasta el alta si ocurre primero en pacientes hospitalizados con sospecha o diagnóstico de covid-19 que requieren suplencia de oxígeno, incluyendo aquellos con ventilación mecánica, que sean menores de 70 años y con más de 7 días de síntomas. amci ® actualmente no existe una terapia dirigida que se a efectiva para el manejo del virus; un número alto de estudios han surgido en los últimos dos meses, la mayoría sin el rigor metodológico suficiente para tomar decisiones adecuadas con respecto al manejo del paciente con infección por sars-cov-2. el conocimiento en la estructura del virus y el mejor entendimiento en la fisiopatología de la enfermedad genera un sinnúmero de potenciales fármacos que han sido ensayados para el manejo de la enfermedad. en tiempos de pandemia, con una patología catastrófica en términos de vidas humanas y costos hospitalarios; es importante encontrar soluciones a desenlaces importantes como mortalidad, días de estancia en uci y en el hospital, aumento en los días libres del ventilador, disminución de complicaciones mayores debido a la enfermedad entre otros. hasta el momento no se ha documentado ninguna terapia específica que pueda impactar sobre estos desenlaces; pero la calidad de los trabajos, tampoco dejan claro sin él no usar ningún tratamiento específico mejora los desenlaces al menos al disminuir el número de complicaciones. este nuevo beta-coronavirus es similar al coronavirus del síndrome respiratorio agudo severa (sars-cov) y del síndrome respiratorio del medio este (mers-cov); por lo tanto, varias moléculas que habían sido evaluadas en este tipo de enfermedad rápidamente se abrieron paso a ensayos clínicos en paciente con covid-19. estos ensayos principalmente observacionales, aleatorios pero abiertos con un número pequeño de pacientes no han permitido sacar adecuadas conclusiones y es frecuente como ver las diferentes guías de las principales sociedades del mundo cambiar de forma frecuente sus recomendaciones; no existes evidencia de estudios clínicos aleatorios y controlados que midan desenlaces fuertes, la premura de un tratamiento efectivo ha sacrificado el rigor metodológico que una investigación requiere. una estructura viral y replicación conocidas generan posibles dianas para que diferentes fármacos puedan ser investigados, antivirales tipo arbidol el cual inhibe la fusión de la membrana en la envoltura viral a algunos receptores; antimaláricos como la hidroxicloroquina y la cloroquina, las cuales inhiben la entrada viral y endocitosis por múltiples mecanismos, así como los efectos inmunomoduladores demostrados en el huésped; antivirales que impiden la replicación como el lopinavir o darunavir inhibiendo las proteasas o la ribavirina, el remdesivir o el favipiravir que actúan como análogos de nucleótidos o fármacos que actúan modulando la respuesta específica del huésped como el tocilizumab el cual se une al receptor de la il-6 inhibiendo el punto de acción de esta; los corticosteroides con múltiples efectos en la modulación del sistema inmunológico del paciente o los fármacos para evitar la respuesta secundaria a esta cascada inflamatoria como son los anticoagulantes. por último, se han buscado estrategias con el fin de mejorar la inmunización pasiva del huésped en el uso del plasma de pacientes convalecientes o el uso de inmunoglobulinas enriquecidas entre otros tratamientos propuestos para esta enfermedad. amci ® a los diferentes medicamentos que han sido usados en la pandemia del sars-cov-2/covid-19. de manera reciente en datos preliminares aún sin publicar horby y col en una rama del ensayo de evaluación aleatorizada de la terapia covid-19 (recovery), estudio aleatorizado, controlado, abierto que compara una gama de posibles tratamientos con la atención habitual en pacientes hospitalizados con covid-19, compararon el uso de la dexametasona a dosis de 6 mg día (oral o intravenosa) una vez al día por 10 días o el alta según lo que ocurriera primero contra el manejo habitual; en 2104 pacientes aleatorizados que recibieron dexametasona se compararon con 4321 pacientes en manejo estándar; 454 (21.6%) pacientes en el grupo de dexametasona y 1065 (24.6%) pacientes en el grupo control murieron a los 28 días, con un riesgo relativo ajustado para la edad (rr 0.83; 95% ic 0.74 a 0.92; p < 0.001). la mortalidad relativa y absoluta variaron significativamente en relación al soporte ventilatorio al momento de la aleatorización; la dexametasona redujo las muertes en una tercera parte de los pacientes que recibieron ventilación mecánica invasiva (29.0% vs. 40.7%, rr 0.65, 95% ic 0.51 a 0.82; p < 0.001), y una quinta parte en los pacientes que reciben oxígeno sin ventilación mecánica invasiva (21.5% vs. 25.0%, rr 0.80, 95% ic 0.70 a 0.92; p = 0.002), pero sin reducir la mortalidad en paciente que no recibieron soporte respiratorio al momento de la aleatorización (17.0% vs. 13.2%, rr 1.22, 95% ic 0.93 a 1.61]; p = 0.14) (423) . no se emite recomendación a favor ni en contra para el inhibidor de la janus quinasa (baricitinib) en los pacientes con sospecha clínica o diagnóstico de covid-19 severo. uno de los reguladores conocidos de la endocitosis es la proteína quinasa 1 asociada a ap2 (aak1); la interrupción de aak1 podría, a su vez, interrumpir el paso del virus a las células y también el ensamblaje intracelular de partículas del virus. uno de los seis fármacos de unión a aak1 de alta afinidad es el inhibidor de la janus quinasa (jak1 y jak2), llamado baricitinib, que también se une a la quinasa asociada a la ciclina g, otro regulador de la endocitosis (23) . el baricitinib alcanza concentraciones plasmáticas suficientes para inhibir aak1 con 2 mg o 4 mg una vez al día; por su baja unión a proteínas plasmáticas y a su mínima interacción con las enzimas cyp, permite combinarlo con los antivirales. sin embargo, algunos piensan que el bloqueo de la señal jak-stat por baricitinib puede producir un deterioro de la respuesta antiviral mediada por interferón, con un posible efecto facilitador sobre la evolución de la infección por sars-cov-2; otras limitantes son la linfopenia (no dar si < 500 cel./ mm 3 ) y el aumento de la cpk. (24, 25) . cantini y cols, en abril 2020, en italia, administraron baricitinib a 4 mg/día vía oral por 2 semanas a 12 pacientes con covid-19 moderado y los compararon con un grupo control; la terapia mejoró significativamente los parámetros clínicos, respiratorios y de laboratorio (pcr); ninguno de los pacientes requirió uci vs 33% del grupo control, sin eventos adversos. se amci ® trata de un estudio piloto de seguridad e impacto clínico en pacientes que no estaban en uci (472) . ¿en pacientes hospitalizados con sospecha o diagnóstico de covid-19 el uso de n-acetil cisteína modifica el curso clínico de la enfermedad o genera beneficios en desenlaces clínicos de interés? basados en evidencia indirecta para el manejo del sdra y resultados observaciones en covid-19, se podría utilizar el uso de n-acetil cisteina a dosis de 200mg/kg/día durante los primeros cinco días del sdra, aunque no se ha demostrado impacto en la mortalidad, su utilización parece relacionarse con una disminución significativa en la estancia en la unidad de cuidados intensivos y con disminución de los marcadores inflamatorios en pacientes con covid-19 . la severidad de la infección en covid-19, en gran parte depende de la respuesta inmunológica de cada persona, sin embargo, se encuentran 3 mecanismos fisiopatológicos de relevancia. sobreproducción de moco en vía aérea superior e inferior, que en parte explica la dificultad en la mecánica ventilatoria y los retos de ventilación en estos pacientes, la descarga desmedida de citoquinas proinflamatorias que se asocian a la falla multiorgánica y la coagulopatía asociada a la disfunción endotelial. esto mecanismos fisiopatológicos son comunes en el sdra, incluido los casos asociados a covid-19(616). amci ® enfermo con falla respiratoria aguda, la cual engloba falla respiratoria hipóxica (tipo 1), falla respiratoria hipercápnica aguda (tipo 2), sdra y lesión pulmonar aguda, se revisaron 13 ensayos clínicos, más de 1712 pacientes. el análisis del grupo de n acetilcisteína intravenoso mostró una reducción de estancia en uci, de 4.7 días, con una heterogeneidad muy baja del 25%, con valoración de la evidencia calificada como de alta calidad y baja probabilidad de sesgo (621) . en covid-19, fue utilizada con recuperación completa en un caso severo de un paciente con déficit de glucosa 6 fosfato deshidrogenasa (g6pd), con control de la hemolisis y resolución del compromiso pulmonar. en pacientes sin déficit de g6pd, también ha sido asociada a mejoría clínica y disminución significativa de los niveles de pcr y ferritina (622) . en una revisión de costo efectividad nacional, se identificaron 222 referencias, 3 de ellos era revisiones sistemáticas de la literatura, dos de las cuales incluían metaanálisis (lu 2019 y zhang 2017), y fueron incluidos en la evaluación. estos estudios incluyeron información de ensayos clínicos que comparaban la aplicación de nac intravenosa frente a placebo o cuidado usual en pacientes con sdra. los tres estudios reportan como resultado de mortalidad rr de 0.83 con ic al 95% de 0.62 a 1.11 (lu 2019), rr de 0.64 con ic al 95% de 0.32 a 1.30 (lewis 2019) y rr de 0.73 con ic al 95% de 0.50 a 1.07 (zhang 2017) . para el tiempo de estancia en uci solo las revisiones con metaanálisis reportaron resultados, encontrando una diferencia de promedio de días de estancia de -4.47 días con ic al 95% de -8.79 a -0.14 (lu 2019) y de -4.56 días con ic al 95% de -7.32 a -1.80 (zhang 2017). una de las revisiones reportó que en ninguno de los estudios analizados se presentaron eventos adversos. no se encontraron resultados para los desenlaces de infección, sobreinfección, ni uso y tipo de antibiótico utilizado. en el análisis se encontró una reducción estadísticamente significativa de los días de estancia en uci de los pacientes que recibieron tratamiento con n-acetilcisteína intravenosa con dosis entre 150 y 200 mg/kg/día durante los primeros cinco días del sdra, en comparación con los pacientes que recibieron placebo o manejo usual. no se reportó diferencia estadísticamente significativa en la reducción de la mortalidad de los pacientes que recibieron nac. (623) calidad de vida 1. ¿cómo podemos medir la calidad de vida, en los pacientes con covid-19 que egresan de la uci? se recomienda utilizar los marcadores disponibles de severidad y del riesgo de mortalidad por covid-19 en los pacientes internados en la uci. amci ® las secuelas inmediatas en los pacientes víctimas del devastador ataque sistémico del covid-19 durante su estancia en la uci son valorables, pero no se dispone de herramientas que permita medir el grado de afectación de la calidad de vida de estos pacientes posterior al egreso de la uci o de alta hospitalaria, por lo tanto, se sugiere realizar estudios de creación, validación y utilización de instrumentos de valoración de la calidad de vida en pacientes con covid-19 posteriores al alta hospitalaria. parte importante de los pacientes con diagnóstico de covid-19 que ingresan a la uci, evolucionan tórpidamente presentando deterioro progresivo de los diferentes órganos llegando en pocos días a una falla multiorgánica (327) , estos pacientes presentan características clínicas y de laboratorio que se relacionan de manera significativa con mayor severidad y riesgo de mortalidad (294, 624) . a pesar de conocer con alguna precisión el riesgo de severidad y mortalidad de los pacientes que ingresan a la uci, no disponemos de un score que nos permita evaluar y predecir el grado de afectación en la calidad de vida de los pacientes que logran sobrevivir. aproximadamente un 6,1% del total de pacientes con enfermedad por covid-19 ingresan a uci, y de estos 2,3% sometidos a ventilación mecánica (327); lamentablemente los pacientes con enfermedad severa que logran sobrevivir y recuperarse han sido sometidos a una larga estancia en la uci y a ventilación mecánica invasiva con una intubación prolongada, que puede producir disfunción en la deglución impidiendo a la persona alimentarse de forma correcta y segura. es importante diagnosticar esta disfagia en los pacientes que se están recuperando del covid-19 y tratarla correctamente desde el principio para evitar complicaciones importantes como la malnutrición y la deshidratación, así como el riesgo de neumonía aspirativa. además de la disfagia, la fibrosis pulmonar y el riesgo de trombos son los problemas más frecuentes, pero no los únicos. una de las características de la enfermedad severa por covid-19 es que el virus provoca una enfermedad multiorgánica, con un amplio y heterogéneo abanico de secuelas cuyo alcance todavía se desconoce y aunque el órgano más afectado es el pulmón, puede afectar también otros órganos o sistemas incluido el snc, que en los casos más graves puede presentar encefalitis, delirios, desorientación y confusión, síntomas que pueden persistir tras el alta de la uci. otra secuela frecuente son las polineuropatías, esta afectación suele comenzar con una sensación de hormigueo en las extremidades y en los pacientes con covid-19 se presenta además con un cuadro de miositis que provoca debilidad y cansancio al caminar, a veces incluso en reposo; en algunos pacientes se presenta tal debilidad que dificulta llevar el alimento a la boca e incluso deglutirlo. sin embargo, la primera y más frecuente de las manifestaciones neurológicas del covid-19 es la pérdida del olfato, que a veces perdura como secuela tiempo después del alta. un estudio en 900 pacientes ingresados en el hospital clínico san carlos de madrid revela que el 70% había sufrido anosmia en mayor o menor grado. la importancia de este síntoma radica en que las fosas nasales pueden ser la vía de acceso del virus al sistema nervioso central. amci ® otras posibles secuelas neurológicas asociadas a la infección por covid-19 son la ageusia, la cefalea y amnesia a corto y mediano plazo. también son importantes las secuelas que afectan al sistema cardiovascular. un estudio publicado en la journal o the american medical association advierte que un 20% de los pacientes presenta una elevación de las enzimas que indican daño en el miocardio. la inflamación que provoca el virus puede provocar directamente ese daño y también puede agravar el estado de pacientes que ya tengan una patología cardiovascular de base, muchas miocarditis son reversibles, pero hay una parte importante que deja como secuela una pérdida de la función contráctil. todavía se desconoce el alcance y es difícil medir el impacto de la enfermedad sobre el corazón porque en algunos casos, los síntomas de insuficiencia cardíaca se confunden con los de la neumonía. otra de las complicaciones más frecuentes, y potencialmente más grave, afecta al mecanismo de coagulación de la sangre. durante el ingreso hospitalario se han visto numerosos casos de ictus. la secuela más importante es el riesgo de que se formen trombos, que pueden ir al pulmón o al cerebro, y si se producen en las arterias, pueden dar lugar a un infarto, aunque este efecto es mucho menos frecuente. eso explica que algunos pacientes de covid-19 dados de alta hayan tenido que volver a ingresar por trombosis. finalmente es importante tener presente que a las afectaciones que haya podido producir el virus, hay que sumar las secuelas neurológicas propias de una estancia prolongada en una unidad de cuidados intensivos que también pueden ser graves y a veces no se distinguen bien unas de otras. debilidad muscular, desorientación, depresión y problemas psicológicos son secuelas muy habituales entre los pacientes que salen de la uci por enfermedades diferentes. por la anterior razón es difícil, por ahora, saber qué es efecto directo del virus y que puede derivarse del proceso de hospitalización. aún es difícil decir si los daños a largo plazo dependen del propio virus o de los efectos adversos del proceso tratante. sin embargo, este análisis de las posibles secuelas del covid-19 en el cuerpo, se presenta con más dudas que certezas. como es habitual en medicina, las causas pueden ser múltiples y muchas veces reflejan la participación de varias complicaciones que se han podido dar durante el proceso infeccioso directo o por la hospitalización, la información sobre los mecanismos de invasión del sars-cov-2 en todos los órganos sigue siendo, por ahora, escasa. y también lo es nuestro conocimiento sobre los efectos adversos de los medicamentos, muchos de ellos experimentales, que se han utilizado durante esta crisis. gran parte de lo que conocemos actualmente sobre los efectos de este virus proviene de la experiencia clínica de otros colegas y de las historias de pacientes que han sufrido la enfermedad, quedando todavía mucho por descubrir. dado el actual panorama, diferentes hospitales e instituciones de salud se preparan en torno a la rehabilitación, habilitando ya unidades multidisciplinares poscovid-19 para el seguimiento de estos pacientes y algunos centros están contactando con los pacientes dados de alta para evaluar su estado y hacer un seguimiento a su salud. también están en marcha varios estudios multicéntricos para evaluar el alcance de las secuelas, prácticamente todos los centros sanitarios deberán tener pautas de seguimiento y control para los pacientes ya dados de alta, creándose necesario la utilización simultánea de amci ® instrumentos de medición de calidad de vida, que en nuestro país colombia, ya se han utilizado previamente con este fin (625, 626) . con este instrumento de medición de la calidad de vida se realizaron algunos estudios piloto tanto en pacientes crónicos como en la población general con el fin de determinar la comprensión del instrumento y factibilidad de aplicación del mismo en cuanto a la consistencia interna, la revisión realizada por vilagut y cols demostró que la aplicación de la escala arrojó en diversos estudios un alfa de cronbach igual o superior a 0.7 en todas las escalas excepto en función social (626) . y aunque un número cada vez mayor de estudios mide los resultados físicos, cognitivos, de salud mental y de calidad de vida relacionada con la salud (cvrs) en los sobrevivientes adultos de la uci, los datos sobre las propiedades de medición de tales instrumentos son escasos y, en general, de calidad deficiente a justa. se necesitan análisis empíricos que evalúen el rendimiento de los instrumentos en adultos sobrevivientes de la uci para avanzar en la investigación en este campo (627) . finalmente, el conocimiento de las secuelas y complicaciones dejadas por la infección del covid-19, permitirá identificar importantes variables clínicas que acompañan a esta enfermedad y que afectan de manera importante la calidad de vida de los pacientes que padecen la enfermedad severa en la unidad de cuidados intensivos. en la actualidad no existen estudios para evaluar el riesgo de malnutrición aguda en pacientes hospitalizados por sars-cov-2. experiencias con otras infecciones virales por influenza, se han identificado como factores asociados con mortalidad, la presencia de malnutrición, la adquisición de infección intrahospitalarias, la falla respiratoria y la presencia de infiltrados en la radiografía de tórax (628) . las guías espen 2020 recomiendan utilizar el must o el nrs-2002(2), para la tamización del riesgo nutricional, estos puntajes de tamización previamente han sido validados en múltiples patologías y contextos clínicos; sin embargo, existen otros puntajes útiles desde la perspectiva clínica como la valoración global subjetiva, mini-nutritional asessment(629), puntaje nutric (630) y la global leadership initiative on malnutrition (glim) (631) . el proceso de diagnóstico nutricional debe involucrar, dos componentes: la identificación del riesgo con la utilización de alguno de los puntajes previamente validados en otros contextos y posteriormente el diagnóstico de los pacientes con malnutrición y la valoración de la gravedad de ésta; en este último paso es importante la valoración del índice de masa corporal, los hábitos de consumo calórico y proteico, la presencia de inflamación, los trastornos gastrointestinales, las enfermedades de base y siempre que sea factible el cálculo de la masa muscular. tabla 20. en vista del riesgo de infección al personal de salud, no siempre será necesario la visita nutricional al paciente, ésta podría ayudarse con entrevista al familiar, interrogatorio vía amci ® telefónica y sólo en caso necesario el examen del paciente para lo cual se requiere el uso de equipo de protección personal completo. esta estrategia de interrogatorio al familiar o al paciente por vía remota o telefónica puede ayudar a identificar los patrones de consumo y los hábitos nutricionales de riesgo y en caso de ser necesario la valoración nutricional disminuye el tiempo de exposición a un ambiente contaminado. para la atención presencial de pacientes en el ámbito de cuidado intensivo, es necesario definir cuál es el riesgo que existe de infección para el personal de salud, para aclarar esta pregunta se debe definir si hay un riesgo de generación de aerosoles(88). aunque no existen pautas específicas para la nutrición en pacientes con covid-19, las diferentes sociedades científicas han desarrollado guías de pauta clínica para la nutrición de pacientes con esta enfermedad (632, 633) . idealmente la nutrición debe ser iniciada de forma temprana, esto se refiere al inicio en las primeras 24 a 36 horas del ingreso a cuidado intensivo o en las primeras 12 horas luego de la intubación y el inicio de la ventilación mecánica(633) y se prefiere la vía enteral. aunque no existen estudios para evaluar el momento del inicio de la nutrición en pacientes con infección por sars-cov2, el inicio temprano de la nutrición ha mostrado beneficios en términos de mortalidad y reducción de infecciones con dicha estrategia (634, 635) . adicionalmente es importante, evaluar el riesgo de morbilidad y mortalidad asociado a la malnutrición aguda en el ámbito del paciente crítico, en los pacientes que no se alcance la meta de aporte calórico y proteico por vía enteral o que exista contraindicación para ésta, se debe considerar el inicio de nutrición por vía parenteral, especialmente cuando su riesgo nutricional agudo sea elevado (puntaje nutric ≥5, nrs ≥5) (636) (637) . el choque no es una contraindicación para la utilización de nutrición enteral (638) y no es una indicación para el uso de nutrición parenteral, quizás la mejor estrategia, es vigilar la presencia de disfunción gastrointestinal, en combinación con la presencia de intolerancia a la nutrición enteral, especialmente en pacientes con acidosis láctica en progreso y cuando sea necesario escalar la dosis de vasopresores o exista incapacidad para la reducción de éstos. no es necesario medir el residuo gástrico de rutina, es preferible iniciar procinéticos de forma rutinaria. la sonda debe colocarse con cuidado de evitar riesgo de contaminación, preferiblemente al entubar al paciente. algunos pacientes pueden presentar diarrea, ya que se ha descubierto la presencia de la proteína ace2 (receptor del virus sars-cov-2) en células del esófago, estómago, duodeno y recto. no existe evidencia que indique que la nutrición enteral durante la posición prono aumente el riesgo de complicaciones. sugerimos no suspender nutrición enteral al durante la pronación, se debe iniciar con dosis trófica de 20 ml/h. amci ® se recomienda una estrecha monitorización de la tolerancia a la nutrición enteral para pacientes en posición prono. se recomienda para aumentar la tolerancia de la ne a los pacientes en posición prona, una elevación del tórax entre 10-25º (posición de trendelenburg inversa) no realizar endoscopias digestivas para ubicación de sondas avanzadas recomendaciones de nutrición parenteral los pacientes con covid-19 pueden requerir niveles significativos de sedación y bloqueo neuromuscular, lo que puede aumentar la incidencia de intolerancia gastrointestinal. la nutrición parenteral (np) debe utilizarse donde la alimentación enteral no está disponible o no logra completar el 60% de los requerimientos. si existen limitaciones para la ruta enteral, se podría recomendar nutrición 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